TY - JOUR
T1 - A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis
AU - Zheng, Huakun
AU - Wang, Baiyu
AU - Hua, Xiuting
AU - Gao, Ruiting
AU - Wang, Yuhao
AU - Zhang, Zixin
AU - Zhang, Yixing
AU - Mei, Jing
AU - Huang, Yongji
AU - Huang, Yumin
AU - Lin, Hui
AU - Zhang, Xingtan
AU - Lin, Dongmei
AU - Lan, Siren
AU - Liu, Zhongjian
AU - Lu, Guodong
AU - Wang, Zonghua
AU - Ming, Ray
AU - Zhang, Jisen
AU - Lin, Zhanxi
N1 - This work was supported by grants from the Major Special Project of Fujian Province ( 2021NZ029009 ) and the Natural Science foundation of Fujian Province ( 2019J01665 ).
PY - 2023/9/11
Y1 - 2023/9/11
N2 - JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.
AB - JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.
KW - Cenchrus grass
KW - allotetrapolyploid
KW - centromere architecture
KW - evolutionary trajectory
KW - genome assembly
KW - photosynthetic efficiency
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UR - http://www.scopus.com/inward/citedby.url?scp=85164330540&partnerID=8YFLogxK
U2 - 10.1016/j.xplc.2023.100633
DO - 10.1016/j.xplc.2023.100633
M3 - Article
C2 - 37271992
AN - SCOPUS:85164330540
SN - 2590-3462
VL - 4
JO - Plant Communications
JF - Plant Communications
IS - 5
M1 - 100633
ER -