Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life

Alex Di Genova, Gino Nardocci, Rodrigo Maldonado-Agurto, Christian Hodar, Camilo Valdivieso, Pamela Morales, Felipe Gajardo, Raquel Marina, Rodrigo A. Gutiérrez, Ariel Orellana, Veronica Cambiazo, Mauricio González, Alvaro Glavic, Marco A. Mendez, Alejandro Maass, Miguel L. Allende, Martin A. Montecino*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.

Original languageEnglish
Pages (from-to)305-315
Number of pages11
JournalGenomics
Volume114
Issue number1
DOIs
StatePublished - Jan 2022
Externally publishedYes

Bibliographical note

Funding Information:
This work is part of the Chilean 1000 Genomes Initiative and is carried out within the framework of the Earth Biogenome Project ( www.earthbiogenome.org ). Funding has been provided by ANID/FONDAP 15090007 and 15200002, ANID/FONDECYT 1180606 (to MLA), ANID/FONDECYT 3190720 (to RMA) and ANID/FONDECYT 1200419 (to M Mendez). This research was partially supported by the supercomputing infrastructure of the NLHPC (ECM-02) and ANID-PIA AFB 170001.

Funding Information:
The authors thank Dr. Juan C. Opazo for his technical support with the Phylogenetic Analysis by Maximum Likelihood (PAML) analysis. This work is part of the Chilean 1000 Genomes Initiative and is carried out within the framework of the Earth Biogenome Project (www.earthbiogenome.org). Funding has been provided by ANID/FONDAP 15090007 and 15200002, ANID/FONDECYT 1180606 (to MLA), ANID/FONDECYT 3190720 (to RMA) and ANID/FONDECYT 1200419 (to M Mendez). This research was partially supported by the supercomputing infrastructure of the NLHPC (ECM-02) and ANID-PIA AFB 170001.

Publisher Copyright:
© 2021

Keywords

  • Altiplano
  • Desert pupfish
  • DNA repair
  • High-altitude
  • microRNAs
  • Orestias ascotanensis

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