Genome biology of the paleotetraploid perennial biomass crop Miscanthus

被引：85

作者：

Mitros, Therese ^{[1
,2
]}

Session, Adam M. ^{[1
,3
]}

James, Brandon T. ^{[2
,4
]}

Wu, Guohong Albert ^{[3
]}

Belaffif, Mohammad B. ^{[2
,4
]}

Clark, Lindsay V. ^{[5
,6
]}

Shu, Shengqiang ^{[3
]}

Dong, Hongxu ^{[5
]}

Barling, Adam ^{[5
]}

Holmes, Jessica R. ^{[5
,6
]}

Mattick, Jessica E. ^{[5
,7
]}

Bredeson, Jessen V. ^{[1
]}

Liu, Siyao ^{[5
,8
]}

Farrar, Kerrie ^{[9
]}

Glowacka, Katarzyna ^{[10
,11
]}

Jezowski, Stanislaw ^{[10
]}

Barry, Kerrie ^{[3
]}

Chae, Won Byoung ^{[5
,12
]}

Juvik, John A. ^{[5
]}

Gifford, Justin ^{[5
]}

Oladeinde, Adebosola ^{[5
]}

Yamada, Toshihiko ^{[13
]}

Grimwood, Jane ^{[3
,4
]}

Putnam, Nicholas H. ^{[14
]}

De Vega, Jose ^{[15
]}

Barth, Susanne ^{[16
]}

Klaas, Manfred ^{[16
]}

Hodkinson, Trevor ^{[17
]}

Li, Laigeng ^{[18
]}

Jin, Xiaoli ^{[19
]}

Peng, Junhua ^{[20
]}

Yu, Chang Yeon ^{[21
]}

Heo, Kweon ^{[21
]}

Yoo, Ji Hye ^{[21
]}

Ghimire, Bimal Kumar ^{[22
]}

Donnison, Iain S. ^{[9
]}

Schmutz, Jeremy ^{[3
,4
]}

Hudson, Matthew E. ^{[2
,5
,23
]}

Sacks, Erik J. ^{[2
,5
,23
]}

Moose, Stephen P. ^{[2
,5
,23
]}

Swaminathan, Kankshita ^{[2
,4
]}

Rokhsar, Daniel S. ^{[1
,2
,3
,24
,25
]}

机构：

[1] Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA

[2] Univ Illinois, DOE Ctr Adv Bioenergy & Bioprod Innovat CABBI, Urbana, IL 61801 USA

[3] US DOE, Joint Genome Inst, Berkeley, CA 94720 USA

[4] HudsonAlpha Biotechnol Inst, 601 Genome Way Northwest, Huntsville, AL 35806 USA

[5] Univ Illinois, Dept Crop Sci, 1102S Goodwin Ave, Urbana, IL 61801 USA

[6] Univ Illinois, Roy J Carver Biotechnol Ctr, High Performance Biol Comp, 206 West Gregory Dr, Urbana, IL 61801 USA

[7] Loyola Univ Chicago, Stritch Sch Med, Dept Microbiol & Immunol, Maywood, IL 60153 USA

[8] Univ N Carolina, Dept Genet Curriculum Bioinformat & Computat Biol, Chapel Hill, NC 27514 USA

[9] Aberystwyth Univ, Inst Biol Environm & Rural Sci IBERS, Aberystwyth SY23 3EE, Ceredigion, Wales

[10] Polish Acad Sci, Inst Plant Genet, PL-60479 Poznan, Poland

[11] Univ Nebraska, Dept Biochem, Lincoln, NE 68588 USA

[12] Dankook Univ, Dept Environm Hort, Cheonan 31116, South Korea

[13] Field Sci Ctr Northern Biosphere, Kita Ku, 10 Chome 3 Kita 11 Jonishi, Sapporo, Hokkaido 0600811, Japan

[14] Dovetail Genom, 100 Enterprise Way, Scotts Valley, CA 95066 USA

[15] Norwich Res Pk Innovat Ctr, Earlham Inst, Norwich NR4 7UZ, Norfolk, England

[16] Oak Pk Res Ctr, Teagasc Crops Environm & Land Use Programme, Carlow R93X E12, Ireland

[17] Univ Dublin, Trinity Coll Dublin, Sch Nat Sci, Bot, Dublin D2, Ireland

[18] Chinese Acad Sci, Inst Plant Physiol & Ecol, 300 Fenglin Rd, Shanghai 200032, Peoples R China

[19] Zhejiang Univ, Dept Agron, Hangzhou 310058, Peoples R China

[20] HuaZhi Rice Biotech Co, Changsha 410125, Hunan, Peoples R China

[21] Kangwon Natl Univ, Dept Appl Plant Sci, Chunchon 200701, Gangwon, South Korea

[22] Konkuk Univ, Dept Appl Biosci, Seoul 05029, South Korea

[23] Univ Illinois, Carl R Woese Inst Genom Biol, 1206 West Gregory Dr, Urbana, IL 61801 USA

[24] Grad Univ, Okinawa Inst Sci & Technol, Okinawa 9040495, Japan

[25] Chan Zuckerberg BioHub, 499 Illinois St, San Francisco, CA 94158 USA

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

基金：

英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会;

关键词：

ARABIDOPSIS; EVOLUTION; OVEREXPRESSION; SACCHARIFLORUS; PHYLOGENIES; ANNOTATION; COLLECTION; FRAMEWORK; DOMINANCE; SINENSIS;

D O I：

10.1038/s41467-020-18923-6

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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. x 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. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.

引用

页数：11

共 77 条

[51] MIPS PlantsDB: a database framework for comparative plant genome research [J].

Nussbaumer, Thomas ;

Martis, Mihaela M. ;

Roessner, Stephan K. ;

Pfeifer, Matthias ;

Bader, Kai C. ;

Sharma, Sapna ;

Gundlach, Heidrun ;

Spannagl, Manuel .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D1144-D1151

[52] Chromosome-scale shotgun assembly using an in vitro method for long-range linkage [J].

Putnam, Nicholas H. ;

O'Connell, Brendan L. ;

Stites, Jonathan C. ;

Rice, Brandon J. ;

Blanchette, Marco ;

Calef, Robert ;

Troll, Christopher J. ;

Fields, Andrew ;

Hartley, Paul D. ;

Sugnet, Charles W. ;

Haussler, David ;

Rokhsar, Daniel S. ;

Green, Richard E. .

GENOME RESEARCH, 2016, 26 (03) :342-350

[53] Genome Size of Three Miscanthus Species [J].

Rayburn, A. Lane ;

Crawford, Joseph ;

Rayburn, Charlotte M. ;

Juvik, John A. .

PLANT MOLECULAR BIOLOGY REPORTER, 2009, 27 (02) :184-188

[54] r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock [J].

Sanderson, MJ .

BIOINFORMATICS, 2003, 19 (02) :301-302

[55] Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss [J].

Schnable, James C. ;

Springer, Nathan M. ;

Freeling, Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (10) :4069-4074

[56] Genome evolution in the allotetraploid frog Xenopus laevis [J].

Session, Adam M. ;

Uno, Yoshinobu ;

Kwon, Taejoon ;

Hapman, Jarrod A. C. ;

Toyoda, Atsushi ;

Takahashi, Shuji ;

Fukui, Akimasa ;

Hikosaka, Akira ;

Suzuki, Atsushi ;

Kondo, Mariko ;

van Heeringen, Simon J. ;

Quigley, Ian ;

Heinz, Sven ;

Ogino, Hajime ;

Ochi, Haruki ;

Hellsten, Uffe ;

Lyons, Jessica B. . ;

Simakov, Oleg ;

Putnam, Nicholas ;

Stites, Jonathan ;

Kuroki, Yoko ;

Tanaka, Toshiaki ;

Michiue, Tatsuo ;

Watanabe, Minoru ;

Ogdanovic, Ozren B. ;

Lister, Ryan ;

Georgiou, Georgios ;

Paranjpe, Sarita S. ;

Van Kruijsbergen, Ila ;

Shu, Shengquiang ;

Carlson, Joseph ;

Kinoshita, Tsutomu ;

Ohta, Yuko ;

Mawaribuchi, Shuuji ;

Jenkins, Jerry ;

Grimwood, Jane ;

Schmutz, Jeremy ;

Mitros, Therese ;

Mozaffari, Sahar V. ;

Suzuki, Yutaka ;

Haramoto, Yoshikazu ;

Yamamoto, Takamasa S. ;

Takagi, Chiyo ;

Heald, Rebecca ;

Miller, Kelly ;

Haudenschild, Christian ;

Kitzman, Jacob ;

Nakayama, Takuya ;

Zutsu, Yumi I. ;

Robert, Jacques .

NATURE, 2016, 538 (7625) :336-+

[57] Insights into bilaterian evolution from three spiralian genomes [J].

Simakov, Oleg ;

Marletaz, Ferdinand ;

Cho, Sung-Jin ;

Edsinger-Gonzales, Eric ;

Havlak, Paul ;

Hellsten, Uffe ;

Kuo, Dian-Han ;

Larsson, Tomas ;

Lv, Jie ;

Arendt, Detlev ;

Savage, Robert ;

Osoegawa, Kazutoyo ;

de Jong, Pieter ;

Grimwood, Jane ;

Chapman, Jarrod A. ;

Shapiro, Harris ;

Aerts, Andrea ;

Otillar, Robert P. ;

Terry, Astrid Y. ;

Boore, Jeffrey L. ;

Grigoriev, Igor V. ;

Lindberg, David R. ;

Seaver, Elaine C. ;

Weisblat, David A. ;

Putnam, Nicholas H. ;

Rokhsar, Daniel S. .

NATURE, 2013, 493 (7433) :526-531

[58] BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs [J].

Simao, Felipe A. ;

Waterhouse, Robert M. ;

Ioannidis, Panagiotis ;

Kriventseva, Evgenia V. ;

Zdobnov, Evgeny M. .

BIOINFORMATICS, 2015, 31 (19) :3210-3212

[59]

Smit A., 2008, RepeatModeler Open-1.0

[60]

Smit A., 2013, REPEATMASKER OPEN 40

← 1 2 3 4 5 6 7 8 →