Banana Slug Genomics

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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=====

  * [[http://en.wikipedia.org/wiki/Aplysia_californica|California sea hare]], //Aplysia californica//
    * Animalia, Mollusca, Gastropoda, **Heterobranchia**, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia
    * There are 74 published protein structures from this organism, mostly Acetylcholine Binding Protein 
    * [[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.
      * 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
    * [[http://www.ncbi.nlm.nih.gov/nuccore/AASC00000000.2|AplCal2.0 Assembly]]
      * Submitted 07/17/2009 by Broad Institute in Cambridge, MA.
      * made using 13.26x coverage of ABI reads
      * [[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://en.wikipedia.org/wiki/Biomphalaria_glabrata|Bloodfluke Planorb]], //Biomphalaria glabrata//
    * Animalia, Mollusca, Gastropoda, Heterobranchia, Euthyneura, **Panpulmonata**, Hygrophila, Planorboidea, Planorbidae; Biomphalaria
    * the host for the medically important trematode parasite,[[http://en.wikipedia.org/wiki/Schistosoma_mansoni|Schistosoma mansoni]]
    * [[http://www.ncbi.nlm.nih.gov/nuccore/APKA00000000.1/|BB02 Assembly]]
      * Submitted 09/06/2013 by Washington University
      * Assembled by Newbler v. July 2011 using 27.5x coverage of 454 FLX Titanium reads
      * largest contig: 526,532 bp (major outlier 2nd biggest is 100,139 bp)
      * 408,321 contigs, total length is 898,888,039 bp
      * 14,225 scaffolds, scaffold length is 652,954,618 bases
      * N50 scaffold length of 42kb
    * [[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
      * Assembled by SOAPdenovo v. 1.05 using 100x coverage of Illumina HiSeq 2000 reads
      * Largest contig: 212,823 bp
      * 30,459 contigs, total length is 491,850,583 bp
      * 7,658 scaffolds, total scaffold length is 557,717,710 bases
      * 26,086 proteins
    * [[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
      * [[http://genome.jgi.doe.gov/Lotgi1/Lotgi1.info.html|main page]]
      * 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
    * [[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
      * 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
  * [[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
      * Assembled with GS De Novo Assembler v. 2.5.3. using 3x coverage of 454 reads
      * Not Scaffolded, only partial genome represented
      * largest Contig: 8,717 bp
      * 1,057 contigs, total length is 905,680 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)]]


===== Relevant Data =====

  * Protein, transcripts, and more details for Sea Hare, //Aplysia californica//
    * [[http://www.ncbi.nlm.nih.gov/genome/proteins/443?genome_assembly_id=29153|protein sequences]]
    * 25041 Predicted protein sequences and 13 known proteins from mitochondrial genes
    * [[http://www.ncbi.nlm.nih.gov/pubmed/21328528|Developmental transcriptome of Aplysia californica]]
    * [[https://genome.ucsc.edu/cgi-bin/hgGateway?db=aplCal|AplCal2 genome browser]]


  * Giant Chinese land snail, //Mastigeulota kiangsinensis//, complete mitochondria
    * Eukaryota, Metazoa, Lophotrochozoa, Mollusca, Gastropoda, Heterobranchia, Euthyneura, Panpulmonata, Eupulmonata, Stylommatophora, **Sigmurethra**, Helicoidea, Bradybaenidae, Mastigeulota.
    * http://www.ncbi.nlm.nih.gov/nuccore/NC_024935.1
    * [[http://www.ncbi.nlm.nih.gov/pubmed/25185698|The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae).]]
  * Giant African land snail, //Achatina fulica//, complete mitochondria
    * Eukaryota, Metazoa, Lophotrochozoa, Mollusca, Gastropoda, Heterobranchia, Euthyneura, Panpulmonata, Eupulmonata, Stylommatophora, **Sigmurethra**, Achatinoidea, Achatinidae, Achatina.
    * http://www.ncbi.nlm.nih.gov/nuccore/NC_024601.1
    * [[http://www.ncbi.nlm.nih.gov/pubmed/24975387|Complete mitochondrial genome of the giant African snail, Achatina fulica (Mollusca: Achatinidae): a novel location of putative control regions (CR) in the mitogenome within Pulmonate species.]]
  * Garden snail, //Helix aspersa (Cornu aspersum)//, complete mitochondria
    * Eukaryota, Metazoa, Lophotrochozoa, Mollusca, Gastropoda, Heterobranchia, Euthyneura, Panpulmonata, Eupulmonata, Stylommatophora, **Sigmurethra**, Helicoidea, Helicidae, Helix.
    * http://www.ncbi.nlm.nih.gov/nuccore/NC_021747.1
    * [[http://www.ncbi.nlm.nih.gov/pubmed/23826260|The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca): intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura.]]
  * Common octopus, //Octopus vulgaris//, complete mitochondria (a common out-group for gastropod mitochondria genome analysis)
    * Eukaryota, Metazoa, Lophotrochozoa, **Mollusca**, Cephalopoda, Coleoidea, Neocoleoidea, Octopodiformes, Octopoda, Incirrata, Octopodidae
    * http://www.ncbi.nlm.nih.gov/nuccore/53793887
    * [[http://www.ncbi.nlm.nih.gov/pubmed/15297602|Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes.]]



===== Relevant Publications =====

[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890673/|DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae)]]

[[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]]

[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389214/|Annotated Checklist of the Terrestrial Gastropods of Nepal]]

[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2287175/|From sea to land and beyond – New insights into the evolution of euthyneuran Gastropoda (Mollusca)]]

[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088622/|A phylogeny of the land snails (Gastropoda: Pulmonata)]]

[[http://www.ncbi.nlm.nih.gov/pubmed/15245403|Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slug Prophysaon coeruleum]]

[[http://www.ncbi.nlm.nih.gov/pubmed/25368439|Physella acuta: atypical mitochondrial gene order among panpulmonates (Gastropoda).]]

[[http://dx.doi.org/10.1371/journal.pone.0061970|Animal Mitochondria, Positive Selection and Cyto-Nuclear Coevolution: Insights from Pulmonates]]

[[http://www.ncbi.nlm.nih.gov/pubmed/25103445|Exceptionally large mitochondrial fragments to the nucleus in sequenced mollusk genomes]]

[[http://www.ncbi.nlm.nih.gov/pubmed/16230032|Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura]]


======= 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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