Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Peng Fei Ma; Yun Long Liu; Cen Guo; Guihua Jin; Zhen Hua Guo; Ling Mao; Yi Zhou Yang; Liang Zhong Niu; Yu Jiao Wang; Lynn G. Clark; Elizabeth A. Kellogg; Zu Chang Xu; Xia Ying Ye; Jing Xia Liu; Meng Yuan Zhou; Yan Luo; Yang Yang; Douglas E. Soltis; Jeffrey L. Bennetzen; Pamela S. Soltis; De Zhu Li

doi:10.1038/s41588-024-01683-0

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Peng Fei Ma, Yun Long Liu, Cen Guo, Guihua Jin, Zhen Hua Guo, Ling Mao, Yi Zhou Yang, Liang Zhong Niu, Yu Jiao Wang, Lynn G. Clark, Elizabeth A. Kellogg, Zu Chang Xu, Xia Ying Ye, Jing Xia Liu, Meng Yuan Zhou, Yan Luo, Yang Yang, Douglas E. Soltis, Jeffrey L. Bennetzen, Pamela S. SoltisDe Zhu Li

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Abstract

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

Original language	English
Pages (from-to)	710-720
Number of pages	11
Journal	Nature Genetics
Volume	56
Issue number	4
DOIs	https://doi.org/10.1038/s41588-024-01683-0
State	Published - Apr 2024

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Ma, P. F., Liu, Y. L., Guo, C., Jin, G., Guo, Z. H., Mao, L., Yang, Y. Z., Niu, L. Z., Wang, Y. J., Clark, L. G., Kellogg, E. A., Xu, Z. C., Ye, X. Y., Liu, J. X., Zhou, M. Y., Luo, Y., Yang, Y., Soltis, D. E., Bennetzen, J. L., ... Li, D. Z. (2024). Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nature Genetics, 56(4), 710-720. https://doi.org/10.1038/s41588-024-01683-0

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title = "Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance",

abstract = "Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.",

author = "Ma, {Peng Fei} and Liu, {Yun Long} and Cen Guo and Guihua Jin and Guo, {Zhen Hua} and Ling Mao and Yang, {Yi Zhou} and Niu, {Liang Zhong} and Wang, {Yu Jiao} and Clark, {Lynn G.} and Kellogg, {Elizabeth A.} and Xu, {Zu Chang} and Ye, {Xia Ying} and Liu, {Jing Xia} and Zhou, {Meng Yuan} and Yan Luo and Yang Yang and Soltis, {Douglas E.} and Bennetzen, {Jeffrey L.} and Soltis, {Pamela S.} and Li, {De Zhu}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = apr,

doi = "10.1038/s41588-024-01683-0",

language = "English",

volume = "56",

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Ma, PF, Liu, YL, Guo, C, Jin, G, Guo, ZH, Mao, L, Yang, YZ, Niu, LZ, Wang, YJ, Clark, LG, Kellogg, EA, Xu, ZC, Ye, XY, Liu, JX, Zhou, MY, Luo, Y, Yang, Y, Soltis, DE, Bennetzen, JL, Soltis, PS & Li, DZ 2024, 'Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance', Nature Genetics, vol. 56, no. 4, pp. 710-720. https://doi.org/10.1038/s41588-024-01683-0

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AU - Ma, Peng Fei

AU - Liu, Yun Long

AU - Guo, Cen

AU - Jin, Guihua

AU - Guo, Zhen Hua

AU - Mao, Ling

AU - Yang, Yi Zhou

AU - Niu, Liang Zhong

AU - Wang, Yu Jiao

AU - Clark, Lynn G.

AU - Kellogg, Elizabeth A.

AU - Xu, Zu Chang

AU - Ye, Xia Ying

AU - Liu, Jing Xia

AU - Zhou, Meng Yuan

AU - Luo, Yan

AU - Yang, Yang

AU - Soltis, Douglas E.

AU - Bennetzen, Jeffrey L.

AU - Soltis, Pamela S.

AU - Li, De Zhu

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N2 - Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

AB - Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

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VL - 56

SP - 710

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JO - Nature Genetics

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ER -

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

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