2017
DOI: 10.1101/151431
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Comparative transcriptomics provides insight into the evolution of cold response in Pooideae

Abstract: Background: Understanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but conserved cold-response genes that might have played a role in the cold adaptation to temperate climate remain unidentified.

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Cited by 3 publications
(5 citation statements)
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“…Based on our findings, there is evidence that the E-O transition affected the molecular evolution of cold adaptive mechanisms in all investigated Pooideae lineages. By the time of the E-O transition, all major Pooideae lineages had already diverged (Marcussen et al 2014;Grønvold et al 2017) and this supports the indications in our data that cold adaptation largely evolved separately in different Pooideae lineages.…”
Section: Pooideae Lineages Evolved Specific Cold Adaptation By Expandsupporting
confidence: 90%
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“…Based on our findings, there is evidence that the E-O transition affected the molecular evolution of cold adaptive mechanisms in all investigated Pooideae lineages. By the time of the E-O transition, all major Pooideae lineages had already diverged (Marcussen et al 2014;Grønvold et al 2017) and this supports the indications in our data that cold adaptation largely evolved separately in different Pooideae lineages.…”
Section: Pooideae Lineages Evolved Specific Cold Adaptation By Expandsupporting
confidence: 90%
“…In another study (Grønvold et al, 2017) we compared the molecular cold response from the five Pooideae species Nardus stricta, Stipa lagascae, Melica nutans, Brachypodium distachyon (same populations/accessions as described above) and Hordeum vulgare (cultivar 'Igri', provided by Prof. Åsmund Bjørnstad). The transcriptomic data produced in Grønvold et al 2017 was used as basis for the investigation of cold acclimation genes.…”
Section: Transcriptomic Data and Differential Gene Expressionmentioning
confidence: 99%
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“…Rice (O. sativa) and B. distachyon Med15 homologs were identified using the Department of Energy-Joint Genome Institute Phytozome database (https://phytozome.jgi.doe.gov), barley (H. vulgare) homologs from the 2017 genome sequence 81 , and bread wheat (T. aestivum) from the reference genome sequence (IWGSC RefSeq v1.0). We accessed publicly available leaf RNAseq data for eight grass species (Supplementary Table 13) 82,83 , performed de novo transcriptome assembly using Trinity 84 (version r20140717) using the parameters "--min_kmer_cov 2 --normalize_max_read_cov 20 -trimmomatic", and identified Med15 homologs using BLAST. PRANK (v.140603) and RAxML (v8.2.9) were used for codon-based alignment and phylogenetic tree construction, respectively [85][86][87] .…”
Section: Methodsmentioning
confidence: 99%
“…The data consisted of a total of 6,321,262,514 reads downloaded from the EMBL (European Molecular Biology Lab)/EBI (European Bioinformatics Institute)-European Nucleotide Archive (ENA) database and the National Center for Biotechnology Information (NCBI) Short Sequence Read Archive (SRA) database. The sequences were obtained from a wide range of studies on different environmental factors and stress treatments including low temperature (vernalisation) [23, 24], photoperiod [25], drought [15], salinity [14, 17, 26], heat stress [18], disease infection [NCBI-GEO (Gene Expression Omnibus) accession GSE83676] and excessive nutrients [16]. Some of the sequences were obtained from studies on domestication [19, 20], tissue development ([21, 22], NCBI-GEO accession GSE87377) and whole genome sequencing in barley [11].…”
Section: Methodsmentioning
confidence: 99%