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What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

Citation

Birkeland, Siri et al. (2022), What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?, Dryad, Dataset, https://doi.org/10.5061/dryad.hhmgqnkjh

Abstract

Little is known about the evolution of cold tolerance in polar plant species and how they differ from temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. We conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22 °C, and after 3h, 6h, and 24h at 2 °C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. Most differentially expressed genes were species-specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, ~200 were shared among the three Arctic species and A. thaliana, while ~100 were exclusively shared among the three Arctic species. Our results show that cold response differs markedly between Arctic Brassicaceae species, but likely builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation. 

Methods

These transcriptomes were generated for a comparative study of cold response in Arctic Brassicaceae. Each transcriptome is generated from 16 samples of leaf RNA, sampled at different time points and temperatures:

  • 4 replicates at 0h (22 °C)
  • 4 replicates at 3h with 2 °C
  • 4 replicates at 6h with 2 °C
  • 4 replicates at 24h with 2 °C

One replicate = one pot with several seeds from genetically identical plants (all plants were siblings derived from selfed parents, and selfing is assumed to be the predominant mode of reproduction in the wild). After RNA sequencing on an Illumina HiSeq 3000, we did de novo transcriptome assemblies using trinity https://github.com/trinityrnaseq/trinityrnaseq/wiki with the integrated trimmomatic option. 

After assembly, we used EnTAP https://entap.readthedocs.io/en/latest/ to filter the raw transcriptomes to reduce inflated transcript estimates (both raw and filtered transcriptomes are deposited). 

The final transcriptomes are all over >90 % complete in terms of BUSCOs. 

Funding

The Research Council of Norway, Award: RCN 240223

The Research Council of Norway, Award: RCN 287465