CaveCrawler: an interactive analysis suite for cavefish bioinformatics

Annabel Perry, Suzanne E. McGaugh, Alex C. Keene, Heath Blackmon

Research output: Contribution to journalArticlepeer-review

Abstract

The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.

Original languageEnglish (US)
Article numberjkac132
JournalG3: Genes, Genomes, Genetics
Volume12
Issue number8
DOIs
StatePublished - Aug 2022

Bibliographical note

Funding Information:
This work was supported by an NIH NIGMS R35GM138098 to HB, NIH R01 1R01GM127872 to ACK, and SEM, NIH R21 NS122166 to ACK, and the Texas A&M University College of Science Undergraduate Research Opportunities Program to AP.

Publisher Copyright:
© 2022 Genetics Society of America. All rights reserved.

Keywords

  • arpin
  • Astyanax mexicanus
  • database
  • genomics
  • model organism

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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