Conus_miliaris_blastx_annotation

Parsed BLASTx report for C. miliaris. Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database, annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot database. Matches with an e-value < 10-5 were retained

Conus_miliaris_populations_expression_files.tar

Annotated tab-delimited expression count files (raw counts and FPKM values) with the number of reads mapping back to each transcript for all transcripts as well as toxin related only transcripts for all populations (Easter Island, Guam, and American Samoa) of Conus miliaris

Guam_TRI_6_14.fa

Transcript assembly for 8 individuals of Conus miliaris collected from Guam. Assembly was created from 130,566,380 100-bp paired-end reads. Transcripts were assembled with Trinity (version 20140413p1). Tissue source: venom ducts

Easter_Island_TRI_6_14.fa

Transcript assembly for 8 individuals of Conus miliaris collected from Easter Island. Assembly was created from 131,525,916 100-bp paired-end reads. Transcripts were assembled with Trinity (version 20140413p1). Tissue source: venom ducts

Conus_miliaris_SNPs.tar

VCF file of 585,736 high-quality single nucleotide polymorphisms (SNPs) identified from 22 C. miliaris individuals from Easter Island, Guam and American Samoa

Conus_miliaris_TRI_6_14.fa

Transcript assembly for Conus miliaris. Assembly consists of 22 individuals collected from Easter Island, Guam and American Samoa. Assembly was created from 100 bp paired-end reads. Reads were first normalized then assembled with Trinity (version 20140413p1). Tissue source: venom ducts

American_samoa_TRI_6_14.fa

Transcript assembly for 6 individuals of Conus miliaris collected from American Samoa. Assembly was created from 87,201,606 100 bp paired-end reads. Transcripts were assembled with Trinity (version 20140413p1). Tissue source: venom ducts

Easter_Island_blastx_annotation

Parsed BLASTx report for C. miliaris from Easter Island. Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database, annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot database. Matches with an e-value < 10-5 were retained

American_Samoa_blastx_annotation

Parsed BLASTx report for C. miliaris from American Samoa. Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database, annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot database. Matches with an e-value < 10-5 were retained

Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp <i>Halocaridina rubra</i> Holthuis 1963 (Atyidae:Decapoda)

<p>The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of <i>Halocaridina rubra</i>, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the <i>tRNA-Lys</i> and <i>tRNA-Asp</i> intergenic region; (2) a 317-bp insertion between the <i>NAD6</i> and <i>CytB</i> genes confined to a single lineage and representing a partial duplication of <i>CytB</i>; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the <i>H. rubra</i> genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from <i>H. rubra</i> suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.</p