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Multiple genetic trajectories to extreme abiotic stress adaptation in Arctic Brassicaceae

Citation

Birkeland, Siri et al. (2020), Multiple genetic trajectories to extreme abiotic stress adaptation in Arctic Brassicaceae, Dryad, Dataset, https://doi.org/10.5061/dryad.v41ns1rs0

Abstract

Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. The Arctic is one of the most hostile environments on Earth, and the few plant species inhabiting this region typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic, and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general. 

Methods

These are the Arctic de novo transcriptome assemblies made for the study (based on leaf tissue). The transcriptomes have been assembled with Trinity v.2.4.0, and then filtered so that only the highest expressed isoforms are retained. Coding regions have been predicted with TransDecoder v.3.0.0. For detailed material and methods, see the published paper. 

Usage Notes

Sample details:

CbA_topISO_121218_SHORT.FILTERED.cds/CbA_topISO_121218_SHORT.FILTERED.pep.fasta; Cardamine bellidifolia from Alaska/Yukon (border) (cds file/peptide file)

CbS_topISO_121218_SHORT.FILTERED.cds/CbS_topISO_121218_SHORT.FILTERED.pep.fasta; Cardamine bellidifolia from Svalbard (cds file/peptide file)

CgA_topISO_121218_SHORT.FILTERED.cds/CgA_topISO_121218_SHORT.FILTERED.pep.fasta; Cochlearia groenlandica from Alaska (cds file/peptide file)

CgS_topISO_121218_SHORT.FILTERED.cds/CgS_topISO_121218_SHORT.FILTERED.pep.fasta; Cochelaria groenlandica from Svalbard (cds file/peptide file)

DnA_topISO_121218_SHORT.FILTERED.cds/DnA_topISO_121218_SHORT.FILTERED.pep.fasta; Draba nivalis from Alaska (cds file/peptide file)

DnN_topISO_121218_SHORT.FILTERED.cds/DnN_topISO_121218_SHORT.FILTERED.pep.fasta; Draba nivalis from mainland Norway (cds file/peptide file)

Funding

The Research Council of Norway, Award: RCN 240223