Data from "Fishing in troubled waters: Revealing genomic signatures of local adaptation in response to freshwater pollutants in two macroinvertebrates"

Published: 3 April 2018| Version 1 | DOI: 10.17632/v4sp99g5dg.1
Contributors:
Hannah Weigand,
Martina Weiss,
Florian Leese,
Huimin Cai,
Yongping Li,
Christine Zhang

Description

Geneset: Genes in the Glossosoma conformis draft genome were predicted using ab initio and homology-based approaches. Augustus was used for ab initio predictions. For the homology-based approach, protein datasets from related species (Apis mellifera, Nasonia vitripennis, Drosophila melanogaster, Anopheles gambiae, Plutella xylostella, Bombyx mori, Tribolium castaneum, Pediculus humanus, Acyrthosiphon pisum, Daphnia pulex, Caenorhabditis elegans and Homo sapiens) were aligned to the draft genome assemblies using BLASTp (cutoff: 10-5), and gene models were generated by GeneWise. A consensus gene set that merged ab initio and homology-based predictions was created using GLEAN. The three resulting data files contain a table with summary information per predicted gene (Glossosoma_conformis.gff), the predicted mRNA sequences (Glossosoma_conformis.cds) and the predicted protein sequences (Glossosoma_conformis.pep). Functional annotation: Gene functions were assigned to the Geneset of the Glossosoma conformis draft genome using BLASTp (cutoff: 10-5) against KEGG (release 58), non-redundant protein sequences (NCBI release 20150222), Swiss-Prot, and TrEMBL (Uniprot release 201203). Conserved protein domains were assessed by InterPro and InterProScan. Separate files are provided for each database. nuclear RNA: Nuclear RNA sequences in the Glossosoma conformis draft genome were identified in the draft genome assembly. tRNA genes were identified using tRNAscan-SE with default parameters. miRNA and snRNA were identified using the INFERNAL software by searching against the Rfam database (release 9.1) with default parameters. rRNA genes were identified by BLASTn (cutoff: 10-5) searches against conserved invertebrate rRNA sequences. Separate files are provided for each type of RNA Glossosoma conformis.pop: Final dataset of Dugesia gonocephala after all filtering steps used for population genetics and selection tests. Dugesia gonocephala.pop: Final dataset of Dugesia gonocephala after all filtering steps used for population genetics and selection tests.

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Categories

Population Genetics, Aquatic Ecology

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