Comparative transcriptomics provides insight into the evolution of cold response in Pooideae

Grønvold, Lars; Schubert, Marian; Sandve, SR; Fjellheim, Siri; Tr, Hvidsten

doi:10.1101/151431

Cited by 3 publications

(5 citation statements)

References 97 publications

(122 reference 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%

“…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%

“…For five cold acclimation gene families (C-repeat binding factor genes (CBFIII and CBFIV), dehydrin genes (DHN), chloroplast targeting cold-regulated genes (ctCOR), ice-recrystallization inhibition protein genes (IRIP) and fructosyltransferase genes (FST)) we extracted previously identified H. vulgare genes (Table S1) and downloaded translated amino acid (AA) from GenBank. These reference sequences were used in protein BLAST searches against translated de novo transcript sequences produced by Grønvold et al 2017. Potential cold acclimation gene transcripts were identified by discarding protein BLAST results with a maximum bitscore < 90, and e-value > 1E-021.…”

Section: Identification Of Cold Acclimation Candidate Genesmentioning

confidence: 99%

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Evolution of cold acclimation in temperate grasses (Pooideae)

Schubert

Groenvold

Sandve

et al. 2017

Preprint

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In the past 50 million years climate cooling has triggered the expansion of temperate biomes. During this period, many extant plant lineages in temperate biomes evolved from tropical ancestors and adapted to seasonality and cool conditions. Among the Poaceae (grass family), one of the subfamilies that successfully shifted from tropical to temperate biomes is the Pooideae (temperate grasses). Subfamily Pooideae contains the most important crops cultivated in the temperate regions including wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the need of well-adapted cultivars, extensive research has produced a large body of knowledge about the mechanisms underlying cold adaptation in cultivated Pooideae species. Especially cold acclimation, a process which increases the frost tolerance during a period of non-freezing cold, plays an important role. Because cold adaptation is largely unexplored in lineages that diverged early in the evolution of the Pooideae, little is known about the evolutionary history of cold acclimation in the Pooideae. Here we test if several species of early diverging lineages exhibit increased frost tolerance after a period of cold acclimation.We further investigate the conservation of five well-studied gene families that are known to be involved in the cold acclimation of Pooideae crop species. Our results indicate that cold acclimation exists in early diverging lineages, but that genes involved in regulation of cold acclimation are not conserved. The investigated gene families show signs of lineage-specific evolution and support the hypothesis that gene family expansion is an important mechanism in adaptive evolution.

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Section: Pooideae Lineages Evolved Specific Cold Adaptation By Expandsupporting

confidence: 90%

Section: Transcriptomic Data and Differential Gene Expressionmentioning

confidence: 99%

Section: Identification Of Cold Acclimation Candidate Genesmentioning

confidence: 99%

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Evolution of cold acclimation in temperate grasses (Pooideae)

Schubert

Groenvold

Sandve

et al. 2017

Preprint

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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%

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex

et al. 2020

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Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.

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“…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%

A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

Liu

Stiller

et al. 2019

BMC Genomics

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BackgroundIt has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.ResultsIn this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones.ConclusionsWe demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.

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Comparative transcriptomics provides insight into the evolution of cold response in Pooideae

Cited by 3 publications

References 97 publications

Evolution of cold acclimation in temperate grasses (Pooideae)

Evolution of cold acclimation in temperate grasses (Pooideae)

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex

A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

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