Abstract 5109: National cyberinfrastructure and bioinformatic analysis support available to the cancer research community

Papudeshi, Bhavya; Ganote, Carrie; Sanders, Sheri; Doak, Thomas G.

doi:10.1158/1538-7445.am2019-5109

Cited by 1 publication

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“…We used Trim Galore v.0.4.4 (https://github.com/FelixKrueger/TrimGalore) to remove adapter sequences from the PE reads, trim read ends with Phred‐scaled scores <20, and eliminate PE reads if any or both were <75 bp after trimming. For de novo transcriptome assembly, we used a multiassembler pipeline outlined in the National Center for Genome Analysis Support de novo Transcriptome Workflow and Workshops (Sanders et al, 2019). This approach uses assemblies from multiple programs (i.e., Trinity [Haas et al, 2013], TransABySS [Robertson et al, 2010], Velvet‐Oases [Schulz et al, 2012], and SOAPdenovo‐Trans [Xie et al, 2014]) that are then combined into a single assembly.…”

Section: Methodsmentioning

confidence: 99%

Genetic characterization of potential venom resistance proteins in California ground squirrels (Otospermophilus beecheyi) using transcriptome analyses

Ochoa

Hassinger²,

Holding

et al. 2022

J Exp Zool Pt B

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Understanding the molecular basis of adaptations in coevolving species requires identifying the genes that underlie reciprocally selected phenotypes, such as those involved in venom in snakes and resistance to the venom in their prey. In this regard, California ground squirrels (CGS; Otospermophilus beecheyi) are eaten by northern Pacific rattlesnakes (Crotalus oreganus oreganus), but individual squirrels may still show substantial resistance to venom and survive bites. A recent study using proteomics identified venom interactive proteins (VIPs) in the blood serum of CGS. These VIPs represent possible resistance proteins, but the sequences of genes encoding them are unknown despite the value of such data to molecular studies of coevolution. To address this issue, we analyzed a de novo assembled transcriptome from CGS liver tissue—where many plasma proteins are synthesized—and other tissues from this species. We then examined VIP sequences in terms of three characteristics that identify them as possible resistance proteins: evidence for positive selection, high liver expression, and nonsynonymous variation across CGS populations. Based on these characteristics, we identified five VIPs (i.e., α‐2‐macroglobulin, α‐1‐antitrypsin‐like protein GS55‐LT, apolipoprotein A‐II, hibernation‐associated plasma protein HP‐20, and hibernation‐associated plasma protein HP‐27) as the most likely candidates for resistance proteins among VIPs identified to date. Four of these proteins have been previously implicated in conferring resistance to the venom in mammals, validating our approach. When combined with the detailed information available for rattlesnake venom proteins, these results set the stage for future work focused on understanding coevolutionary interactions at the molecular level between these species.

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