Gradual evolution of allopolyploidy in Arabidopsis suecica

J 2021

Gradual evolution of allopolyploidy in Arabidopsis suecica

BURNS, Robin, Terezie MALÍK MANDÁKOVÁ, Joanna GUNIS, Luz Mayela SOTO-JIMÉNEZ, Chang LIU et. al.

Základní údaje

Originální název

Gradual evolution of allopolyploidy in Arabidopsis suecica

Autoři

BURNS, Robin, Terezie MALÍK MANDÁKOVÁ (203 Česká republika, domácí), Joanna GUNIS, Luz Mayela SOTO-JIMÉNEZ, Chang LIU, Martin LYSÁK (203 Česká republika, domácí), Polina Yu. NOVIKOVA a Magnus NORDBORG (garant)

Vydání

Nature Ecology & Evolution, Nature Research, 2021, 2397-334X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

40500 4.5 Other agricultural sciences

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 19.100

Kód RIV

RIV/00216224:14740/21:00119687

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1038/s41559-021-01525-w

UT WoS

000686439900004

Klíčová slova anglicky

RIBOSOMAL-RNA GENES; NUCLEOLAR DOMINANCE; TRANSPOSABLE ELEMENTS; GENOME ASSEMBLIES; BRASSICA-NAPUS; CD-HIT; POLYPLOIDY; EXPRESSION; COTTON; ELIMINATION

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 5. 2022 15:21, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Arabidopsis suecica is a natural allotetraploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. Comparative analysis of genome and transcriptome data shows no evidence for major genomic changes linked to structural and functional alterations in A. suecica but reveals changes to the meiotic machinery and cyto-nuclear processes. Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.

Návaznosti

GA19-03442S, projekt VaV

Název: Geny pro ribozomální RNA - cestovatelé v čase a genomech

Investor: Grantová agentura ČR, Geny pro ribozomální RNA - cestovatelé v čase a genomech

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

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

Citovat

BURNS, Robin, Terezie MALÍK MANDÁKOVÁ, Joanna GUNIS, Luz Mayela SOTO-JIMÉNEZ, Chang LIU, Martin LYSÁK, Polina Yu. NOVIKOVA a Magnus NORDBORG. Gradual evolution of allopolyploidy in Arabidopsis suecica. Nature Ecology & Evolution. Nature Research, 2021, roč. 5, č. 10, s. 1367-1381, 29 s. ISSN 2397-334X. Dostupné z: https://dx.doi.org/10.1038/s41559-021-01525-w.

@article{1838357,
   author = {Burns, Robin and Malík Mandáková, Terezie and Gunis, Joanna and SotoandJiménez, Luz Mayela and Liu, Chang and Lysák, Martin and Novikova, Polina Yu. and Nordborg, Magnus},
   article_number = {10},
   doi = {http://dx.doi.org/10.1038/s41559-021-01525-w},
   keywords = {RIBOSOMAL-RNA GENES; NUCLEOLAR DOMINANCE; TRANSPOSABLE ELEMENTS; GENOME ASSEMBLIES; BRASSICA-NAPUS; CD-HIT; POLYPLOIDY; EXPRESSION; COTTON; ELIMINATION},
   language = {eng},
   issn = {2397-334X},
   journal = {Nature Ecology & Evolution},
   title = {Gradual evolution of allopolyploidy in Arabidopsis suecica},
   url = {https://www.nature.com/articles/s41559-021-01525-w},
   volume = {5},
   year = {2021}
}

TY  - JOUR
ID  - 1838357
AU  - Burns, Robin - Malík Mandáková, Terezie - Gunis, Joanna - Soto-Jiménez, Luz Mayela - Liu, Chang - Lysák, Martin - Novikova, Polina Yu. - Nordborg, Magnus
PY  - 2021
TI  - Gradual evolution of allopolyploidy in Arabidopsis suecica
JF  - Nature Ecology & Evolution
VL  - 5
IS  - 10
SP  - 1367-1381
EP  - 1367-1381
PB  - Nature Research
SN  - 2397334X
KW  - RIBOSOMAL-RNA GENES
KW  - NUCLEOLAR DOMINANCE
KW  - TRANSPOSABLE ELEMENTS
KW  - GENOME ASSEMBLIES
KW  - BRASSICA-NAPUS
KW  - CD-HIT
KW  - POLYPLOIDY
KW  - EXPRESSION
KW  - COTTON
KW  - ELIMINATION
UR  - https://www.nature.com/articles/s41559-021-01525-w
N2  - Arabidopsis suecica is a natural allotetraploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. Comparative analysis of genome and transcriptome data shows no evidence for major genomic changes linked to structural and functional alterations in A. suecica but reveals changes to the meiotic machinery and cyto-nuclear processes. Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
ER  -

BURNS, Robin, Terezie MALÍK MANDÁKOVÁ, Joanna GUNIS, Luz Mayela SOTO-JIMÉNEZ, Chang LIU, Martin LYSÁK, Polina Yu. NOVIKOVA a Magnus NORDBORG. Gradual evolution of allopolyploidy in Arabidopsis suecica. \textit{Nature Ecology \&{} Evolution}. Nature Research, 2021, roč.~5, č.~10, s.~1367-1381, 29 s. ISSN~2397-334X. Dostupné z: https://dx.doi.org/10.1038/s41559-021-01525-w.

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