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Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

文献类型： 外文期刊

作者： Sun, Yanling 1 ; Liu, Yang 1 ; Shi, Jinfeng 1 ; Wang, Lun 4 ; Liang, Chengzhi 1 ; Yang, Jun 5 ; Chen, Jinfeng 2 ; Chen, Mingsheng 1 ;

作者机构： 1.Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing 100101, Peoples R China

2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China

3.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects &, Beijing 100101, Peoples R China

4.Shanxi Acad Agr Sci, Inst Crop Germplasm Resources, Taiyuan 030031, Peoples R China

5.Shanghai Chenshan Bot Garden, Shanghai Key Lab Plant Funct Genom & Resources, Shanghai 201602, Peoples R China

6.Chinese Acad Sci, CAS Ctr Excellence Mol Plant Sci, Natl Key Lab Plant Mol Genet, Shanghai 200032, Peoples R China

关键词： broomcorn millet; polyploid; diploidization; gene loss; transposable element

期刊名称：PLANT JOURNAL （ 影响因子：7.2； 五年影响因子：7.9 ）

ISSN： 0960-7412

年卷期： 2023 年 113 卷 4 期

页码：

收录情况： SCI

摘要： Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome-scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at similar to 4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about similar to 0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element-rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.

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