Banana Slug Genomics

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======= Mollusk Genomics =======

As of May 11, 2015 there are 6 different assembled mollusk(taxid:6447) genomes on NCBI database

[[http://www.ncbi.nlm.nih.gov/assembly/organism/6447/all/|Mollusk Assemblies]]

  * [[http://en.wikipedia.org/wiki/Aplysia_californica|California sea hare]], //Aplysia californica//
    * Animalia, Mollusca, Gastropoda, **Heterobranchia**, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia
    * [[http://www.ncbi.nlm.nih.gov/nuccore/AASC00000000|AplCal3.0 Assembly]] representative genome
      * Submitted 05/15/2013 by [[http://www.broadinstitute.org/|Broad Institute]] in Cambridge, MA. 
      * Largest Contig: 174,336 bp
    * [[http://www.ncbi.nlm.nih.gov/nuccore/AASC00000000.2|AplCal2.0 Assembly]]
      * Submitted 07/17/2009 by Broad Institute in Cambridge, MA.
      * [[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=155184841&clade=other&org=Sea+hare&db=0|UCSC Genome browser page]]
      * Largest Contig: 303,309 bp
  * [[http://genome.wustl.edu/genomes/detail/biomphalaria-glabrata/|Bloodfluke Planorb]], //Biomphalaria glabrata//
    * Animalia, Mollusca, Gastropoda, Heterobranchia, Euthyneura, **Panpulmonata**, Hygrophila, Planorboidea, Planorbidae; Biomphalaria
    * [[http://www.ncbi.nlm.nih.gov/nuccore/APKA00000000.1/|BB02 Assembly]]
      * Submitted 09/06/2013 by Washington University
      * largest Contig: 526,532 bp (major outlier 2nd biggest is 100,139	bp)
    * [[http://www.ncbi.nlm.nih.gov/pubmed/15562597|The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni]]
  * [[http://en.wikipedia.org/wiki/Pacific_oyster|Pacific oyster]], //Crassostrea gigas//
    * Animalia, **Mollusca**, Bivalvia, Pteriomorphia, Ostreoida, Ostreoidea, Ostreidae, Crassostrea
    * [[http://www.ncbi.nlm.nih.gov/nuccore/AFTI00000000.1/|oyster_v9 Assembly]]
      * Submitted 09/19/2012 by BGI-Shenzhen
      * Largest Contig: 212,823 bp
    * [[http://www.ncbi.nlm.nih.gov/pubmed/22992520|The oyster genome reveals stress adaptation and complexity of shell formation.]]
  * [[http://genome.jgi-psf.org/Lotgi1/|Giant owl limpet]], //Lottia gigantea//
    * Animalia, Mollusca, **Gastropoda**, Prosobranchia, Patellogastropoda, Nacellina, Lottiidae
    * [[http://www.ncbi.nlm.nih.gov/nuccore/AMQO00000000.1/|Helro1 Assembly]]
      * Submitted 12/20/2012 by DOE Joint Genome Institute
      * Largest Contig: 745,440 bp
    * [[http://www.ncbi.nlm.nih.gov/pubmed/23254933|Insights into bilaterian evolution from three spiralian genomes]]
  * [[http://en.wikipedia.org/wiki/Mediterranean_mussel|Mediterranean mussel]], //Mytilus galloprovincialis//
    * Animalia, **Mollusca**, Bivalvia, Pteriomorphia, Mytiloida, Mytiloidea, Mytilidae, Mytilinae, Mytilus.
    * [[http://www.ncbi.nlm.nih.gov/nuccore/APJB000000000.1/|mussel1.0 Assembly]]
      * Submitted 05/18/2014 by Deakin University
      * Not Scaffolded, only contigs
      * largest Contig: 39,674 bp
  * [[http://en.wikipedia.org/wiki/Zebra_mussel|Zebra mussel]] //Dreissena polymorpha//
    * Animalia, **Mollusca**, Bivalvia, Heteroconchia, Euheterodonta, Veneroida, Dreissenoidea, Dreissenidae, Dreissena.
    * [[http://www.ncbi.nlm.nih.gov/nuccore/JWHF00000000.1/|ASM80632v1 Assembly]]
      * Submitted 12/22/2014 by University of Girona
      * Not Scaffolded, only partial genome represented
      * largest Contig: 8,717 bp
    * [[http://www.ncbi.nlm.nih.gov/pubmed/25780924|Using Massive Parallel Sequencing for the development, validation, and application of population genetics markers in the invasive bivalve zebra mussel (Dreissena polymorpha)]]





==== Publications ====

[[http://www.ncbi.nlm.nih.gov/pubmed/21672613|Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation.]]

[[http://www.biomedcentral.com/1471-2148/11/295|Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships]]



======= Old Content =======


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.
=== Closest To Banana Slug ===
There are two mitochondrial genomes that are in the same infraorder (//Stylommatophora//; land slugs) as the banana slug:
  - [[http://en.wikipedia.org/wiki/Grove_snail|Cepaea nemoralis]]\\ [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=12206|NC_001816]]\\ mitochondrion, complete genome\\ DNA; circular; Length: 14,100 nt\\ Organelle: mitochondrion\\ Created: 1999/08/24
  - [[http://en.wikipedia.org/wiki/Albinaria|Albinaria coerulea]]\\ [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=11604|NC_001761]]\\ mitochondrion, complete genome\\ DNA; circular; Length: 14,130 nt\\ Organelle: mitochondrion\\ Created: 1999/08/24
Banana Slug Genomics

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