From iscapularis at vectorbase.org Mon Feb 4 13:43:14 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Mon Feb 4 13:45:07 2008 Subject: [Ixodes] Ixodes scapularis Listserv Message-ID: <7B822100FD93C646B5D905DC842F65943C98D2@EXCH05.purdue.lcl> Welcome to the Ixodes scapularis genome listserv! This listserv has been created to communicate information regarding the Ixodes scapularis (Lyme disease tick) genome sequence. This listserv is hosted by VectorBase , an NIAID, NIH Bioinformatics Resource Center for invertebrate vectors of human disease. If you would like to unsubscribe or add others to the distribution list, please go to: http://mail.vectorbase.org:82/mailman/listinfo/iscapularis. Release of the Ixodes scapularis genome assembly The National Institute of Allergy and Infectious Diseases, National Institutes of Health has funded the sequencing, assembly and annotation of the Ixodes scapularis genome through its Microbial Sequencing Centers (the J. Craig Venter Institute (JCVI ) and the Broad Institute ) and the NIAID-funded Bioinformatics Resource Center, VectorBase, at the University of Notre Dame. Whole genome shotgun sequence data have now been generated and assembled, providing 3.8 fold coverage of the Ixodes scapularis genome. The Whole Genome Shotgun project has been deposited at GenBank under the project accession ABJB010000000 (consisting of contig accessions ABJB010000001-ABJB011141594). This first public assembly is deposited as JCVI_ISG_i3_1.0 and has the VectorBase designation IscaW1. Assembly Statistics Total number of sequence reads: 17.4 million Total number of sequence reads placed in the assembly: 7.3 million Estimated fold coverage of the assembly: 3.8 fold Number of contigs deposited at GenBank: 1,141,594 Number of contigs used in assembly: 570,640 Number of scaffolds: 369,495 Total length of combined contigs 1.4 Gb Total length of combined scaffolds (including gaps) 1.8 Gb Annotation Release Preliminary annotations of the assembly by the MSCs and by VB (0.5 gene sets) are expected to be released in April 2008 at VectorBase . Community scientists may submit manual annotations to VectorBase via a web-based submission process. Community annotations will be reviewed by VectorBase annotators and incorporated into a merged, final gene set in accordance with the NIAID approved project plan. This more complete annotation, including functional assignments, is planned for release in GenBank and VectorBase by September 2008. Long-term curation of the sequence and subsequent annotation updates will be the responsibility of VectorBase. Supplementary Data Release Complementary to the sequencing and annotation project described above, the NIAID, NIH has also funded a project to provide additional Ixodes scapularis genome-related resources. As part of this project 183,834 Ixodes scapularis EST sequences have been deposited at GenBank (accession range: EW781064-EW964897). These sequences are also available as part of the Ixodes scapularis gene index at the Dana Faber Cancer Institute Gene Indices . Forty-five BAC clones from a 10X Ixodes scapularis BAC library have also been sequenced and assembled. The assembled BAC sequences are available at GenBank under accession ranges: AC192414-AC192429, AC192742-AC192744, AC200531, and AC205630-AC205654. More than 370,000 BAC clones have also been end sequenced and are available from the NCBI trace archive and at VectorBase. Catherine A. Hill, PhD Assistant Professor Department of Entomology Purdue University 901 West State Street West Lafayette, IN, 47907 Tel: (765) 496 6157 Fax: (765) 496 1219 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080204/14e8f716/attachment.html From iscapularis at vectorbase.org Wed Feb 6 03:04:09 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Wed Feb 6 03:08:40 2008 Subject: [Ixodes] Ixodes scapularis Listserv In-Reply-To: <7B822100FD93C646B5D905DC842F65943C98D2@EXCH05.purdue.lcl> References: <7B822100FD93C646B5D905DC842F65943C98D2@EXCH05.purdue.lcl> Message-ID: <47A969F9.9010903@uiuc.edu> Thanks for the listerve and update, Cate. Congratulations to everyone at the two sequencing centers and especially the JCVI assembly folk for fighting with this beast. I wonder if we can ask for some more details about the assembly, especially why 10 m reads did not make it into the assembly. Obviously 1m contigs with only half of them in scaffolds and around 3.4X depth means that gene building is often going to be hard, much like the available Bombyx mori assemblies, and the resultant gene count inflated by fragments. But at least we have the raw traces so we can manually extend contigs, etc. for genes we care about. I took a quick look around at some of my favorite genes, and found some nice and some not so nice things. First, for the chemoreceptors, I predicted there would be no orthologs of the insect odorant receptors or Ors, since I predicted in 2003 those are novel with terrestriality in insects, and, as with Daphnia, find no ortholog of the highly conserved DmOr83b protein which in insects forms a heterodimeric partner with all the specific Ors, hence most likely no Ors. (Functional olfactory receptors of course could exist within the Gr family below). Second, I expected to find some gustatory receptors or Grs, the broader and more basal family of the insect chemoreceptors superfamily, because I've found a few distant relatives in nematodes. Although there are no obvious orthologs of the carbon dioxide receptors that are highly conserved in insects, or the sugar receptors (and this is the same for Daphnia), I finally found (using TBLASTN searches with E=1000 and the last 20aa or so of the mildly conserved C-terminus of diverse insect Grs), a series of 9 single ORF genes of about 1.2kb that encode a remarkably diverse set of tick Grs. There also appear to be genes related to these with introns, but I can only find the C-terminal third for now. I'll work more on these later - Nasonia, Culex, and Daphnia come first - all done, but manuscripts need writing. Third, I checked some other favorite genes. There is a simple ortholog of telomerase or TERT, with a large 2.5kb ORF encoding most of it, but the N-terminus is missing in a gap. There appears to be a 95% identical version that for some reason was not assembled and I will eventually do it manually. I will also fight with the telomeres themselves, which contain TTAGG repeats - is there a set of fosmid reads I can work from? Fourth, I checked for DNMT1, and find a series of paralogs, some with tons of introns, which seem pleasantly short, but not completely worked up, one with just a couple of short introns, and one single long ORF! Some insects and Daphnia also have multiple DNMT1 paralogs. For DNMT2 a single conserved ortholog was expected and found as a single 1.5kb ORF. I then checked DNMT3, which is more divergent amoungst animals, and it is there, but spread out, with single short exons on each contig. Fifth, I checked SID-1, the apparent RNA transporter implicated in RNAi in nematodes, and with multiple homologs in many insects, but nothing obvious. Sixth, I tried cryptochrome from the circadian rhythms, and it is nicely there, but with one exon per contig. Seventh, I checked Mahya, a follistatin-5 homolog, and it is there, but with many long introns and spread out across several contigs. Eigth, I checked pteropsin, and it finds a whole bunch of opsins, most single ORFs in single contigs, which will be fun to work up and compare with the 46 Daphnia opsins we are writing up now. In summary, remarkably many of these genes are single ORFs in single contigs, so could be built by automated programs. But most cross multiple contigs and will be impossible to build automatically, except as fragments. They will also be hard to deposit manually in the inferential Third Party Annotation database at GenBank, which requires that the genes be completely contained within single contigs. So it looks like a mixed bag. Hugh iscapularis@vectorbase.org wrote: > > > Welcome to the /Ixodes scapularis/ genome listserv! > > > > This listserv has been created to communicate information regarding > the /Ixodes scapularis/ (Lyme disease tick) genome sequence. > > > > This listserv is hosted by VectorBase > , an NIAID, NIH Bioinformatics > Resource Center for invertebrate vectors of human disease. If you > would like to unsubscribe or add others to the distribution list, > please go to: http://mail.vectorbase.org:82/mailman/listinfo/iscapularis. > > > > * Release of the /Ixodes scapularis/ genome assembly * > > The National Institute of Allergy and Infectious Diseases, National > Institutes of Health has funded the sequencing, assembly and > annotation of the /Ixodes scapularis/ genome through its Microbial > Sequencing Centers > (the J. > Craig Venter Institute ( JCVI ) and > the Broad Institute ) and the NIAID-funded > Bioinformatics Resource Center, VectorBase, at the University of Notre > Dame. Whole genome shotgun sequence data have now been generated and > assembled, providing 3.8 fold coverage of the /Ixodes scapularis/ > genome. The Whole Genome Shotgun project has been deposited at > GenBank under the project accession ABJB010000000 > > (consisting of contig accessions ABJB010000001-ABJB011141594). This > first public assembly is deposited as JCVI_ISG_i3_1.0 and has the > VectorBase designation IscaW1. > > > > * Assembly Statistics * > > Total number of sequence reads: 17.4 million > > Total number of sequence reads placed in the assembly: 7.3 million > > Estimated fold coverage of the assembly: 3.8 fold > > Number of contigs deposited at GenBank: 1,141,594 > > Number of contigs used in assembly: 570,640 > > Number of scaffolds: 369,495 > > Total length of combined contigs 1.4 Gb > > Total length of combined scaffolds (including gaps) 1.8 Gb > > > > * Annotation Release * > > Preliminary annotations of the assembly by the MSCs and by VB (0.5 > gene sets) are expected to be released in April 2008 at VectorBase > . Community scientists may > submit manual annotations to VectorBase via a web-based submission > process. Community annotations will be reviewed by VectorBase > annotators and incorporated into a merged, final gene set in > accordance with the NIAID approved project plan. This more complete > annotation, including functional assignments, is planned for release > in GenBank and VectorBase by September 2008. Long-term curation of > the sequence and subsequent annotation updates will be the > responsibility of VectorBase. > > * * > > * Supplementary Data Release * > > Complementary to the sequencing and annotation project described > above, the NIAID, NIH has also funded a project to provide additional > /Ixodes scapularis/ genome-related resources. As part of this project > 183,834 /Ixodes scapularis/ EST sequences have been deposited at > GenBank (accession range: EW781064-EW964897). These sequences are > also available as part of the /Ixodes scapularis/ gene index at the > Dana Faber Cancer Institute Gene Indices > . Forty-five BAC clones from a > 10X /Ixodes scapularis/ BAC library have also been sequenced and > assembled. The assembled BAC sequences are available at GenBank under > accession ranges: AC192414-AC192429, AC192742-AC192744, AC200531, and > AC205630-AC205654. More than 370,000 BAC clones have also been end > sequenced and are available from the NCBI trace archive and at > VectorBase. > > > > > > > > Catherine A. Hill, PhD > > Assistant Professor > > Department of Entomology > > Purdue University > > 901 West State Street > > West Lafayette , IN , 47907 > > Tel: (765) 496 6157 > > Fax: (765) 496 1219 > > > > > >------------------------------------------------------------------------ > >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis > > From iscapularis at vectorbase.org Wed Feb 6 18:32:40 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Wed Feb 6 18:38:49 2008 Subject: [Ixodes] Ixodes scapularis Listserv In-Reply-To: <47A969F9.9010903@uiuc.edu> Message-ID: <7B822100FD93C646B5D905DC842F65943C98E4@EXCH05.purdue.lcl> Hi Hugh, Wow! I am very pleased to hear that you are analyzing the Ixodes data. Thank you for sharing this information on preliminary annotations and initial impressions of the Ixodes contigs with listserv subscribers. This information is incredibly useful for all of us interested in analysis of the Ixodes sequence. I encourage others to discuss their findings through this forum as well. I expect that additional information on the Ixodes assembly will be forthcoming. We will share details via the listserv as they become available. I am very interested in your OR and GR results, especially the apparent lack of a CO2 receptor ortholog and orthologs of the Or83b and sugar receptors conserved in the insects. This is intriguing given the body of evidence re tick chemosensory perception. I hope you will be willing to continue this and other Ixodes analyses. I am aware of several other investigators with an interest in the Ixodes ORs and the OBPs - I will ask them to correspond with you via this listserv. Jason Meyer, a postdoctoral scientist in our group and the Ixodes Community Representative for VectorBase, has been working on the Ixodes non-sensory G-Protein Coupled Receptors (GPCRs). To date, Jason has identified approximately 70 GPCRs in classes A, B and C, including a number of opsins. I'll let Jason tell you more about his findings. In summary, the annotation has been relatively straightforward. The majority of Ixodes GPCRs are remarkably conserved with insect GPCRs, the gene models can be identified within assembled regions, and the gene structures are relatively simple (i.e., many single exon genes and small introns). This was somewhat of a surprise; we were expecting multiple exons and large introns but so far this has not been the case. I am hoping this bodes well for others interested in Ixodes genes, especially highly conserved genes. We would like to hear from others with an interest in these Ixodes non-sensory GPCRs. I will be interested to know your thoughts re gene identification and annotation using the Ixodes scaffolds when these are made available. If possible, I would strongly encourage you to submit any Ixodes gene annotations to VectorBase. As stated in the initial email, we expect that JCVI and VectorBase 0.5 gene sets will be available sometime in April. Community scientists will have an opportunity to submit new/revised gene models as third party annotations via a VectorBase submission tool. These manual annotations will be captured by VectorBase, reviewed by Jason and then incorporated into a merged gene set. Release of this more complete gene set is expected in September this year. Thanks once again and please keep us posted! Cheers, Cate. Catherine A. Hill, PhD Assistant Professor Department of Entomology Purdue University 901 West State Street West Lafayette, IN, 47907 Tel: (765) 496 6157 Fax: (765) 496 1219 -----Original Message----- From: iscapularis-bounces@vectorbase.org [mailto:iscapularis-bounces@vectorbase.org] On Behalf Of iscapularis@vectorbase.org Sent: Wednesday, February 06, 2008 3:04 AM To: iscapularis@vectorbase.org Subject: Re: [Ixodes] Ixodes scapularis Listserv Thanks for the listerve and update, Cate. Congratulations to everyone at the two sequencing centers and especially the JCVI assembly folk for fighting with this beast. I wonder if we can ask for some more details about the assembly, especially why 10 m reads did not make it into the assembly. Obviously 1m contigs with only half of them in scaffolds and around 3.4X depth means that gene building is often going to be hard, much like the available Bombyx mori assemblies, and the resultant gene count inflated by fragments. But at least we have the raw traces so we can manually extend contigs, etc. for genes we care about. I took a quick look around at some of my favorite genes, and found some nice and some not so nice things. First, for the chemoreceptors, I predicted there would be no orthologs of the insect odorant receptors or Ors, since I predicted in 2003 those are novel with terrestriality in insects, and, as with Daphnia, find no ortholog of the highly conserved DmOr83b protein which in insects forms a heterodimeric partner with all the specific Ors, hence most likely no Ors. (Functional olfactory receptors of course could exist within the Gr family below). Second, I expected to find some gustatory receptors or Grs, the broader and more basal family of the insect chemoreceptors superfamily, because I've found a few distant relatives in nematodes. Although there are no obvious orthologs of the carbon dioxide receptors that are highly conserved in insects, or the sugar receptors (and this is the same for Daphnia), I finally found (using TBLASTN searches with E=1000 and the last 20aa or so of the mildly conserved C-terminus of diverse insect Grs), a series of 9 single ORF genes of about 1.2kb that encode a remarkably diverse set of tick Grs. There also appear to be genes related to these with introns, but I can only find the C-terminal third for now. I'll work more on these later - Nasonia, Culex, and Daphnia come first - all done, but manuscripts need writing. Third, I checked some other favorite genes. There is a simple ortholog of telomerase or TERT, with a large 2.5kb ORF encoding most of it, but the N-terminus is missing in a gap. There appears to be a 95% identical version that for some reason was not assembled and I will eventually do it manually. I will also fight with the telomeres themselves, which contain TTAGG repeats - is there a set of fosmid reads I can work from? Fourth, I checked for DNMT1, and find a series of paralogs, some with tons of introns, which seem pleasantly short, but not completely worked up, one with just a couple of short introns, and one single long ORF! Some insects and Daphnia also have multiple DNMT1 paralogs. For DNMT2 a single conserved ortholog was expected and found as a single 1.5kb ORF. I then checked DNMT3, which is more divergent amoungst animals, and it is there, but spread out, with single short exons on each contig. Fifth, I checked SID-1, the apparent RNA transporter implicated in RNAi in nematodes, and with multiple homologs in many insects, but nothing obvious. Sixth, I tried cryptochrome from the circadian rhythms, and it is nicely there, but with one exon per contig. Seventh, I checked Mahya, a follistatin-5 homolog, and it is there, but with many long introns and spread out across several contigs. Eigth, I checked pteropsin, and it finds a whole bunch of opsins, most single ORFs in single contigs, which will be fun to work up and compare with the 46 Daphnia opsins we are writing up now. In summary, remarkably many of these genes are single ORFs in single contigs, so could be built by automated programs. But most cross multiple contigs and will be impossible to build automatically, except as fragments. They will also be hard to deposit manually in the inferential Third Party Annotation database at GenBank, which requires that the genes be completely contained within single contigs. So it looks like a mixed bag. Hugh From iscapularis at vectorbase.org Wed Feb 6 22:24:07 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Wed Feb 6 22:28:38 2008 Subject: [Ixodes] Ixodes scapularis Listserv In-Reply-To: <7B822100FD93C646B5D905DC842F65943C98E4@EXCH05.purdue.lcl> References: <7B822100FD93C646B5D905DC842F65943C98E4@EXCH05.purdue.lcl> Message-ID: <47AA79D7.8020503@uiuc.edu> Thanks Cate, Your colleagues interested in Ors and OBPs in Ixodes will have a struggle on their hands. I will of course do my usual job with the Grs (some of which are surely now independently evolved functional olfactory receptors), and as with Anopheles, Aedes, and recently Culex, communicate all gene model changes to VectorBase once the official annotation is released (so that I can reference those gene numbers). I doubt they will all be simple single exons in single contigs, and when they cross contigs the automated programs will not be able to annotate them correctly (except perhaps for those in scaffolds of course). Culex was typical for the Grs - of the single copy genes, 30% were perfect, 30% needed slight to major modifications, and 30% were completely absent, and complicated alternatively spliced genes were concatenated, as expected. Your experience with the GPCRs is also reassuring that the tick genome will prove to be manageable after all because the genes are "normal", even unexpectedly lacking in introns, unlike Bombyx where there are tons of repeats in introns and between genes. Perhaps the 10m reads that did not make it into the assembly are all the repetitive stuff, what Celera called "chaff" on the original Dm assembly, at the centromeres. That would mean that while it cost a lot to get the useful stuff, at least it is decipherable. This genome might well present an interesting exception to the rule of intron content versus size developed by Michael Lynch down the road from you. One thing that would be most useful if someone can do it, is ask what percentage of ESTs (after clustering) are present in the assembly (say with at least a 100 bp and 90% match), and then what percentage are in the raw traces to see how much might yet be missing from the assembly (this analysis was very revealing for the first bee assembly). If anyone is missing an otherwise highly conserved gene, they should also try TBLASTN searches of the 17m raw traces to see if it is there - this can be done using NETBLAST from NCBI - I'm willing to do it for anyone. I did it for SID1, and there is just one trace that might have a tiny piece of it, but I'm not convinced, so conclude it is not in this genome (or was in such an unusual part of it that it did not clone, which seems unlikely given the large size of this gene). Hugh iscapularis@vectorbase.org wrote: >Hi Hugh, > >Wow! I am very pleased to hear that you are analyzing the Ixodes data. >Thank you for sharing this information on preliminary annotations and >initial impressions of the Ixodes contigs with listserv subscribers. >This information is incredibly useful for all of us interested in >analysis of the Ixodes sequence. I encourage others to discuss their >findings through this forum as well. > >I expect that additional information on the Ixodes assembly will be >forthcoming. We will share details via the listserv as they become >available. > >I am very interested in your OR and GR results, especially the apparent >lack of a CO2 receptor ortholog and orthologs of the Or83b and sugar >receptors conserved in the insects. This is intriguing given the body >of evidence re tick chemosensory perception. I hope you will be willing >to continue this and other Ixodes analyses. I am aware of several other >investigators with an interest in the Ixodes ORs and the OBPs - I will >ask them to correspond with you via this listserv. > >Jason Meyer, a postdoctoral scientist in our group and the Ixodes >Community Representative for VectorBase, has been working on the Ixodes >non-sensory G-Protein Coupled Receptors (GPCRs). To date, Jason has >identified approximately 70 GPCRs in classes A, B and C, including a >number of opsins. I'll let Jason tell you more about his findings. In >summary, the annotation has been relatively straightforward. The >majority of Ixodes GPCRs are remarkably conserved with insect GPCRs, the >gene models can be identified within assembled regions, and the gene >structures are relatively simple (i.e., many single exon genes and small >introns). This was somewhat of a surprise; we were expecting multiple >exons and large introns but so far this has not been the case. I am >hoping this bodes well for others interested in Ixodes genes, especially >highly conserved genes. We would like to hear from others with an >interest in these Ixodes non-sensory GPCRs. > >I will be interested to know your thoughts re gene identification and >annotation using the Ixodes scaffolds when these are made available. If >possible, I would strongly encourage you to submit any Ixodes gene >annotations to VectorBase. As stated in the initial email, we expect >that JCVI and VectorBase 0.5 gene sets will be available sometime in >April. Community scientists will have an opportunity to submit >new/revised gene models as third party annotations via a VectorBase >submission tool. These manual annotations will be captured by >VectorBase, reviewed by Jason and then incorporated into a merged gene >set. Release of this more complete gene set is expected in September >this year. > >Thanks once again and please keep us posted! > >Cheers, >Cate. > >Catherine A. Hill, PhD >Assistant Professor >Department of Entomology >Purdue University >901 West State Street >West Lafayette, IN, 47907 >Tel: (765) 496 6157 >Fax: (765) 496 1219 > > >-----Original Message----- >From: iscapularis-bounces@vectorbase.org >[mailto:iscapularis-bounces@vectorbase.org] On Behalf Of >iscapularis@vectorbase.org >Sent: Wednesday, February 06, 2008 3:04 AM >To: iscapularis@vectorbase.org >Subject: Re: [Ixodes] Ixodes scapularis Listserv > >Thanks for the listerve and update, Cate. Congratulations to everyone at > >the two sequencing centers and especially the JCVI assembly folk for >fighting with this beast. I wonder if we can ask for some more details >about the assembly, especially why 10 m reads did not make it into the >assembly. Obviously 1m contigs with only half of them in scaffolds and >around 3.4X depth means that gene building is often going to be hard, >much like the available Bombyx mori assemblies, and the resultant gene >count inflated by fragments. But at least we have the raw traces so we >can manually extend contigs, etc. for genes we care about. > >I took a quick look around at some of my favorite genes, and found some >nice and some not so nice things. > >First, for the chemoreceptors, I predicted there would be no orthologs >of the insect odorant receptors or Ors, since I predicted in 2003 those >are novel with terrestriality in insects, and, as with Daphnia, find no >ortholog of the highly conserved DmOr83b protein which in insects forms >a heterodimeric partner with all the specific Ors, hence most likely no >Ors. (Functional olfactory receptors of course could exist within the Gr > >family below). > >Second, I expected to find some gustatory receptors or Grs, the broader >and more basal family of the insect chemoreceptors superfamily, because >I've found a few distant relatives in nematodes. Although there are no >obvious orthologs of the carbon dioxide receptors that are highly >conserved in insects, or the sugar receptors (and this is the same for >Daphnia), I finally found (using TBLASTN searches with E=1000 and the >last 20aa or so of the mildly conserved C-terminus of diverse insect >Grs), a series of 9 single ORF genes of about 1.2kb that encode a >remarkably diverse set of tick Grs. There also appear to be genes >related to these with introns, but I can only find the C-terminal third >for now. I'll work more on these later - Nasonia, Culex, and Daphnia >come first - all done, but manuscripts need writing. > >Third, I checked some other favorite genes. There is a simple ortholog >of telomerase or TERT, with a large 2.5kb ORF encoding most of it, but >the N-terminus is missing in a gap. There appears to be a 95% identical >version that for some reason was not assembled and I will eventually do >it manually. I will also fight with the telomeres themselves, which >contain TTAGG repeats - is there a set of fosmid reads I can work from? > >Fourth, I checked for DNMT1, and find a series of paralogs, some with >tons of introns, which seem pleasantly short, but not completely worked >up, one with just a couple of short introns, and one single long ORF! >Some insects and Daphnia also have multiple DNMT1 paralogs. For DNMT2 a >single conserved ortholog was expected and found as a single 1.5kb ORF. >I then checked DNMT3, which is more divergent amoungst animals, and it >is there, but spread out, with single short exons on each contig. > >Fifth, I checked SID-1, the apparent RNA transporter implicated in RNAi >in nematodes, and with multiple homologs in many insects, but nothing >obvious. > >Sixth, I tried cryptochrome from the circadian rhythms, and it is nicely > >there, but with one exon per contig. > >Seventh, I checked Mahya, a follistatin-5 homolog, and it is there, but >with many long introns and spread out across several contigs. > >Eigth, I checked pteropsin, and it finds a whole bunch of opsins, most >single ORFs in single contigs, which will be fun to work up and compare >with the 46 Daphnia opsins we are writing up now. > >In summary, remarkably many of these genes are single ORFs in single >contigs, so could be built by automated programs. But most cross >multiple contigs and will be impossible to build automatically, except >as fragments. They will also be hard to deposit manually in the >inferential Third Party Annotation database at GenBank, which requires >that the genes be completely contained within single contigs. So it >looks like a mixed bag. > >Hugh > > >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis > > From iscapularis at vectorbase.org Wed Feb 6 22:48:01 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Wed Feb 6 22:52:30 2008 Subject: [Ixodes] Ixodes scapularis common name Message-ID: <47AA7F71.7090905@uiuc.edu> I see in the NCBI files that the common name is given as black-legged tick, while I've been using deer tick for it. I checked Wikipedia, and they give both. Hardly the most authoritative source, but these days the first place I check for most anything. I think I'll stick with deer tick if possible. Anyone interested in updating the Wikipedia page, it could use some help! Hugh From iscapularis at vectorbase.org Thu Feb 7 05:39:53 2008 From: iscapularis at vectorbase.org (iscapularis@vectorbase.org) Date: Thu Feb 7 05:43:36 2008 Subject: [Ixodes] Ixodes scapularis common name In-Reply-To: <47AA7F71.7090905@uiuc.edu> References: <47AA7F71.7090905@uiuc.edu> Message-ID: Ahem, folks..... we adopted the Linnaean system in 1759 (or was it 1735?) precisely because of the issues raised by Hugh.... The only "authoritative" name is Ixodes scapularis (I. dammini afficianados notwithstanding!). "Black-legged tick" and "deer tick" are equally "non-authoritative" so feel free to use either (or neither)! Reuben ************ At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: >I see in the NCBI files that the common name is given as >black-legged tick, while I've been using deer tick for it. I checked >Wikipedia, and they give both. Hardly the most authoritative source, >but these days the first place I check for most anything. I think >I'll stick with deer tick if possible. Anyone interested in updating >the Wikipedia page, it could use some help! Hugh >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis -- W. Reuben Kaufman, Leverhulme Visiting Professor, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, England, UK BA2 7AY Tel: + 44 - (0)1225 - 386318 Fax: + 44 - (0)1225 - 386779 E-mail: reuben.kaufman@ualberta.ca Personal Web Address: http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080207/c14bbc86/attachment-0001.html From reuben.kaufman at ualberta.ca Thu Feb 7 06:43:40 2008 From: reuben.kaufman at ualberta.ca (Reuben Kaufman) Date: Thu Feb 7 06:47:22 2008 Subject: [Ixodes] Ixodes scapularis common name Message-ID: Let me correct myself (pedantic professor that I am) before we get a flurry of objections: Linnaeus published successive editions of Systema Naturae beginning in 1735.... That's a far cry, of course, from his system being universally adopted then .... Now that I got myself started, however, I'm probing around a bit to see if I can nail that down a bit more. Cheers all, Reuben Ahem, folks..... we adopted the Linnaean system in 1759 (or was it 1735?) precisely because of the issues raised by Hugh.... The only "authoritative" name is Ixodes scapularis (I. dammini afficianados notwithstanding!). "Black-legged tick" and "deer tick" are equally "non-authoritative" so feel free to use either (or neither)! Reuben ************ At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: >I see in the NCBI files that the common name is given as >black-legged tick, while I've been using deer tick for it. I checked >Wikipedia, and they give both. Hardly the most authoritative source, >but these days the first place I check for most anything. I think >I'll stick with deer tick if possible. Anyone interested in updating >the Wikipedia page, it could use some help! Hugh >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis -- W. Reuben Kaufman, Leverhulme Visiting Professor, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, England, UK BA2 7AY Tel: + 44 - (0)1225 - 386318 Fax: + 44 - (0)1225 - 386779 E-mail: reuben.kaufman@ualberta.ca Personal Web Address: http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080207/d41647fe/attachment.html From durland.fish at yale.edu Thu Feb 7 09:16:55 2008 From: durland.fish at yale.edu (Durland Fish) Date: Thu Feb 7 09:20:59 2008 Subject: [Ixodes] Ixodes scapularis common name In-Reply-To: Message-ID: <200802071417.m17EGva6020847@pantheon-po08.its.yale.edu> I believe quite the opposite is true. I. scapularis has an official common name - black-legged tick - approved by ESA, so using deer tick for I. scapularis is incorrect. There is disagreement over the scientific name which is still unresolved. Although the last published revision has precedence, following it is not compulsory. Authors are free to use either I. scapularis or I. dammini to distinguish between northern and southern forms which have different host-seeking behaviors. As far as I know, the common name of deer tick for I. dammini was never approved by ESA. Durland _____ From: iscapularis-bounces@vectorbase.org [mailto:iscapularis-bounces@vectorbase.org] On Behalf Of iscapularis@vectorbase.org Sent: Thursday, February 07, 2008 5:40 AM To: iscapularis@vectorbase.org Subject: Re: [Ixodes] Ixodes scapularis common name Ahem, folks..... we adopted the Linnaean system in 1759 (or was it 1735?) precisely because of the issues raised by Hugh.... The only "authoritative" name is Ixodes scapularis (I. dammini afficianados notwithstanding!). "Black-legged tick" and "deer tick" are equally "non-authoritative" so feel free to use either (or neither)! Reuben ************ At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: I see in the NCBI files that the common name is given as black-legged tick, while I've been using deer tick for it. I checked Wikipedia, and they give both. Hardly the most authoritative source, but these days the first place I check for most anything. I think I'll stick with deer tick if possible. Anyone interested in updating the Wikipedia page, it could use some help! Hugh _______________________________________________ Iscapularis mailing list Iscapularis@vectorbase.org http://mail.vectorbase.org:82/mailman/listinfo/iscapularis -- W. Reuben Kaufman, Leverhulme Visiting Professor, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, England, UK BA2 7AY Tel: + 44 - (0)1225 - 386318 Fax: + 44 - (0)1225 - 386779 E-mail: reuben.kaufman@ualberta.ca Personal Web Address: http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080207/45060b9b/attachment.html From lorenzabeati at georgiasouthern.edu Thu Feb 7 13:43:28 2008 From: lorenzabeati at georgiasouthern.edu (Lorenza Beati) Date: Thu Feb 7 13:47:10 2008 Subject: [Ixodes] Ixodes scapularis common name In-Reply-To: References: Message-ID: <620d8edf84549ce4b0bac209e89c76df@georgiasouthern.edu> To all of you: I contacted Jim Keirans for the best informed opinion about these issues and here it is: Ixodes scapularis has an "Official Common Name" and it is the blacklegged tick. Note that ther is no hyphen between black and legged. The deer tick is not its official common name nor is it the official common name for any tick as far as I know. [....] Me, Lance, Joel and Hans (NOt sure of the order, but I was senior author) in around 1996 in J. Med Entomol. published a redescription of I scapularis. In that paper I discussed the common names for both I. scapularis and I. dammini. When Spielman et al. described I. dammini they gave it a common name, "Dammin's northeastern deer ixodid." So even if you believed I. dammini to be valid, calling it the deer tick would be incorrect since the original author's gave it a different common name. Voil? Hope this helps Lorenza On 7, Feb 2008, at 6:43, Reuben Kaufman wrote: Let me correct myself (pedantic professor that I am) before we get a flurry of objections: Linnaeus published successive editions of Systema Naturae beginning in 1735.... That's a far cry, of course, from his system being universally adopted then .... Now that I got myself started, however, I'm probing around a bit to see if I can nail that down a bit more. Cheers all, Reuben Ahem, folks..... we adopted the Linnaean system in 1759 (or was it 1735?) precisely because of the issues raised by Hugh.... The only "authoritative" name is Ixodes scapularis (I. dammini afficianados notwithstanding!). "Black-legged tick" and "deer tick" are equally "non-authoritative" so feel free to use either (or neither)! Reuben ************ At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: > I see in the NCBI files that the common name is given as black-legged > tick, while I've been using deer tick for it. I checked Wikipedia, and > they give both. Hardly the most authoritative source, but these days > the first place I check for most anything. I think I'll stick with > deer tick if possible. Anyone interested in updating the Wikipedia > page, it could use some help! Hugh > _______________________________________________ > Iscapularis mailing list > Iscapularis@vectorbase.org > http://mail.vectorbase.org:82/mailman/listinfo/iscapularis -- W. Reuben Kaufman, Leverhulme Visiting Professor, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, England, UK?? BA2 7AY Tel: + 44 - (0)1225 - 386318 Fax: + 44 - (0)1225 - 386779 E-mail: reuben.kaufman@ualberta.ca Personal Web Address: http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php _______________________________________________ Iscapularis mailing list Iscapularis@vectorbase.org http://mail.vectorbase.org:82/mailman/listinfo/iscapularis Dr Lorenza Beati Associate Professor Curator - U.S. National Tick Collection Institute of Arthropodology and Parasitology Georgia Southern University 114 Georgia Ave. P.O. Box 8056 STATESBORO, GA 30460-8056 phone: 912-681-5564 fax: 912-681-0559 e-mail: lorenzabeati@georgiasouthern.edu web page: http://personal.georgiasouthern.edu/~lorenzab/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3417 bytes Desc: not available Url : http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080207/bc1b78ce/attachment.bin From dsonensh at odu.edu Thu Feb 7 14:21:34 2008 From: dsonensh at odu.edu (Daniel Sonenshine) Date: Thu Feb 7 14:25:43 2008 Subject: [Ixodes] Ixodes scapularis common name In-Reply-To: <620d8edf84549ce4b0bac209e89c76df@georgiasouthern.edu> Message-ID: Hi: This settles the issue as far as I'm concerned. The Ent. Soc. America uses approved common names. For Ixodes scapularis, it is the "blacklegged tick", as Jim Keirans noted. Dan Dr. Daniel E. Sonenshine Professor (Emeritus) Department of Biological Sciences Old Dominion University Norfolk, Virginia 23529 Tel (757) 683 - 3612 Fax (757) 683-5283 e-mail: dsonensh@odu.edu Lorenza Beati To Sent by: Reuben Kaufman iscapularis-bounc es@vectorbase.org cc iscapularis@vectorbase.org Subject 02/07/2008 01:47 Re: [Ixodes] Ixodes scapularis PM common name To all of you: I contacted Jim Keirans for the best informed opinion about these issues and here it is: Ixodes scapularis has an "Official Common Name" and it is the blacklegged tick. Note that ther is no hyphen between black and legged. The deer tick is not its official common name nor is it the official common name for any tick as far as I know. [....] Me, Lance, Joel and Hans (NOt sure of the order, but I was senior author) in around 1996 in J. Med Entomol. published a redescription of I scapularis. In that paper I discussed the common names for both I. scapularis and I. dammini. When Spielman et al. described I. dammini they gave it a common name, "Dammin's northeastern deer ixodid." So even if you believed I. dammini to be valid, calling it the deer tick would be incorrect since the original author's gave it a different common name. Voil? Hope this helps Lorenza On 7, Feb 2008, at 6:43, Reuben Kaufman wrote: Let me correct myself (pedantic professor that I am) before we get a flurry of objections: Linnaeus published successive editions of Systema Naturae beginning in 1735.... That's a far cry, of course, from his system being universally adopted then .... Now that I got myself started, however, I'm probing around a bit to see if I can nail that down a bit more. Cheers all, Reuben Ahem, folks..... we adopted the Linnaean system in 1759 (or was it 1735?) precisely because of the issues raised by Hugh.... The only "authoritative" name is Ixodes scapularis (I. dammini afficianados notwithstanding!). "Black-legged tick" and "deer tick" are equally "non-authoritative" so feel free to use either (or neither)! Reuben ************ At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: > I see in the NCBI files that the common name is given as black-legged > tick, while I've been using deer tick for it. I checked Wikipedia, and > they give both. Hardly the most authoritative source, but these days > the first place I check for most anything. I think I'll stick with > deer tick if possible. Anyone interested in updating the Wikipedia > page, it could use some help! Hugh > _______________________________________________ > Iscapularis mailing list > Iscapularis@vectorbase.org > http://mail.vectorbase.org:82/mailman/listinfo/iscapularis -- W. Reuben Kaufman, Leverhulme Visiting Professor, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, England, UK?? BA2 7AY Tel: + 44 - (0)1225 - 386318 Fax: + 44 - (0)1225 - 386779 E-mail: reuben.kaufman@ualberta.ca Personal Web Address: http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php _______________________________________________ Iscapularis mailing list Iscapularis@vectorbase.org http://mail.vectorbase.org:82/mailman/listinfo/iscapularis Dr Lorenza Beati Associate Professor Curator - U.S. National Tick Collection Institute of Arthropodology and Parasitology Georgia Southern University 114 Georgia Ave. P.O. Box 8056 STATESBORO, GA 30460-8056 phone: 912-681-5564 fax: 912-681-0559 e-mail: lorenzabeati@georgiasouthern.edu web page: http://personal.georgiasouthern.edu/~lorenzab/ _______________________________________________ Iscapularis mailing list Iscapularis@vectorbase.org http://mail.vectorbase.org:82/mailman/listinfo/iscapularis From hughrobe at uiuc.edu Thu Feb 7 15:42:01 2008 From: hughrobe at uiuc.edu (Hugh Robertson) Date: Thu Feb 7 15:49:15 2008 Subject: [Ixodes] Ixodes scapularis common name In-Reply-To: References: Message-ID: <47AB6D19.1020109@uiuc.edu> Thanks everyone, as a member of an Entomology Department and the ESA, I'm embarrased to say that I've called it the "deer tick" in publications. I'll stick with "blacklegged tick" from here on out. It is usually possible for GenBank to do global changes in files, so perhaps whoever at JCVI submitted the assembly to GenBank could ask them to remove the hyphen. Hugh Daniel Sonenshine wrote: >Hi: > This settles the issue as far as I'm concerned. The Ent. Soc. America >uses approved common names. For Ixodes scapularis, it is the "blacklegged >tick", as Jim Keirans noted. >Dan > > > >Dr. Daniel E. Sonenshine >Professor (Emeritus) >Department of Biological Sciences >Old Dominion University >Norfolk, Virginia 23529 >Tel (757) 683 - 3612 >Fax (757) 683-5283 >e-mail: dsonensh@odu.edu > > > > Lorenza Beati > rgiasouthern.edu> To > Sent by: Reuben Kaufman > iscapularis-bounc > es@vectorbase.org cc > iscapularis@vectorbase.org > Subject > 02/07/2008 01:47 Re: [Ixodes] Ixodes scapularis > PM common name > > > > > > > > > > >To all of you: >I contacted Jim Keirans for the best informed opinion about these >issues and here it is: > >Ixodes scapularis has an "Official Common Name" and it is the >blacklegged tick. Note that ther is no hyphen between black and >legged. The deer tick is not its official common name nor is it the >official common name for any tick as far as I know. >[....] Me, Lance, Joel and Hans (NOt sure of the order, but I was >senior author) in around 1996 in J. Med Entomol. published a >redescription of I scapularis. In that paper I discussed the common >names for both I. scapularis and I. dammini. When Spielman et al. >described I. dammini they gave it a common name, "Dammin's northeastern >deer ixodid." So even if you believed I. dammini to be valid, calling >it the deer tick would be incorrect since the original author's gave it >a different common name. > >Voil? >Hope this helps >Lorenza > > > > > > >On 7, Feb 2008, at 6:43, Reuben Kaufman wrote: > >Let me correct myself (pedantic professor that I am) before we get a >flurry of objections: > >Linnaeus published successive editions of Systema Naturae beginning in >1735.... That's a far cry, of course, from his system being universally >adopted then .... Now that I got myself started, however, I'm probing >around a bit to see if I can nail that down a bit more. > >Cheers all, >Reuben > > > >Ahem, folks..... we adopted the Linnaean system in 1759 (or was it >1735?) precisely because of the issues raised by Hugh.... > >The only "authoritative" name is Ixodes scapularis (I. dammini >afficianados notwithstanding!). "Black-legged tick" and "deer tick" are >equally "non-authoritative" so feel free to use either (or neither)! > >Reuben >************ > > > >At 9:48 PM -0600 2/6/08, iscapularis@vectorbase.org wrote: > > >>I see in the NCBI files that the common name is given as black-legged >>tick, while I've been using deer tick for it. I checked Wikipedia, and >>they give both. Hardly the most authoritative source, but these days >>the first place I check for most anything. I think I'll stick with >>deer tick if possible. Anyone interested in updating the Wikipedia >>page, it could use some help! Hugh >> _______________________________________________ >> Iscapularis mailing list >> Iscapularis@vectorbase.org >> http://mail.vectorbase.org:82/mailman/listinfo/iscapularis >> >> > >-- > > > > W. Reuben Kaufman, > Leverhulme Visiting Professor, > Department of Biology and Biochemistry, > University of Bath, > Claverton Down, > Bath, England, UK BA2 7AY > Tel: + 44 - (0)1225 - 386318 > Fax: + 44 - (0)1225 - 386779 > E-mail: reuben.kaufman@ualberta.ca > Personal Web Address: > http://www.biology.ualberta.ca/faculty/reuben_kaufman/index.php >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis > >Dr Lorenza Beati >Associate Professor >Curator - U.S. National Tick Collection >Institute of Arthropodology and Parasitology >Georgia Southern University >114 Georgia Ave. >P.O. Box 8056 >STATESBORO, GA 30460-8056 >phone: 912-681-5564 >fax: 912-681-0559 >e-mail: lorenzabeati@georgiasouthern.edu >web page: http://personal.georgiasouthern.edu/~lorenzab/ >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis > > >_______________________________________________ >Iscapularis mailing list >Iscapularis@vectorbase.org >http://mail.vectorbase.org:82/mailman/listinfo/iscapularis > > From mhammond at ebi.ac.uk Thu Feb 7 15:52:43 2008 From: mhammond at ebi.ac.uk (Martin Hammond) Date: Thu Feb 7 15:56:27 2008 Subject: Assembly points (was Re: [Ixodes] Ixodes scapularis Listserv) In-Reply-To: <47A969F9.9010903@uiuc.edu> References: <7B822100FD93C646B5D905DC842F65943C98D2@EXCH05.purdue.lcl> <47A969F9.9010903@uiuc.edu> Message-ID: Hi Hugh, Thanks for the peek at your preliminary gene finding. I'm one of the people working on making a genome-wide set of preliminary gene models on the assembly. Just a couple of points for the list in case anyone is unclear about the assembly. The contigs have been released via GenBank - that includes ~half a million degenerate/low confidence ones as well as the ~half million that are considered the formal assembly. Some of the latter have been joined into scaffolds. We will release the scaffolds, as well as the contigs, via VectorBase as soon as we can, and are delaying only until we can be sure we have a fixed set of identifiers. Some of your single exon fragments of genes will, I'd hope, get linked in scaffolds. But there's no getting around your point that many will be fragments! To partially address your second email, there has been some preliminary looks at how many of the ESTs hit the assembly. It is, unfortunately, true that a significant proportion do not give a high similarity/near full-length match. Also, if I look for at least partial exact matching between the assembly and the relatively small number of Ixodes scapularis proteins in GenBank (a large proportion of which are Jose Ribeiro's sialome ones), some are not found. We plan to do a lot more analysis of this and will keep the list posted when we have some proper numbers. Regards, Martin Martin Hammond VectorBase / EBI On 6 Feb 2008, at 08:04, iscapularis@vectorbase.org wrote: > Thanks for the listerve and update, Cate. Congratulations to > everyone at the two sequencing centers and especially the JCVI > assembly folk for fighting with this beast. I wonder if we can ask > for some more details about the assembly, especially why 10 m reads > did not make it into the assembly. Obviously 1m contigs with only > half of them in scaffolds and around 3.4X depth means that gene > building is often going to be hard, much like the available Bombyx > mori assemblies, and the resultant gene count inflated by > fragments. But at least we have the raw traces so we can manually > extend contigs, etc. for genes we care about. > > I took a quick look around at some of my favorite genes, and found > some nice and some not so nice things. > > First, for the chemoreceptors, I predicted there would be no > orthologs of the insect odorant receptors or Ors, since I predicted > in 2003 those are novel with terrestriality in insects, and, as > with Daphnia, find no ortholog of the highly conserved DmOr83b > protein which in insects forms a heterodimeric partner with all the > specific Ors, hence most likely no Ors. (Functional olfactory > receptors of course could exist within the Gr family below). > > Second, I expected to find some gustatory receptors or Grs, the > broader and more basal family of the insect chemoreceptors > superfamily, because I've found a few distant relatives in > nematodes. Although there are no obvious orthologs of the carbon > dioxide receptors that are highly conserved in insects, or the > sugar receptors (and this is the same for Daphnia), I finally found > (using TBLASTN searches with E=1000 and the last 20aa or so of the > mildly conserved C-terminus of diverse insect Grs), a series of 9 > single ORF genes of about 1.2kb that encode a remarkably diverse > set of tick Grs. There also appear to be genes related to these > with introns, but I can only find the C-terminal third for now. > I'll work more on these later - Nasonia, Culex, and Daphnia come > first - all done, but manuscripts need writing. > > Third, I checked some other favorite genes. There is a simple > ortholog of telomerase or TERT, with a large 2.5kb ORF encoding > most of it, but the N-terminus is missing in a gap. There appears > to be a 95% identical version that for some reason was not > assembled and I will eventually do it manually. I will also fight > with the telomeres themselves, which contain TTAGG repeats - is > there a set of fosmid reads I can work from? > > Fourth, I checked for DNMT1, and find a series of paralogs, some > with tons of introns, which seem pleasantly short, but not > completely worked up, one with just a couple of short introns, and > one single long ORF! Some insects and Daphnia also have multiple > DNMT1 paralogs. For DNMT2 a single conserved ortholog was expected > and found as a single 1.5kb ORF. I then checked DNMT3, which is > more divergent amoungst animals, and it is there, but spread out, > with single short exons on each contig. > > Fifth, I checked SID-1, the apparent RNA transporter implicated in > RNAi in nematodes, and with multiple homologs in many insects, but > nothing obvious. > > Sixth, I tried cryptochrome from the circadian rhythms, and it is > nicely there, but with one exon per contig. > > Seventh, I checked Mahya, a follistatin-5 homolog, and it is there, > but with many long introns and spread out across several contigs. > > Eigth, I checked pteropsin, and it finds a whole bunch of opsins, > most single ORFs in single contigs, which will be fun to work up > and compare with the 46 Daphnia opsins we are writing up now. > > In summary, remarkably many of these genes are single ORFs in > single contigs, so could be built by automated programs. But most > cross multiple contigs and will be impossible to build > automatically, except as fragments. They will also be hard to > deposit manually in the inferential Third Party Annotation database > at GenBank, which requires that the genes be completely contained > within single contigs. So it looks like a mixed bag. > > Hugh > > > iscapularis@vectorbase.org wrote: > >> >> Welcome to the /Ixodes scapularis/ genome listserv! >> >> >> This listserv has been created to communicate information >> regarding the /Ixodes scapularis/ (Lyme disease tick) genome >> sequence. >> >> >> This listserv is hosted by VectorBase > index.php> , an NIAID, NIH Bioinformatics Resource Center for >> invertebrate vectors of human disease. If you would like to >> unsubscribe or add others to the distribution list, please go to: >> http://mail.vectorbase.org:82/mailman/listinfo/iscapularis. >> >> >> * Release of the /Ixodes scapularis/ genome assembly * >> >> The National Institute of Allergy and Infectious Diseases, >> National Institutes of Health has funded the sequencing, assembly >> and annotation of the /Ixodes scapularis/ genome through its >> Microbial Sequencing Centers > genomes/mscs/overview.htm> (the J. Craig Venter Institute ( JCVI >> ) and the Broad Institute > www.broad.mit.edu/> ) and the NIAID-funded Bioinformatics Resource >> Center, VectorBase, at the University of Notre Dame. Whole genome >> shotgun sequence data have now been generated and assembled, >> providing 3.8 fold coverage of the /Ixodes scapularis/ genome. >> The Whole Genome Shotgun project has been deposited at GenBank >> under the project accession ABJB010000000 > www.ncbi.nlm.nih.gov/sites/entrez? >> Db=genomeprj&cmd=ShowDetailView&TermToSearch=16232> (consisting of >> contig accessions ABJB010000001-ABJB011141594). This first public >> assembly is deposited as JCVI_ISG_i3_1.0 and has the VectorBase >> designation IscaW1. >> >> >> * Assembly Statistics * >> >> Total number of sequence reads: 17.4 million >> >> Total number of sequence reads placed in the assembly: 7.3 million >> >> Estimated fold coverage of the assembly: 3.8 fold >> >> Number of contigs deposited at GenBank: 1,141,594 >> >> Number of contigs used in assembly: 570,640 >> >> Number of scaffolds: 369,495 >> >> Total length of combined contigs 1.4 Gb >> >> Total length of combined scaffolds (including gaps) 1.8 Gb >> >> >> * Annotation Release * >> >> Preliminary annotations of the assembly by the MSCs and by VB (0.5 >> gene sets) are expected to be released in April 2008 at VectorBase >> . Community scientists may >> submit manual annotations to VectorBase via a web-based submission >> process. Community annotations will be reviewed by VectorBase >> annotators and incorporated into a merged, final gene set in >> accordance with the NIAID approved project plan. This more >> complete annotation, including functional assignments, is planned >> for release in GenBank and VectorBase by September 2008. Long- >> term curation of the sequence and subsequent annotation updates >> will be the responsibility of VectorBase. >> >> * * >> >> * Supplementary Data Release * >> >> Complementary to the sequencing and annotation project described >> above, the NIAID, NIH has also funded a project to provide >> additional /Ixodes scapularis/ genome-related resources. As part >> of this project 183,834 /Ixodes scapularis/ EST sequences have >> been deposited at GenBank (accession range: EW781064-EW964897). >> These sequences are also available as part of the /Ixodes >> scapularis/ gene index at the Dana Faber Cancer Institute Gene >> Indices . Forty-five BAC >> clones from a 10X /Ixodes scapularis/ BAC library have also been >> sequenced and assembled. The assembled BAC sequences are >> available at GenBank under accession ranges: AC192414-AC192429, >> AC192742-AC192744, AC200531, and AC205630-AC205654. More than >> 370,000 BAC clones have also been end sequenced and are available >> from the NCBI trace archive and at VectorBase. >> >> >> >> >> Catherine A. Hill, PhD >> >> Assistant Professor >> >> Department of Entomology >> >> Purdue University >> >> 901 West State Street >> >> West Lafayette , IN , 47907 >> >> Tel: (765) 496 6157 >> >> Fax: (765) 496 1219 >> >> >> >> --------------------------------------------------------------------- >> --- >> >> _______________________________________________ >> Iscapularis mailing list >> Iscapularis@vectorbase.org >> http://mail.vectorbase.org:82/mailman/listinfo/iscapularis >> > > _______________________________________________ > Iscapularis mailing list > Iscapularis@vectorbase.org > http://mail.vectorbase.org:82/mailman/listinfo/iscapularis