Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species
文献类型：期刊论文
| 作者 | Yuan, Jianbo1,2,3; Zhang, Xiaojun1,2,3; Li, Fuhua1,2,3; Xiang, Jianhai1,2,3
|
| 刊名 | FRONTIERS IN GENETICS
 |
| 出版日期 | 2021-05-03 |
| 卷号 | 12页码:12 |
| 关键词 | penaeid shrimp genome genome assembly genomic characteristic whole genome duplication |
| DOI | 10.3389/fgene.2021.658619 |
| 通讯作者 | Xiang, Jianhai(jhxiang@qdio.ac.cn) |
| 英文摘要 | Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies. |
| 资助项目 | National Natural Science Foundation of China[41876167] ; National Natural Science Foundation of China[31830100] ; National Key Research & Development Program of China[2018YFD0900103] ; National Key Research & Development Program of China[2018YFD0900404] ; Qingdao National Laboratory for Marine Science and Technology[MS2017NO04] ; China Agriculture Research system-48[CARS-48] |
| WOS研究方向 | Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:000651095300001 |
| 出版者 | FRONTIERS MEDIA SA |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/170964]  |
| 专题 | 海洋研究所_实验海洋生物学重点实验室 |
| 通讯作者 | Xiang, Jianhai |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Expt Marine Biol, Qingdao, Peoples R China 2.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Peoples R China 3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China |
| 推荐引用方式 GB/T 7714 | Yuan, Jianbo,Zhang, Xiaojun,Li, Fuhua,et al. Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species[J]. FRONTIERS IN GENETICS,2021,12:12. |
| APA | Yuan, Jianbo,Zhang, Xiaojun,Li, Fuhua,&Xiang, Jianhai.(2021).Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species.FRONTIERS IN GENETICS,12,12. |
| MLA | Yuan, Jianbo,et al."Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species".FRONTIERS IN GENETICS 12(2021):12. |
入库方式： OAI收割
来源：海洋研究所
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