CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

CrusTome_v0.1.0 Prerelease
/ReadMe - this file
/crustome_aa_BLAST.tar.gz - CrusTome database of amino acid sequences in BLAST format
/crustome_aa_DIAMOND.tar.gz - CrusTome database of amino acid sequences in DIAMOND format
/crustome_mrna_BLAST.tar.gz  - CrusTome database of mRNA sequences in BLAST format
/dict - Dictionary file to translate species IDs. For usage with sed/awk see link to Github site below

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Pérez-Moreno JL, Kozma MT, DeLeo DM, Bracken-Grissom HD, Durica DS, Mykles DL. 2023. CrusTome: A transcriptome database resource for large-scale analyses across Crustacea. G3: Genes, Genomes, Genetics.

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead 
to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant 
advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for non-traditional 
model organisms remains limited. Crustaceans, for example, being amongst the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are 
ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in 
publicly available sequence databases. Here, we present CrusTome, a multi-species, multi-tissue, transcriptome database of 201 
assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan outgroups) as an evolving, and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ
genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward incorporation into existing custom pipelines for high-throughput analyses.

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For questions regarding released datasets contact:
  Corresponding Author: Jorge L. Perez-Moreno (Colorado State University)
                        [e-mail] / [e-mail]

  https://github.com/invertome/crustome

PLEASE CITE:

Pérez-Moreno JL, Kozma MT, DeLeo DM, Bracken-Grissom HD, Durica DS, Mykles DL. 2023. CrusTome: A transcriptome database resource for large-scale analyses across Crustacea. G3: Genes, Genomes, Genetics.

Funder Information

Supported by National Science Foundation grants to DLM (IOS-1922701) and DSD (IOS-1922755). In addition, this work was partially funded by two grants awarded from the National Science Foundation: Doctoral Dissertation Improvement Grant (#1701835) awarded to JPM and HBG and the Division of Environmental Biology Bioluminescence and Vision grant (DEB-1556059) awarded to HBG. Samples in the FICC were collected by grants from The Gulf of Mexico Research Initiative (GOMRI), Florida Institute of Oceanography Shiptime Funding awarded to HBG and DMD; the National Science Foundation Division of Environmental Biology Grant 1556059 awarded to HBG; and the National Oceanic and Atmospheric Administration Ocean Exploration Research (NOAA-OER 2015) grant awarded to HBG.