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There are two complete genomes and at least 83 mitochondrial genomes for species in the phylum Mollusca. ---- ==== Complete Genomes:==== There are two mollusk genomes publicly available: * [[http://en.wikipedia.org/wiki/Aplysia_californica|California sea hare]], //Aplysia californica// * Animalia, Mollusca, Gastropoda, Heterobranchia, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia * This is the most complete mollusk genome assembled. * The sequencing and assembly was performed at the [[http://www.broadinstitute.org/|Broad Institute]] in Cambridge, MA. Their project site is [[http://www.broadinstitute.org/science/projects/mammals-models/vertebrates-invertebrates/aplysia/aplysia-genome-sequencing-project]]. * Tom Pringle said //"The other mollusk genome, Aplysia californica (sea hare), was sequenced by Broad using an inbred line. Sizable assembled contigs are now open to tblastn at the wgs division of GenBank (which allows the exons to be determined). Despite the assembly, sequencing continued: 212,159 new traces were added in Nov 07. Millions of traces might not have been used in the Aplcal1.0 assembly; Aplcal2.0 may have subsumed these. There are 256,000 cDNA dating from mid-2009. No publication in sight here either but here one is probably planned."// * It was added to the [[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=155184841&clade=other&org=Sea+hare&db=0|UCSC Genome Browser]] on March 19, 2010. This browser was built on the Aplca2.0 assembly, so presumably uses most of the data Tom refers to. * [[http://genome.jgi-psf.org/Lotgi1/|Giant owl limpet]], //Lottia gigantea// * Mollusca, Gastropoda, Prosobranchia, Patellogastropoda, Nacellina, Lottiidae * [[http://genome.jgi-psf.org/Lotgi1/Lotgi1.info.html|JGI]] says 359.5Mbases, but the scaffold is still over 20,000 contigs, with the largest scaffold only 9.4Mbases. It looks like it has been almost 3 years since anyone did anything on //Lottia gigantea.// * Tom Pringle sent e-mail to genecats that said, //"There are a great many stalled-out JGI genomes like this. The last of 5.3 million traces appeared in May 2005. In Jan 2007, JGI presented the genome at a meeting talk. No paper ever appeared. A quarter million cDNA were seqd by Dec 2007. JGI offers blast of the assembly 1.0 and display on their funky browser. Their gene models are worthless and are not integrated with the cDNA. SuperFamily has analyzed 23,851 models for domains. Nothing has been submitted to Genbank wgs division. No explanation appears on their Lottia web page which has not been updated for several years."// Of the two genomes, the sea hare seems to be taxonomically closer to //Ariolimax dolichophallus//. ==== Mitochondrial Genomes:==== [[http://www.ncbi.nlm.nih.gov/genomes/genlist.cgi?taxid=6447&name=Mollusca|NCBI List of Mullusca genomes]] - This list shows all Mollusk (taxid: 6447) entries in the NCBI genome database. For some reason this list only shows mitochondrial genomes. Even the sea hare is missing (just lists a older mitochondrial sequence from University of Florida. This could indicate that there are other mollusk genomes out there or in progress. === Possibly Closest To Banana Slug === NC_001816 Links Cepaea nemoralis mitochondrion, complete genome DNA; circular; Length: 14,100 nt Organelle: mitochondrion Created: 1999/08/24 2: NC_001761 Links Albinaria coerulea mitochondrion, complete genome DNA; circular; Length: 14,130 nt Organelle: mitochondrion Created: 1999/08/24 * Unordered List Item
Discussion
This page is more or less what I would like to move away from. This is an amalgamation of data that is not part of our project. There is basically no chance that this page will stay current, and when people view our webpage and encounter old data it skews their perspective of our page.
The wiki needs to be concise and relevant, or nobody will take it seriously. Pages like this essentially feel like google searches dropped into a wiki page, it will detract from the site.
It will remain alive in the archive for future classes to deal with.
This page exists as a section of the online “lab notebook” as I was told to treat the wiki when I was studying something relevant to the class. Not every page needs to be intended to be about our project or what we have done. Some pages can just be a convenient summary of information until we add relevant analysis from our data.
Eventually This page will have information from comparing our assemblies to the ones listed on this page.