archive:other_mollusk_genomes
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archive:other_mollusk_genomes [2015/05/11 13:46] JaredC |
archive:other_mollusk_genomes [2015/08/27 19:57] (current) jaredc |
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| ======= Mollusk Genomics ======= | ======= Mollusk Genomics ======= | ||
| - | As of May 11, 2015 there are 6 different assembled mollusk(taxid:6447) genomes on NCBI database | + | As of May 11, 2015 there are 7 different assembled mollusk(taxid:6447) genomes from 6 different organisms on NCBI database. |
| - | [[http://www.ncbi.nlm.nih.gov/assembly/organism/6447/all/|Mollusk Assemblies]] | + | 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// | * [[http://en.wikipedia.org/wiki/Aplysia_californica|California sea hare]], //Aplysia californica// | ||
| - | * Animalia, Mollusca, Gastropoda, **Heterobranchia**, Opisthobranchia, Aplysiomorpha, Aplysioidea, Aplysiidae, Aplysia | + | * Animalia, Mollusca, Gastropoda, Heterobranchia, **Euthyneura**, 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 | * [[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. | + | * Submitted 05/15/2013 by [[http://www.broadinstitute.org/|Broad Institute]] in Cambridge, MA. |
| - | * Largest Contig: 174,336 bp | + | * 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]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/AASC00000000.2|AplCal2.0 Assembly]] | ||
| * Submitted 07/17/2009 by Broad Institute in Cambridge, MA. | * 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]] | * [[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 | * Largest Contig: 303,309 bp | ||
| - | * [[http://genome.wustl.edu/genomes/detail/biomphalaria-glabrata/|Bloodfluke Planorb]], //Biomphalaria glabrata// | + | * [[http://en.wikipedia.org/wiki/Biomphalaria_glabrata|Bloodfluke Planorb]], //Biomphalaria glabrata// |
| * Animalia, Mollusca, Gastropoda, Heterobranchia, Euthyneura, **Panpulmonata**, Hygrophila, Planorboidea, Planorbidae; Biomphalaria | * 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]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/APKA00000000.1/|BB02 Assembly]] | ||
| * Submitted 09/06/2013 by Washington University | * Submitted 09/06/2013 by Washington University | ||
| - | * largest Contig: 526,532 bp (major outlier 2nd biggest is 100,139 bp) | + | * 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://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// | * [[http://en.wikipedia.org/wiki/Pacific_oyster|Pacific oyster]], //Crassostrea gigas// | ||
| Line 27: | Line 49: | ||
| * [[http://www.ncbi.nlm.nih.gov/nuccore/AFTI00000000.1/|oyster_v9 Assembly]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/AFTI00000000.1/|oyster_v9 Assembly]] | ||
| * Submitted 09/19/2012 by BGI-Shenzhen | * Submitted 09/19/2012 by BGI-Shenzhen | ||
| - | * Largest Contig: 212,823 bp | + | * 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://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// | * [[http://genome.jgi-psf.org/Lotgi1/|Giant owl limpet]], //Lottia gigantea// | ||
| Line 33: | Line 59: | ||
| * [[http://www.ncbi.nlm.nih.gov/nuccore/AMQO00000000.1/|Helro1 Assembly]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/AMQO00000000.1/|Helro1 Assembly]] | ||
| * Submitted 12/20/2012 by DOE Joint Genome Institute | * Submitted 12/20/2012 by DOE Joint Genome Institute | ||
| - | * Largest Contig: 745,440 bp | + | * [[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://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// | * [[http://en.wikipedia.org/wiki/Mediterranean_mussel|Mediterranean mussel]], //Mytilus galloprovincialis// | ||
| Line 39: | Line 71: | ||
| * [[http://www.ncbi.nlm.nih.gov/nuccore/APJB000000000.1/|mussel1.0 Assembly]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/APJB000000000.1/|mussel1.0 Assembly]] | ||
| * Submitted 05/18/2014 by Deakin University | * 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 | * Not Scaffolded, only contigs | ||
| * largest Contig: 39,674 bp | * 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// | * [[http://en.wikipedia.org/wiki/Zebra_mussel|Zebra mussel]] //Dreissena polymorpha// | ||
| * Animalia, **Mollusca**, Bivalvia, Heteroconchia, Euheterodonta, Veneroida, Dreissenoidea, Dreissenidae, Dreissena. | * Animalia, **Mollusca**, Bivalvia, Heteroconchia, Euheterodonta, Veneroida, Dreissenoidea, Dreissenidae, Dreissena. | ||
| * [[http://www.ncbi.nlm.nih.gov/nuccore/JWHF00000000.1/|ASM80632v1 Assembly]] | * [[http://www.ncbi.nlm.nih.gov/nuccore/JWHF00000000.1/|ASM80632v1 Assembly]] | ||
| * Submitted 12/22/2014 by University of Girona | * 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 | * Not Scaffolded, only partial genome represented | ||
| * largest Contig: 8,717 bp | * 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)]] | * [[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)]] | ||
| - | ===== Interesting Data ===== | + | ===== 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 | * Giant Chinese land snail, //Mastigeulota kiangsinensis//, complete mitochondria | ||
| * Eukaryota, Metazoa, Lophotrochozoa, Mollusca, Gastropoda, Heterobranchia, Euthyneura, Panpulmonata, Eupulmonata, Stylommatophora, **Sigmurethra**, Helicoidea, Bradybaenidae, Mastigeulota. | * 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/nuccore/NC_024935.1 | ||
| - | * giant African land snail, //Achatina fulica//, complete mitochondria | + | * [[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. | * 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/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.]] | ||
| - | ===== Interesting Publications ===== | + | ===== 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.ncbi.nlm.nih.gov/pubmed/21672613|Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation]] | ||
| Line 72: | Line 127: | ||
| [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088622/|A phylogeny of the land snails (Gastropoda: Pulmonata)]] | [[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]] | ||
| Line 114: | Line 179: | ||
| === 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: | 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/Grove_snail|Cepaea nemoralis]]\\ [[http://www.ncbi.nlm.nih.gov/nuccore/5835415|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 | + | - [[http://en.wikipedia.org/wiki/Albinaria|Albinaria coerulea]]\\ [[http://www.ncbi.nlm.nih.gov/nuccore/5835289|NC_001761]]\\ mitochondrion, complete genome\\ DNA; circular; Length: 14,130 nt\\ Organelle: mitochondrion\\ Created: 1999/08/24 |
archive/other_mollusk_genomes.1431352017.txt.gz · Last modified: 2015/05/11 13:46 by JaredC
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