Parallelism in gene expression between foothill and alpine
ecotypes in Arabidopsis arenosa

J 2021

Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ, F. KOLAR et. al.

Základní údaje

Originální název

Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa

Autoři

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ (203 Česká republika, garant, domácí) a F. KOLAR

Vydání

Plant Journal, Hoboken (USA), Wiley-Blackwell, 2021, 0960-7412

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.091

Kód RIV

RIV/00216224:14740/21:00119676

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1111/tpj.15105

UT WoS

000604347500001

Klíčová slova anglicky

parallel evolution; gene expression; alpine adaptation; Arabidopsis arenosa; gene-environment interaction; plasticity; common garden experiment

Štítky

CF PLANT, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 4. 2022 08:17, Mgr. Michal Petr

Anotace

V originále

Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.

Návaznosti

GA17-13029S, projekt VaV

Název: Chybějící souvislosti: evoluce genomu v tribu Camelineae (brukvovité)

Investor: Grantová agentura ČR, Chybějící souvislosti: evoluce genomu v tribu Camelineae (brukvovité)

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ a F. KOLAR. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. Plant Journal. Hoboken (USA): Wiley-Blackwell, 2021, roč. 105, č. 5, s. 1211-1224. ISSN 0960-7412. Dostupné z: https://dx.doi.org/10.1111/tpj.15105.

@article{1837998,
   author = {Wos, G. and Bohutinska, M. and Noskova, J. and Malík Mandáková, Terezie and Kolar, F.},
   article_location = {Hoboken (USA)},
   article_number = {5},
   doi = {http://dx.doi.org/10.1111/tpj.15105},
   keywords = {parallel evolution; gene expression; alpine adaptation; Arabidopsis arenosa; gene-environment interaction; plasticity; common garden experiment},
   language = {eng},
   issn = {0960-7412},
   journal = {Plant Journal},
   title = {Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15105},
   volume = {105},
   year = {2021}
}

TY  - JOUR
ID  - 1837998
AU  - Wos, G. - Bohutinska, M. - Noskova, J. - Malík Mandáková, Terezie - Kolar, F.
PY  - 2021
TI  - Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa
JF  - Plant Journal
VL  - 105
IS  - 5
SP  - 1211-1224
EP  - 1211-1224
PB  - Wiley-Blackwell
SN  - 09607412
KW  - parallel evolution
KW  - gene expression
KW  - alpine adaptation
KW  - Arabidopsis arenosa
KW  - gene-environment interaction
KW  - plasticity
KW  - common garden experiment
UR  - https://onlinelibrary.wiley.com/doi/10.1111/tpj.15105
N2  - Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.
ER  -

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ a F. KOLAR. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. \textit{Plant Journal}. Hoboken (USA): Wiley-Blackwell, 2021, roč.~105, č.~5, s.~1211-1224. ISSN~0960-7412. Dostupné z: https://dx.doi.org/10.1111/tpj.15105.

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