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Mollusk Genomics

As of May 11, 2015 there are 7 different assembled mollusk(taxid:6447) genomes from 6 different organisms on NCBI database.

The slender banana slug, Ariolimax dolichophallus, is of Mollusca, Gastropoda, Heterobranchia, Euthyneura, Panpulmonata, Eupulmonata, Stylommatophora, Sigmurethra, Arionoidea, Ariolimacidae, Ariolimacinae, Ariolimax. The closest clade to the banana slug is in bold when known.

Mollusk Assemblies

  • California sea hare, Aplysia californica
    • Animalia, Mollusca, Gastropoda, Heterobranchia, Euthyneura, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia
    • There are 74 published protein structures from this organism, mostly Acetylcholine Binding Protein
    • AplCal3.0 Assembly representative genome
      • Submitted 05/15/2013 by Broad Institute in Cambridge, MA.
      • Assembled with allpaths v. R40582 using 66X coverage of HiSeq reads
      • Length including gaps: 927296314
      • Length excluding gaps: 737783370
      • Number of scaffolds: 4331
      • Scaffold N50 including gaps: 917541
      • Scaffold N90 including gaps: 207684
      • Scaffold N50 excluding gaps: 780203
      • Scaffold N90 excluding gaps: 172466
      • Number of contigs: 164544
      • Contig N50: 9584
      • Contig N90: 1577
      • Longest contig: 174336
      • Longest ungapped scaffold: 498004
      • 25,024 protein sequences
      • Submitted 07/17/2009 by Broad Institute in Cambridge, MA.
      • made using 13.26x coverage of ABI reads
      • Largest Contig: 303,309 bp
  • Bloodfluke Planorb, Biomphalaria glabrata
  • Pacific oyster, Crassostrea gigas
  • Giant owl limpet, Lottia gigantea
    • Animalia, Mollusca, Gastropoda, Prosobranchia, Patellogastropoda, Nacellina, Lottiidae
      • Submitted 12/20/2012 by DOE Joint Genome Institute
      • Assembled with JGI Jazz v. 08/24/2006 using 8.87x coverage of Sanger reads
      • Largest contig: 745,440 bp
      • 18,335 contigs, total length is 298,896,825 bp
      • 4,475 scaffolds, total scaffold length is 359,505,668 bp
      • 51/1.87 Mbp scaffold N50
      • 23,822 Protein sequences
  • Mediterranean mussel, Mytilus galloprovincialis
    • Animalia, Mollusca, Bivalvia, Pteriomorphia, Mytiloida, Mytiloidea, Mytilidae, Mytilinae, Mytilus.
      • Submitted 05/18/2014 by Deakin University
      • Assembled with Velvet v. 1.1.06 using 17.0x coverage of Illumina HiSeq reads
      • Not Scaffolded, only contigs
      • largest Contig: 39,674 bp
      • 2,315,965 Contigs, total length is 1,622,683,383 bp
  • Zebra mussel Dreissena polymorpha

Relevant Data

Relevant Publications

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:

  • California sea hare, Aplysia californica
    • Animalia, Mollusca, Gastropoda, Heterobranchia, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia
    • This is the most complete mollusk genome assembled.
    • 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 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.
  • Giant owl limpet, Lottia gigantea
    • Mollusca, Gastropoda, Prosobranchia, Patellogastropoda, Nacellina, Lottiidae
    • 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:

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:

  1. Cepaea nemoralis
    NC_001816
    mitochondrion, complete genome
    DNA; circular; Length: 14,100 nt
    Organelle: mitochondrion
    Created: 1999/08/24
  2. Albinaria coerulea
    NC_001761
    mitochondrion, complete genome
    DNA; circular; Length: 14,130 nt
    Organelle: mitochondrion
    Created: 1999/08/24

Discussion

, 2015/07/18 13:28

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.

, 2015/07/24 05:17

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.

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archive/other_mollusk_genomes.txt · Last modified: 2015/08/27 12:57 by jaredc