Data from: "Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem" in Genomic Resources Notes accepted 1 June 2014 to 31 July 2014

No description availabl

cd_hit_data

A compressed file consisting of 10 cd hit files (2 for each of the 5 anchialine shrimp species) files used to generate orthologous clusters from the five anchialine shrimp species. One file (ending in .cd-hit_filtered) contains the putative ORFs used to generate clusters while the other file (ending in .cd-hit_filtered.clstr) contains statistics and information on the clusters

Antecaridina_lauensis_pep

Antecaridina lauensis .pep file containing amino acid sequences for putative ORFs as called by the program TransDecode

generate_Trinotate_report

This script will generate a tab-delimited report from a Trinotate annotation compressed file. See comments for usage, and if script is modified, please provide proper attribution

Metabetaeus_minutus_cds

Metabetaeus minutus .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecode

Metabetaeus_lohena_cds

Metabetaeus lohena .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecode

Metabetaeus_minutus_gff

Metabetaeus minutus .gff file containing mapping information for the putative ORFs as called by the program TransDecode

Trinotate

This script will generate a Trinotate annotation compressed file for a .fasta Trinity assembly. See comments for usage, and if script is modified, please provide proper attribution

Performance of Single and Concatenated Sets of Mitochondrial Genes at Inferring Metazoan Relationships Relative to Full Mitogenome Data

<div><p>Mitochondrial (mt) genes are some of the most popular and widely-utilized genetic loci in phylogenetic studies of metazoan taxa. However, their linked nature has raised questions on whether using the entire mitogenome for phylogenetics is overkill (at best) or pseudoreplication (at worst). Moreover, no studies have addressed the comparative phylogenetic utility of mitochondrial genes across individual lineages within the entire Metazoa. To comment on the phylogenetic utility of individual mt genes as well as concatenated subsets of genes, we analyzed mitogenomic data from 1865 metazoan taxa in 372 separate lineages spanning genera to subphyla. Specifically, phylogenies inferred from these datasets were statistically compared to ones generated from all 13 mt protein-coding (PC) genes (i.e., the “supergene” set) to determine which single genes performed “best” at, and the minimum number of genes required to, recover the “supergene” topology. Surprisingly, the popular marker COX1 performed poorest, while ND5, ND4, and ND2 were most likely to reproduce the “supergene” topology. Averaged across all lineages, the longest ∼2 mt PC genes were sufficient to recreate the “supergene” topology, although this average increased to ∼5 genes for datasets with 40 or more taxa. Furthermore, concatenation of the three “best” performing mt PC genes outperformed that of the three longest mt PC genes (i.e, ND5, COX1, and ND4). Taken together, while not all mt PC genes are equally interchangeable in phylogenetic studies of the metazoans, some subset can serve as a proxy for the 13 mt PC genes. However, the exact number and identity of these genes is specific to the lineage in question and cannot be applied indiscriminately across the Metazoa.</p></div

Caridina_rubella_gff

Caridina rubella .gff file containing mapping information for the putative ORFs as called by the program TransDecode