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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 [2015/08/27 19:57] (current)
jaredc
@@ Line 1: / Line 1: @@
+======= 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, **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
+      * 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.
@@ Line 34: / Line 177: @@
 [[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/nuccore/5835415|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/nuccore/5835289|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
-:
-NC_001761
-Links
-    Albinaria coerulea mitochondrion, complete genome
-    DNA; circular; Length: 14,130 nt
-    Organelle: mitochondrion
-    Created: 1999/08/24
-   * Unordered List Item

Banana Slug Genomics

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