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archive:other_mollusk_genomes [2010/04/02 00:47] karplus Added Tom Pringle quote for sea hare |
archive:other_mollusk_genomes [2015/05/11 21:15] jaredc |
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+ | ======= Mollusk Genomics ======= | ||
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+ | As of May 11, 2015 there are 7 different assembled mollusk(taxid:6447) genomes from 6 different organisms on NCBI database. | ||
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+ | 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. | ||
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+ | =====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. | ||
+ | * 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. | ||
+ | * [[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 | ||
+ | * [[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) | ||
+ | * 14,225 scaffolds, total length is 652,954,618 bases | ||
+ | * [[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 | ||
+ | * 45,393 protein sequences | ||
+ | * [[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 | ||
+ | * 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 | ||
+ | * 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)]] | ||
+ | |||
+ | |||
+ | ===== Relevant Data ===== | ||
+ | |||
+ | * Protein & transcript 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]] | ||
+ | * | ||
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+ | * 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.]] | ||
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+ | |||
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+ | ===== 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)]] | ||
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+ | [[http://www.ncbi.nlm.nih.gov/pubmed/21672613|Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation]] | ||
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+ | [[http://www.biomedcentral.com/1471-2148/11/295|Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships]] | ||
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+ | [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389214/|Annotated Checklist of the Terrestrial Gastropods of Nepal]] | ||
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+ | [[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]] | ||
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+ | [[http://www.ncbi.nlm.nih.gov/pubmed/25368439|Physella acuta: atypical mitochondrial gene order among panpulmonates (Gastropoda).]] | ||
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+ | [[http://dx.doi.org/10.1371/journal.pone.0061970|Animal Mitochondria, Positive Selection and Cyto-Nuclear Coevolution: Insights from Pulmonates]] | ||
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+ | [[http://www.ncbi.nlm.nih.gov/pubmed/25103445|Exceptionally large mitochondrial fragments to the nucleus in sequenced mollusk genomes]] | ||
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+ | [[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. | There are two complete genomes and at least 83 mitochondrial genomes for species in the phylum Mollusca. | ||
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[[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. | [[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 === | + | === Closest To Banana Slug === |
- | + | There are two mitochondrial genomes that are in the same infraorder (//Stylommatophora//; land slugs) as the banana slug: | |
- | NC_001816 | + | - [[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 |
- | Links | + | - [[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 |
- | 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 | + |