Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes
文献类型：期刊论文
| 作者 | Jiang, Chunxi1,2,3,5; Yang, Hongsheng1,2,3,5 ; Liu, Bohong1,2,3,5; Sun, Lina1
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| 刊名 | COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
 |
| 出版日期 | 2024-12-01 |
| 卷号 | 52页码:10 |
| 关键词 | Genome variations Genome survey Mitochondrial genome Sea cucumbers Comparative analysis |
| ISSN号 | 1744-117X |
| DOI | 10.1016/j.cbd.2024.101328 |
| 通讯作者 | Sun, Lina(sunlina@qdio.ac.cn) |
| 英文摘要 | Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that Colochirus anceps, Colochirus quadrangularis, and Pseudocolochirus violaceus within the order Dendrochirotida have significantly larger genomes (2238-3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39-72.52 %). While Holothuria edulis and Holothuria atra exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species Apostichopus californicus of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species Synapta maculata of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (P = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies. |
| WOS关键词 | HOLOTHUROIDEA ; PHYLOGENY ; DIVERSITY |
| 资助项目 | National Natural Science Foundation of China[42276143] ; Key Research and Development Pro-gram of Shandong[2021LZGC029] ; Taishan Scholars Program[tsqn202306279] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:001319778900001 |
| 出版者 | ELSEVIER SCIENCE INC |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/199170]  |
| 专题 | 海洋研究所_海洋生态与环境科学重点实验室 |
| 通讯作者 | Sun, Lina |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, 7 Nanhai Rd, Qingdao 266071, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Key Lab Breeding Biotechnol & Sustainable Aquacult, Qingdao 266071, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 5.Qingdao Marine Sci & Technol Ctr, Lab Marine Ecol & Environm Sci, Qingdao 266237, Peoples R China |
| 推荐引用方式 GB/T 7714 | Jiang, Chunxi,Yang, Hongsheng,Liu, Bohong,et al. Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes[J]. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS,2024,52:10. |
| APA | Jiang, Chunxi,Yang, Hongsheng,Liu, Bohong,&Sun, Lina.(2024).Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes.COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS,52,10. |
| MLA | Jiang, Chunxi,et al."Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes".COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 52(2024):10. |
入库方式： OAI收割
来源：海洋研究所
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