Repeat-sequence turnover shifts fundamentally in species with large genomes

Petr Novák; Maïté S. Guignard; Pavel Neumann; Laura J. Kelly; Jelena Mlinarec; Andrea Koblížková; Steven Dodsworth; Aleš Kovařík; Jaume Pellicer; Wencai Wang; Jiří Macas; Ilia J. Leitch; Andrew R. Leitch

doi:10.1038/s41477-020-00785-x

Repeat-sequence turnover shifts fundamentally in species with large genomes

Petr Novák, Maïté S. Guignard, Pavel Neumann, Laura J. Kelly, Jelena Mlinarec, Andrea Koblížková, Steven Dodsworth, Aleš Kovařík, Jaume Pellicer, Wencai Wang, Jiří Macas^*, Ilia J. Leitch, Andrew R. Leitch

^*Corresponding author for this work

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Abstract

Given the 2,400-fold range of genome sizes (0.06–148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.

Original language	English
Pages (from-to)	1325-1329
Number of pages	5
Journal	Nature Plants
Volume	6
Issue number	11
DOIs	https://doi.org/10.1038/s41477-020-00785-x
Publication status	Published - 19 Oct 2020

Keywords

UKRI
NERC
NE/G020256/1

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Novák_et_al_2020_AAM
This is a post-peer-review, pre-copyedit version of an article published in Novák, P., Guignard, M.S., Neumann, P. et al. Repeat-sequence turnover shifts fundamentally in species with large genomes. Nat. Plants 6, 1325–1329 (2020). The final authenticated version is available online at: https://doi.org/10.1038/s41477-020-00785-x.
Accepted author manuscript (Post-print), 2.08 MB

https://qmro.qmul.ac.uk/xmlui/handle/123456789/67178

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@article{fff0ee1733bf4df19ce6884d1ec25358,

title = "Repeat-sequence turnover shifts fundamentally in species with large genomes",

abstract = "Given the 2,400-fold range of genome sizes (0.06–148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55\% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.",

keywords = "UKRI, NERC, NE/G020256/1",

author = "Petr Nov{\'a}k and Guignard, \{Ma{\"i}t{\'e} S.\} and Pavel Neumann and Kelly, \{Laura J.\} and Jelena Mlinarec and Andrea Kobl{\'i}{\v z}kov{\'a} and Steven Dodsworth and Ale{\v s} Kova{\v r}{\'i}k and Jaume Pellicer and Wencai Wang and Ji{\v r}{\'i} Macas and Leitch, \{Ilia J.\} and Leitch, \{Andrew R.\}",

note = "Funding Information: We thank Natural Environment Research Council (NE/G020256/1), the Czech Academy of Sciences (RVO:60077344) and Ram{\'o}n y Cajal Fellowship (RYC-2017-2274) funded by the Ministerio de Ciencia y Tecnolog{\'i}a (Gobierno de Espa{\~n}a) for support. In addition, the work was supported by the European Regional Development Fund–European Social Fund project ELIXIR-CZ–Capacity Building (no. CZ.02.1.01/0.0/0.0/16\_013/00 01777) and ELIXIR-CZ research infrastructure project (LM2015047) for the access to computing and storage facilities. We also thank Natural Environment Research Council for funding a studentship to S.D. and the China Scholarship Council for funding W.W. Finally, we thank R.A. Nichols for helpful advice and J. Marquardt for supplying DNA of H. non-scripta. Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature Limited.",

year = "2020",

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doi = "10.1038/s41477-020-00785-x",

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AU - Novák, Petr

AU - Guignard, Maïté S.

AU - Neumann, Pavel

AU - Kelly, Laura J.

AU - Mlinarec, Jelena

AU - Koblížková, Andrea

AU - Dodsworth, Steven

AU - Kovařík, Aleš

AU - Pellicer, Jaume

AU - Wang, Wencai

AU - Macas, Jiří

AU - Leitch, Ilia J.

AU - Leitch, Andrew R.

N1 - Funding Information: We thank Natural Environment Research Council (NE/G020256/1), the Czech Academy of Sciences (RVO:60077344) and Ramón y Cajal Fellowship (RYC-2017-2274) funded by the Ministerio de Ciencia y Tecnología (Gobierno de España) for support. In addition, the work was supported by the European Regional Development Fund–European Social Fund project ELIXIR-CZ–Capacity Building (no. CZ.02.1.01/0.0/0.0/16_013/00 01777) and ELIXIR-CZ research infrastructure project (LM2015047) for the access to computing and storage facilities. We also thank Natural Environment Research Council for funding a studentship to S.D. and the China Scholarship Council for funding W.W. Finally, we thank R.A. Nichols for helpful advice and J. Marquardt for supplying DNA of H. non-scripta. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2020/10/19

Y1 - 2020/10/19

N2 - Given the 2,400-fold range of genome sizes (0.06–148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.

AB - Given the 2,400-fold range of genome sizes (0.06–148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.

KW - UKRI

KW - NERC

KW - NE/G020256/1

UR - https://www.scopus.com/pages/publications/85092727877

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VL - 6

SP - 1325

EP - 1329

JO - Nature Plants

JF - Nature Plants

IS - 11

ER -

Repeat-sequence turnover shifts fundamentally in species with large genomes

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