The genome of Draba nivalis shows signatures of adaptation to
the extreme environmental stresses of the Arctic

J 2021

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

NOWAK, M.D.; S. BIRKELAND; Terezie MANDÁKOVÁ; R.R. CHOUDHURY; Xinyi GUO et al.

Základní údaje

Originální název

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

Autoři

Vydání

Molecular Ecology Resources, HOBOKEN, WILEY, 2021, 1755-098X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 8.678

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/21:00118890

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

adaptation; Arctic; Brassicaceae; chromosome‐ scale assembly; linkage map

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 1. 2022 13:55, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.

Návaznosti

GA15-18545S, projekt VaV

Název: Evoluce genomu a časoprostorová diversita v tribu Arabideae

Investor: Grantová agentura ČR, Evoluce genomu a časoprostorová diversita v tribu Arabideae

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

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

Citovat

NOWAK, M.D.; S. BIRKELAND; Terezie MANDÁKOVÁ; R.R. CHOUDHURY; Xinyi GUO; A.L.S. GUSTAFSSON; A. GIZAW; A. SCHRODER-NIELSEN; M. FRACASSETTI; A.K. BRYSTING; L. RIESEBERG; T. SLOTTE; C. PARISOD; Martin LYSÁK a C. BROCHMANN. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Molecular Ecology Resources. HOBOKEN: WILEY, 2021, roč. 21, č. 3, s. 661-676. ISSN 1755-098X. Dostupné z: https://doi.org/10.1111/1755-0998.13280.

@article{1752937,
   author = {Nowak, M.D. and Birkeland, S. and Mandáková, Terezie and Choudhury, R.R. and Guo, Xinyi and Gustafsson, A.L.S. and Gizaw, A. and SchroderandNielsen, A. and Fracassetti, M. and Brysting, A.K. and Rieseberg, L. and Slotte, T. and Parisod, C. and Lysák, Martin and Brochmann, C.},
   article_location = {HOBOKEN},
   article_number = {3},
   doi = {https://doi.org/10.1111/1755-0998.13280},
   keywords = {adaptation; Arctic; Brassicaceae; chromosome‐ scale assembly; linkage map},
   language = {eng},
   issn = {1755-098X},
   journal = {Molecular Ecology Resources},
   title = {The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13280},
   volume = {21},
   year = {2021}
}

TY  - JOUR
ID  - 1752937
AU  - Nowak, M.D. - Birkeland, S. - Mandáková, Terezie - Choudhury, R.R. - Guo, Xinyi - Gustafsson, A.L.S. - Gizaw, A. - Schroder-Nielsen, A. - Fracassetti, M. - Brysting, A.K. - Rieseberg, L. - Slotte, T. - Parisod, C. - Lysák, Martin - Brochmann, C.
PY  - 2021
TI  - The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
JF  - Molecular Ecology Resources
VL  - 21
IS  - 3
SP  - 661-676
EP  - 661-676
PB  - WILEY
SN  - 1755098X
KW  - adaptation
KW  - Arctic
KW  - Brassicaceae
KW  - chromosome‐ scale assembly
KW  - linkage map
UR  - https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13280
N2  - The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
ER  -

NOWAK, M.D.; S. BIRKELAND; Terezie MANDÁKOVÁ; R.R. CHOUDHURY; Xinyi GUO; A.L.S. GUSTAFSSON; A. GIZAW; A. SCHRODER-NIELSEN; M. FRACASSETTI; A.K. BRYSTING; L. RIESEBERG; T. SLOTTE; C. PARISOD; Martin LYSÁK a C. BROCHMANN. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. \textit{Molecular Ecology Resources}. HOBOKEN: WILEY, 2021, roč.~21, č.~3, s.~661-676. ISSN~1755-098X. Dostupné z: https://doi.org/10.1111/1755-0998.13280.

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