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Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Yuan, Jianbo1,2,3; Zhang, Xiaojun1,2,3; Wang, Min4,5; Sun, Yamin6; Liu, Chengzhang1,2,3; Li, Shihao1,2,3; Yu, Yang1,2,3; Gao, Yi1,2,3; Liu, Fei1,2,3; Zhang, Xiaoxi1; Kong, Jie7; Fan, Guangyi8; Zhang, Chengsong1,2,3; Feng, Lu4,5; Xiang, Jianhai1,2,3; Li, Fuhua1,2,3
2021-02-11
Source PublicationCOMMUNICATIONS BIOLOGY
Volume4Issue:1Pages:14
Corresponding AuthorFeng, Lu(fenglu63@nankai.edu.cn) ; Xiang, Jianhai(jhxiang@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
AbstractSimple 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.
DOI10.1038/s42003-021-01716-y
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaLife Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS SubjectBiology ; Multidisciplinary Sciences
WOS IDWOS:000617223400001
PublisherNATURE RESEARCH
Citation statistics
Cited Times:11[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/170085
Collection实验海洋生物学重点实验室
Corresponding AuthorFeng, Lu; Xiang, Jianhai; Li, Fuhua
Affiliation1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Expt Marine Biol, Qingdao, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Peoples R China
4.Minist Educ, Key Lab Mol Microbiol & Technol, Tianjin, Peoples R China
5.Nankai Univ, TEDA Inst Biol Sci & Biotechnol, TEDA, Tianjin, Peoples R China
6.Tianjin Biochip Corp, Tianjin 300457, Peoples R China
7.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Utilizat Marine Fisheries Res, Minist Agr, Qingdao, Peoples R China
8.BGI Shenzhen, BGI Qingdao, Qingdao, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences;  Center for Ocean Mega-Science, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences;  Center for Ocean Mega-Science, Chinese Academy of Sciences
Recommended Citation
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.
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