Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp

doi:10.1038/s42003-021-01716-y

CORC > 海洋研究所 > 中国科学院海洋研究所 > 实验海洋生物学重点实验室

	Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
	Yuan, Jianbo 2,3,5; Zhang, Xiaojun 2,3,5; Wang, Min 6,7; Sun, Yamin 4; Liu, Chengzhang 2,3,5; Li, Shihao 2,3,5; Yu, Yang 2,3,5; Gao, Yi 2,3,5; Liu, Fei 2,3,5; Zhang, Xiaoxi 3
刊名	COMMUNICATIONS BIOLOGY
	2021-02-11
卷号	4 期号:1 页码:14
DOI	10.1038/s42003-021-01716-y
通讯作者	Feng, Lu(fenglu63@nankai.edu.cn) ; Xiang, Jianhai(jhxiang@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
英文摘要	Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. However, penaeid shrimp genomes have a high proportion of SSRs (>23%), raising the question of whether these SSRs play important functional and evolutionary roles in these SSR-rich species. Here, we show that SSRs drive genome plasticity and adaptive evolution in two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. Assembly and comparison of genomes of these two shrimp species at the chromosome-level revealed that transposable elements serve as carriers for SSR expansion, which is still occurring. The remarkable genome plasticity identified herein might have been shaped by significant SSR expansions. SSRs were also found to regulate gene expression by multi-omics analyses, and be responsible for driving adaptive evolution, such as the variable osmoregulatory capacities of these shrimp under low-salinity stress. These data provide strong evidence that SSRs are an important driver of the adaptive evolution in penaeid shrimp. This study focuses on the role of simple sequence repeats (SSRs) in the evolution of the genomes of two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. They observed a significant expansion in SSRs in the genomes of these species (similar to 23%) compared what is seen in other animal genomes (similar to 1%) and suggest a possible mechanistic relationship between SSRs and transposable elements.
资助项目	National Key Research & Development Program of China[2018YFD0900103] ; National Natural Science Foundation of China[41876167] ; National Natural Science Foundation of China[31830100] ; Senior User Project of RV KEXUE[KEXUE2018G19] ; Qingdao National Laboratory for Marine Science and Technology[MS2017NO04] ; China Agriculture Research system-48[CARS-48] ; High Performance Computing Center, Institute of Oceanology, CAS
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
语种	英语
出版者	NATURE RESEARCH
WOS记录号	WOS:000617223400001
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/170084]
专题	海洋研究所_实验海洋生物学重点实验室
通讯作者	Feng, Lu; Xiang, Jianhai; Li, Fuhua
作者单位	1.BGI Shenzhen, BGI Qingdao, Qingdao, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Expt Marine Biol, Qingdao, Peoples R China 4.Tianjin Biochip Corp, Tianjin 300457, Peoples R China 5.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Peoples R China 6.Minist Educ, Key Lab Mol Microbiol & Technol, Tianjin, Peoples R China 7.Nankai Univ, TEDA Inst Biol Sci & Biotechnol, TEDA, Tianjin, Peoples R China 8.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Utilizat Marine Fisheries Res, Minist Agr, Qingdao, Peoples R China
推荐引用方式 GB/T 7714	Yuan, Jianbo,Zhang, Xiaojun,Wang, Min,et al. Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp[J]. COMMUNICATIONS BIOLOGY,2021,4(1):14.
APA	Yuan, Jianbo.,Zhang, Xiaojun.,Wang, Min.,Sun, Yamin.,Liu, Chengzhang.,...&Li, Fuhua.(2021).Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp.COMMUNICATIONS BIOLOGY,4(1),14.
MLA	Yuan, Jianbo,et al."Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp".COMMUNICATIONS BIOLOGY 4.1(2021):14.