archive:other_mollusk_genomes
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archive:other_mollusk_genomes [2015/05/11 15:58] JaredC |
archive:other_mollusk_genomes [2015/08/27 19:57] (current) jaredc |
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| * [[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. | ||
| Line 30: | Line 31: | ||
| * [[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://en.wikipedia.org/wiki/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// | ||
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| * [[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 |
| - | * 45,393 protein sequences | + | * 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// | ||
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| * [[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 | * 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]] | ||
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| * [[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)]] | ||
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| ===== Relevant Data ===== | ===== Relevant Data ===== | ||
| - | * Protein & transcript details for Sea Hare, //Aplysia californica// | + | * 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]] | * [[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 | * 25041 Predicted protein sequences and 13 known proteins from mitochondrial genes | ||
| * [[http://www.ncbi.nlm.nih.gov/pubmed/21328528|Developmental transcriptome of Aplysia californica]] | * [[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]] |
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| === 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.1431359893.txt.gz · Last modified: 2015/05/11 15:58 by JaredC
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