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archive:other_mollusk_genomes [2015/05/11 11:52]
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 different assembled mollusk(taxid:​6447) genomes on NCBI database+As of May 11, 2015 there are 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. 
 +      * 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.
-  ​* [[http://​genome.wustl.edu/genomes/detail/biomphalaria-glabrata/​|Bloodfluke Planorb]], //​Biomphalaria glabrata//+      * 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     * 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
 +      * 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//   * [[http://​en.wikipedia.org/​wiki/​Pacific_oyster|Pacific oyster]], //​Crassostrea gigas//
     * Animalia, **Mollusca**,​ Bivalvia, Pteriomorphia,​ Ostreoida, Ostreoidea, Ostreidae, Crassostrea     * Animalia, **Mollusca**,​ Bivalvia, Pteriomorphia,​ Ostreoida, Ostreoidea, Ostreidae, Crassostrea
     * [[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
 +      * 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 27: 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
 +      * [[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 32: 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
 +      * 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 
-    * Not Scaffolded, only partial genome represented+      * 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)]]     * [[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).]]
  
-==== Publications ====+[[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/​21672613|Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation.]]+[[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 90: 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.1431345151.txt.gz · Last modified: 2015/05/11 11:52 by jaredC