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.

Basic information

Original name

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

Authors

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, guarantor, belonging to the institution) and F. KOLAR

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.091

RIV identification code

RIV/00216224:14740/21:00119676

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000604347500001

Keywords in English

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

Abstract

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.

Links

GA17-13029S, research and development project

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

Investor: Czech Science Foundation

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

WOS, G., M. BOHUTINSKA, J. NOSKOVA, Terezie MALÍK MANDÁKOVÁ and F. KOLAR. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. Plant Journal. Hoboken (USA): Wiley-Blackwell, 2021, vol. 105, No 5, p. 1211-1224. ISSN 0960-7412. Available from: 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 and F. KOLAR. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. \textit{Plant Journal}. Hoboken (USA): Wiley-Blackwell, 2021, vol.~105, No~5, p.~1211-1224. ISSN~0960-7412. Available from: https://dx.doi.org/10.1111/tpj.15105.

Detailed Information on Publication Record