Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Triticum aestivum L.)

被引：3

作者：

Cui, Licao ^{[1
,2
]}

Cheng, Hao ^{[1
,3
]}

Yang, Zhe ^{[1
]}

Xia, Chuan ^{[1
]}

Zhang, Lichao ^{[1
]}

Kong, Xiuying ^{[1
]}

机构：

[1] Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China

[2] Jiangxi Agr Univ, Coll Biosci & Engn, Nanchang 330045, Peoples R China

[3] Northwest A&F Univ, Coll Life Sci, State Key Lab Crop Stress Biol Arid Areas, Yangling 712100, Peoples R China

来源：

PLANTS-BASEL | 2023年 / 12卷 / 17期

关键词：

wheat; gene duplication; evolutionary rate; domestication; polyploidization; POSITIVE SELECTION; WHOLE-GENOME; CODON USAGE; POPULATION GENOMICS; ESCHERICHIA-COLI; DIVERGENCE; EXPRESSION; WILD; DOMESTICATION; POLYPLOIDY;

D O I：

10.3390/plants12173021

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Wheat (Triticum aestivum L.) is a staple food crop that provides 20% of total human calorie consumption. Gene duplication has been considered to play an important role in evolution by providing new genetic resources. However, the evolutionary fates and biological functions of the duplicated genes in wheat remain to be elucidated. In this study, the resulting data showed that the duplicated genes evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity when compared to non-duplicated genes. Our analysis further revealed functions of duplicated genes in various biological processes with significant enrichment to environmental stresses. In addition, duplicated genes derived from dispersed, proximal, tandem, transposed, and whole-genome duplication differed in abundance, evolutionary rate, gene compactness, expression pattern, and genetic diversity. Tandem and proximal duplicates experienced stronger selective pressure and showed a more compact gene structure with diverse expression profiles than other duplication modes. Moreover, genes derived from different duplication modes showed an asymmetrical evolutionary pattern for wheat A, B, and D subgenomes. Several candidate duplication hotspots associated with wheat domestication or polyploidization were characterized as potential targets for wheat molecular breeding. Our comprehensive analysis revealed the evolutionary trajectory of duplicated genes and laid the foundation for future functional studies on wheat.

引用

页数：22

共 89 条

[1] Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes [J].

Akhunov, Eduard D. ;

Akhunova, Alina R. ;

Anderson, Olin D. ;

Anderson, James A. ;

Blake, Nancy ;

Clegg, Michael T. ;

Coleman-Derr, Devin ;

Conley, Emily J. ;

Crossman, Curt C. ;

Deal, Karin R. ;

Dubcovsky, Jorge ;

Gill, Bikram S. ;

Gu, Yong Q. ;

Hadam, Jakub ;

Heo, Hwayoung ;

Huo, Naxin ;

Lazo, Gerard R. ;

Luo, Ming-Cheng ;

Ma, Yaqin Q. ;

Matthews, David E. ;

McGuire, Patrick E. ;

Morrell, Peter L. ;

Qualset, Calvin O. ;

Renfro, James ;

Tabanao, Dindo ;

Talbert, Luther E. ;

Tian, Chao ;

Toleno, Donna M. ;

Warburton, Marilyn L. ;

You, Frank M. ;

Zhang, Wenjun ;

Dvorak, Jan .

BMC GENOMICS, 2010, 11

[2] The Amborella Genome and the Evolution of Flowering Plants [J].

Albert, Victor A. ;

Barbazuk, W. Bradley ;

dePamphilis, Claude W. ;

Der, Joshua P. ;

Leebens-Mack, James ;

Ma, Hong ;

Palmer, Jeffrey D. ;

Rounsley, Steve ;

Sankoff, David ;

Schuster, Stephan C. ;

Soltis, Douglas E. ;

Soltis, Pamela S. ;

Wessler, Susan R. ;

Wing, Rod A. ;

Albert, Victor A. ;

Ammiraju, Jetty S. S. ;

Barbazuk, W. Bradley ;

Chamala, Srikar ;

Chanderbali, Andre S. ;

dePamphilis, Claude W. ;

Der, Joshua P. ;

Determann, Ronald ;

Leebens-Mack, James ;

Ma, Hong ;

Ralph, Paula ;

Rounsley, Steve ;

Schuster, Stephan C. ;

Soltis, Douglas E. ;

Soltis, Pamela S. ;

Talag, Jason ;

Tomsho, Lynn ;

Walts, Brandon ;

Wanke, Stefan ;

Wing, Rod A. ;

Albert, Victor A. ;

Barbazuk, W. Bradley ;

Chamala, Srikar ;

Chanderbali, Andre S. ;

Chang, Tien-Hao ;

Determann, Ronald ;

Lan, Tianying ;

Soltis, Douglas E. ;

Soltis, Pamela S. ;

Arikit, Siwaret ;

Axtell, Michael J. ;

Ayyampalayam, Saravanaraj ;

Barbazuk, W. Bradley ;

Burnette, James M., III ;

Chamala, Srikar ;

De Paoli, Emanuele .

SCIENCE, 2013, 342 (6165) :1467-+

[3] Shifting the limits in wheat research and breeding using a fully annotated reference genome [J].

Appels, Rudi ;

Eversole, Kellye ;

Feuillet, Catherine ;

Keller, Beat ;

Rogers, Jane ;

Stein, Nils ;

Pozniak, Curtis J. ;

Choulet, Frederic ;

Distelfeld, Assaf ;

Poland, Jesse ;

Ronen, Gil ;

Sharpe, Andrew G. ;

Pozniak, Curtis ;

Barad, Omer ;

Baruch, Kobi ;

Keeble-Gagnere, Gabriel ;

Mascher, Martin ;

Ben-Zvi, Gil ;

Josselin, Ambre-Aurore ;

Himmelbach, Axel ;

Balfourier, Francois ;

Gutierrez-Gonzalez, Juan ;

Hayden, Matthew ;

Koh, ChuShin ;

Muehlbauer, Gary ;

Pasam, Raj K. ;

Paux, Etienne ;

Rigault, Philippe ;

Tibbits, Josquin ;

Tiwari, Vijay ;

Spannagl, Manuel ;

Lang, Daniel ;

Gundlach, Heidrun ;

Haberer, Georg ;

Mayer, Klaus F. X. ;

Ormanbekova, Danara ;

Prade, Verena ;

Simkova, Hana ;

Wicker, Thomas ;

Swarbreck, David ;

Rimbert, Helene ;

Felder, Marius ;

Guilhot, Nicolas ;

Kaithakottil, Gemy ;

Keilwagen, Jens ;

Leroy, Philippe ;

Lux, Thomas ;

Twardziok, Sven ;

Venturini, Luca ;

Juhasz, Angela .

SCIENCE, 2018, 361 (6403) :661-+

[4] Wild emmer genome architecture and diversity elucidate wheat evolution and domestication [J].

Avni, Raz ;

Nave, Moran ;

Barad, Omer ;

Baruch, Kobi ;

Twardziok, Sven O. ;

Gundlach, Heidrun ;

Hale, Iago ;

Mascher, Martin ;

Spannagl, Manuel ;

Wiebe, Krystalee ;

Jordan, Katherine W. ;

Golan, Guy ;

Deek, Jasline ;

Ben-Zvi, Batsheva ;

Ben-Zvi, Gil ;

Himmelbach, Axel ;

MacLachlan, Ron P. ;

Sharpe, Andrew G. ;

Fritz, Allan ;

Ben-David, Roi ;

Budak, Hikmet ;

Fahima, Tzion ;

Korol, Abraham ;

Faris, Justin D. ;

Hernandez, Alvaro ;

Mikel, Mark A. ;

Levy, Avraham A. ;

Steffenson, Brian ;

Maccaferri, Marco ;

Tuberosa, Roberto ;

Cattivelli, Luigi ;

Faccioli, Primetta ;

Ceriotti, Aldo ;

Kashkush, Khalil ;

Pourkheirandish, Mohammad ;

Komatsuda, Takao ;

Eilam, Tamar ;

Sela, Hanan ;

Sharon, Amir ;

Ohad, Nir ;

Chamovitz, Daniel A. ;

Mayer, Klaus F. X. ;

Stein, Nils ;

Ronen, Gil ;

Peleg, Zvi ;

Pozniak, Curtis J. ;

Akhunov, Eduard D. ;

Distelfeld, Assaf .

SCIENCE, 2017, 357 (6346) :93-96

[5]

BENNETZEN JL, 1982, J BIOL CHEM, V257, P3026

[6] Ohno's dilemma: Evolution of new genes under continuous selection [J].

Bergthorsson, Ulfar ;

Andersson, Dan I. ;

Roth, John R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (43) :17004-17009

[7] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[8] Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus [J].

Cao, Yunpeng ;

Jiang, Lan ;

Wang, Lihu ;

Cai, Yongping .

BIOMOLECULES, 2019, 9 (09)

[9] Evidence for the fixation of gene duplications by positive selection in Drosophila [J].

Cardoso-Moreira, Margarida ;

Arguello, J. Roman ;

Gottipati, Srikanth ;

Harshman, L. G. ;

Grenier, Jennifer K. ;

Clark, Andrew G. .

GENOME RESEARCH, 2016, 26 (06) :787-798

[10] TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data [J].

Chen, Chengjie ;

Chen, Hao ;

Zhang, Yi ;

Thomas, Hannah R. ;

Frank, Margaret H. ;

He, Yehua ;

Xia, Rui .

MOLECULAR PLANT, 2020, 13 (08) :1194-1202

← 1 2 3 4 5 6 7 8 9 →