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

<p>CrusTome_v0.1.0 Prerelease<br> /ReadMe - this file<br> /crustome_aa_BLAST.tar.gz - CrusTome database of amino acid sequences in BLAST format<br> /crustome_aa_DIAMOND.tar.gz - CrusTome database of amino acid sequences in DIAMOND format<br> /crustome_mrna_BLAST.tar.gz &nbsp;- CrusTome database of mRNA sequences in BLAST format<br> /dict - Dictionary file to translate species IDs. For usage with sed/awk see link to Github site below<br> &nbsp;<br> * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *<br> * &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; Please note, most of the data files contained in this DOI are&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; compressed into GZip files (.gz extension).&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; Mac and Linux OS&#39;s can extract this file type natively.&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; Windows OS requires software to extract the archive. &nbsp;7-Zip&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; (http://www.7-zip.org) is free and open source software that will&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * &nbsp; allow windows PCs to open and decompress the archive.&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br> * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *<br> &nbsp;<br> <strong><em>P&eacute;rez-Moreno JL, Kozma MT, DeLeo DM, Bracken-Grissom HD, Durica DS, Mykles DL. 2023. CrusTome: A transcriptome database resource&nbsp;for large-scale analyses across Crustacea. G3: Genes, Genomes, Genetics.</em></strong></p> <p><strong>CrusTome: A transcriptome database resource for large-scale analyses across Crustacea</strong></p> <p>Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead&nbsp;<br> to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant&nbsp;<br> advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for non-traditional&nbsp;<br> model organisms remains limited. Crustaceans, for example, being amongst the most numerous, diverse, and widely distributed taxa&nbsp;on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are&nbsp;<br> ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in&nbsp;<br> publicly available sequence databases. Here, we present CrusTome, a multi-species, multi-tissue, transcriptome database of 201&nbsp;<br> assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan outgroups) as an evolving,&nbsp;and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ<br> genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for&nbsp;sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward incorporation&nbsp;into existing custom pipelines for high-throughput analyses.</p> <p>&nbsp;<br> * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *<br> &nbsp;<br> For questions regarding released datasets contact:<br> &nbsp; Corresponding Author: Jorge L. Perez-Moreno (Colorado State University)<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; jorgepm@colostate.edu / jpere645@fiu.edu<br> &nbsp;<br> <strong>&nbsp; https://github.com/invertome/crustome</strong></p> <p>&nbsp;</p> <p>&nbsp;<br> <strong>PLEASE CITE:</strong></p> <p>P&eacute;rez-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.</p> <p>&nbsp;</p> <p><strong>Funder Information</strong></p> <p>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.</p>