Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Therese Mitros; Adam M. Session; Brandon T. James; Guohong Albert Wu; Mohammad B. Belaffif; Lindsay V. Clark; Shengqiang Shu; Hongxu Dong; Adam Barling; Jessica R. Holmes; Jessica E. Mattick; Jessen V. Bredeson; Siyao Liu; Kerrie Farrar; Katarzyna Głowacka; Stanisław Jeżowski; Kerrie Barry; Won Byoung Chae; John A. Juvik; Justin Gifford; Adebosola Oladeinde; Toshihiko Yamada; Jane Grimwood; Nicholas H. Putnam; Jose De Vega; Susanne Barth; Manfred Klaas; Trevor Hodkinson; Laigeng Li; Xiaoli Jin; Junhua Peng; Chang Yeon Yu; Kweon Heo; Ji Hye Yoo; Bimal Kumar Ghimire; Iain S. Donnison; Jeremy Schmutz; Matthew E. Hudson; Erik J. Sacks; Stephen P. Moose; Kankshita Swaminathan; Daniel S. Rokhsar

doi:10.1038/s41467-020-18923-6

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Therese Mitros
, Adam M. Session
, Brandon T. James
, Guohong Albert Wu
, Mohammad B. Belaffif
, Lindsay V. Clark
, Shengqiang Shu
, Hongxu Dong
, Adam Barling
, Jessica R. Holmes
, Jessica E. Mattick
, Jessen V. Bredeson
, Siyao Liu
, Kerrie Farrar
, Katarzyna Głowacka
, Stanisław Jeżowski
, Kerrie Barry
, Won Byoung Chae
, John A. Juvik
, Justin Gifford

Adebosola Oladeinde, Toshihiko Yamada, Jane Grimwood, Nicholas H. Putnam, Jose De Vega, Susanne Barth, Manfred Klaas, Trevor Hodkinson, Laigeng Li, Xiaoli Jin, Junhua Peng, Chang Yeon Yu, Kweon Heo, Ji Hye Yoo, Bimal Kumar Ghimire, Iain S. Donnison, Jeremy Schmutz, Matthew E. Hudson, Erik J. Sacks, Stephen P. Moose, Kankshita Swaminathan, Daniel S. Rokhsar^*

^*Corresponding author for this work

Institute of Biological, Environmental, and Rural Sciences

University of California, Berkeley
University of Illinois Urbana-Champaign
Joint Genome Institute
HudsonAlpha Institute for Biotechnology
Loyola University Chicago
University of North Carolina at Chapel Hill
Institute of Plant Genetics, Polish Academy of Sciences
University of Nebraska–Lincoln
Dankook University
Field Science Center for Northern Biosphere
Dovetail Genomics (United States)
Teagasc - The Irish Agriculture and Food Development Authority
Trinity College Dublin
Shanghai Institutes for Biological Sciences
Zhejiang University
HuaZhi Rice Biotech Company
Kangwon National University
Konkuk University
Okinawa Institute of Science and Technology Graduate University
Chan Zuckerberg Biohub San Francisco
Earlham Institute

Research output: Contribution to journal › Article › peer-review

95 Citations (Scopus)

627 Downloads (Pure)

Abstract

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Original language	English
Article number	5442
Number of pages	11
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-18923-6
Publication status	Published - 28 Oct 2020

Keywords

Biomass
Chromosomes, Plant/genetics
DNA Transposable Elements
Diploidy
Evolution, Molecular
Gene Expression Regulation, Plant
Genetic Variation
Genome, Plant
Genomics
Models, Genetic
Phylogeny
Poaceae/classification
Polyploidy
Saccharum/genetics
Seasons
Sorghum/genetics

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10.1038/s41467-020-18923-6Licence: CC BY

ArticleFinal published version, 2.07 MBLicence: CC BY
Supplementary InformationFinal published version, 3.4 MBLicence: CC BY
Description of Supplementary DataFinal published version, 182 KBLicence: CC BY
Supplementary DataFinal published version, 59.1 MBLicence: CC BY
Source DataFinal published version, 16.4 MBLicence: CC BY

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Mitros, T., Session, A. M., James, B. T., Wu, G. A., Belaffif, M. B., Clark, L. V., Shu, S., Dong, H., Barling, A., Holmes, J. R., Mattick, J. E., Bredeson, J. V., Liu, S., Farrar, K., Głowacka, K., Jeżowski, S., Barry, K., Chae, W. B., Juvik, J. A., ... Rokhsar, D. S. (2020). Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications, 11(1), Article 5442. https://doi.org/10.1038/s41467-020-18923-6

@article{85887f2bbcbb4db4839f34751481e100,

title = "Genome biology of the paleotetraploid perennial biomass crop Miscanthus",

abstract = "Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.",

keywords = "Biomass, Chromosomes, Plant/genetics, DNA Transposable Elements, Diploidy, Evolution, Molecular, Gene Expression Regulation, Plant, Genetic Variation, Genome, Plant, Genomics, Models, Genetic, Phylogeny, Poaceae/classification, Polyploidy, Saccharum/genetics, Seasons, Sorghum/genetics",

author = "Therese Mitros and Session, \{Adam M.\} and James, \{Brandon T.\} and Wu, \{Guohong Albert\} and Belaffif, \{Mohammad B.\} and Clark, \{Lindsay V.\} and Shengqiang Shu and Hongxu Dong and Adam Barling and Holmes, \{Jessica R.\} and Mattick, \{Jessica E.\} and Bredeson, \{Jessen V.\} and Siyao Liu and Kerrie Farrar and Katarzyna G{\l}owacka and Stanis{\l}aw Je{\.z}owski and Kerrie Barry and Chae, \{Won Byoung\} and Juvik, \{John A.\} and Justin Gifford and Adebosola Oladeinde and Toshihiko Yamada and Jane Grimwood and Putnam, \{Nicholas H.\} and \{De Vega\}, Jose and Susanne Barth and Manfred Klaas and Trevor Hodkinson and Laigeng Li and Xiaoli Jin and Junhua Peng and Yu, \{Chang Yeon\} and Kweon Heo and Yoo, \{Ji Hye\} and Ghimire, \{Bimal Kumar\} and Donnison, \{Iain S.\} and Jeremy Schmutz and Hudson, \{Matthew E.\} and Sacks, \{Erik J.\} and Moose, \{Stephen P.\} and Kankshita Swaminathan and Rokhsar, \{Daniel S.\}",

note = "Funding: BBS/E/W/0012843A",

year = "2020",

month = oct,

day = "28",

doi = "10.1038/s41467-020-18923-6",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Springer Nature",

number = "1",

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Mitros, T, Session, AM, James, BT, Wu, GA, Belaffif, MB, Clark, LV, Shu, S, Dong, H, Barling, A, Holmes, JR, Mattick, JE, Bredeson, JV, Liu, S, Farrar, K, Głowacka, K, Jeżowski, S, Barry, K, Chae, WB, Juvik, JA, Gifford, J, Oladeinde, A, Yamada, T, Grimwood, J, Putnam, NH, De Vega, J, Barth, S, Klaas, M, Hodkinson, T, Li, L, Jin, X, Peng, J, Yu, CY, Heo, K, Yoo, JH, Ghimire, BK, Donnison, IS, Schmutz, J, Hudson, ME, Sacks, EJ, Moose, SP, Swaminathan, K & Rokhsar, DS 2020, 'Genome biology of the paleotetraploid perennial biomass crop Miscanthus', Nature Communications, vol. 11, no. 1, 5442. https://doi.org/10.1038/s41467-020-18923-6

TY - JOUR

T1 - Genome biology of the paleotetraploid perennial biomass crop Miscanthus

AU - Mitros, Therese

AU - Session, Adam M.

AU - James, Brandon T.

AU - Wu, Guohong Albert

AU - Belaffif, Mohammad B.

AU - Clark, Lindsay V.

AU - Shu, Shengqiang

AU - Dong, Hongxu

AU - Barling, Adam

AU - Holmes, Jessica R.

AU - Mattick, Jessica E.

AU - Bredeson, Jessen V.

AU - Liu, Siyao

AU - Farrar, Kerrie

AU - Głowacka, Katarzyna

AU - Jeżowski, Stanisław

AU - Barry, Kerrie

AU - Chae, Won Byoung

AU - Juvik, John A.

AU - Gifford, Justin

AU - Oladeinde, Adebosola

AU - Yamada, Toshihiko

AU - Grimwood, Jane

AU - Putnam, Nicholas H.

AU - De Vega, Jose

AU - Barth, Susanne

AU - Klaas, Manfred

AU - Hodkinson, Trevor

AU - Li, Laigeng

AU - Jin, Xiaoli

AU - Peng, Junhua

AU - Yu, Chang Yeon

AU - Heo, Kweon

AU - Yoo, Ji Hye

AU - Ghimire, Bimal Kumar

AU - Donnison, Iain S.

AU - Schmutz, Jeremy

AU - Hudson, Matthew E.

AU - Sacks, Erik J.

AU - Moose, Stephen P.

AU - Swaminathan, Kankshita

AU - Rokhsar, Daniel S.

N1 - Funding: BBS/E/W/0012843A

PY - 2020/10/28

Y1 - 2020/10/28

N2 - Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

AB - Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

KW - Biomass

KW - Chromosomes, Plant/genetics

KW - DNA Transposable Elements

KW - Diploidy

KW - Evolution, Molecular

KW - Gene Expression Regulation, Plant

KW - Genetic Variation

KW - Genome, Plant

KW - Genomics

KW - Models, Genetic

KW - Phylogeny

KW - Poaceae/classification

KW - Polyploidy

KW - Saccharum/genetics

KW - Seasons

KW - Sorghum/genetics

UR - https://www.scopus.com/pages/publications/85094845165

UR - https://www.nature.com/articles/s41467-020-18923-6#Sec16

U2 - 10.1038/s41467-020-18923-6

DO - 10.1038/s41467-020-18923-6

M3 - Article

C2 - 33116128

AN - SCOPUS:85094845165

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 5442

ER -

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Abstract

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Kerrie Farrar

BBSRC Core Strategic Programme in Resilient Crops: Miscanthus

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Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Abstract

Keywords

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Kerrie Farrar

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BBSRC Core Strategic Programme in Resilient Crops: Miscanthus

Cite this