Repeat proliferation and partial endoreplication jointly shape
the patterns of genome size evolution in orchids

J 2021

Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids

CHUMOVA, Z., E. ZAVESKA, P. HLOUSKOVA, J. PONERT, P.A. SCHMIDT et. al.

Základní údaje

Originální název

Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids

Autoři

CHUMOVA, Z., E. ZAVESKA, P. HLOUSKOVA, J. PONERT, P.A. SCHMIDT, M. CERTNER, Terezie MALÍK MANDÁKOVÁ (203 Česká republika, garant, domácí) a P. TRAVNICEK

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

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.091

Kód RIV

RIV/00216224:14740/21:00124335

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1111/tpj.15306

UT WoS

000653836100001

Klíčová slova anglicky

genome size evolution; Hyb‐ Seq; partial endoreplication; phylogenetic generalized least squares; Pleurothallidinae; repetitive elements

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 1. 3. 2022 13:41, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.

Návaznosti

LM2015047, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

Citovat

CHUMOVA, Z., E. ZAVESKA, P. HLOUSKOVA, J. PONERT, P.A. SCHMIDT, M. CERTNER, Terezie MALÍK MANDÁKOVÁ a P. TRAVNICEK. Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. Plant Journal. Hoboken (USA): Wiley-Blackwell, 2021, roč. 107, č. 2, s. 511-524. ISSN 0960-7412. Dostupné z: https://dx.doi.org/10.1111/tpj.15306.

@article{1837999,
   author = {Chumova, Z. and Zaveska, E. and Hlouskova, P. and Ponert, J. and Schmidt, P.A. and Certner, M. and Malík Mandáková, Terezie and Travnicek, P.},
   article_location = {Hoboken (USA)},
   article_number = {2},
   doi = {http://dx.doi.org/10.1111/tpj.15306},
   keywords = {genome size evolution; Hyb‐ Seq; partial endoreplication; phylogenetic generalized least squares; Pleurothallidinae; repetitive elements},
   language = {eng},
   issn = {0960-7412},
   journal = {Plant Journal},
   title = {Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids},
   url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15306},
   volume = {107},
   year = {2021}
}

TY  - JOUR
ID  - 1837999
AU  - Chumova, Z. - Zaveska, E. - Hlouskova, P. - Ponert, J. - Schmidt, P.A. - Certner, M. - Malík Mandáková, Terezie - Travnicek, P.
PY  - 2021
TI  - Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids
JF  - Plant Journal
VL  - 107
IS  - 2
SP  - 511-524
EP  - 511-524
PB  - Wiley-Blackwell
SN  - 09607412
KW  - genome size evolution
KW  - Hyb‐ Seq
KW  - partial endoreplication
KW  - phylogenetic generalized least squares
KW  - Pleurothallidinae
KW  - repetitive elements
UR  - https://onlinelibrary.wiley.com/doi/10.1111/tpj.15306
N2  - Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.
ER  -

CHUMOVA, Z., E. ZAVESKA, P. HLOUSKOVA, J. PONERT, P.A. SCHMIDT, M. CERTNER, Terezie MALÍK MANDÁKOVÁ a P. TRAVNICEK. Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. \textit{Plant Journal}. Hoboken (USA): Wiley-Blackwell, 2021, roč.~107, č.~2, s.~511-524. ISSN~0960-7412. Dostupné z: https://dx.doi.org/10.1111/tpj.15306.

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