Genome characterization and comparative analysis among three swimming crab species
In this study we sequenced the genomes of three economically important swimming crabs Portunus trituberculatus, Charybdis japonica, and Callinectes sapidus using the next-generation sequencing approach and made a basic assembly. The genomes of the three species are characterized with high heterozygo...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Marine Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.895119/full |
| _version_ | 1828396863678578688 |
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| author | Ming Liu Shanshan Ge Shivish Bhandari Chunlei Fan Yu Jiao Chunlei Gai Youhong Wang Hongjun Liu |
| author_facet | Ming Liu Shanshan Ge Shivish Bhandari Chunlei Fan Yu Jiao Chunlei Gai Youhong Wang Hongjun Liu |
| author_sort | Ming Liu |
| collection | DOAJ |
| description | In this study we sequenced the genomes of three economically important swimming crabs Portunus trituberculatus, Charybdis japonica, and Callinectes sapidus using the next-generation sequencing approach and made a basic assembly. The genomes of the three species are characterized with high heterozygosity (>1.2%) and high repeat content (>50%). Genome comparative analysis revealed 40 long conserved fragments (>5,000 bp) among the three species, most of them are involved in cardiac-related biological process. Relative higher genome similarity was found between P. trituberculatus and C. japonica that are belong to different subfamilies, compared to that between P. trituberculatus and C. sapidus which are from the same subfamily. It is inconsistent with their phylogenetic evolutionary trees inferred from previous mitochondrial DNA coding fragments and a conserved ANK2 protein fragment from this study. We speculated that the high genome similarity between P. trituberculatus and C. japonica might be attributed to their same inhabit range in which the genome is subject to the same environment selection, and the inconsistence between genome similarity and phylogenetic relationship is caused by the different evolutionary rates of coding DNA and non-coding DNA under environment selection. |
| first_indexed | 2024-12-10T08:37:32Z |
| format | Article |
| id | doaj.art-e23cdf648c1e417390627471562ff03b |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-10T08:37:32Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-e23cdf648c1e417390627471562ff03b2022-12-22T01:55:56ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452022-07-01910.3389/fmars.2022.895119895119Genome characterization and comparative analysis among three swimming crab speciesMing Liu0Shanshan Ge1Shivish Bhandari2Chunlei Fan3Yu Jiao4Chunlei Gai5Youhong Wang6Hongjun Liu7Patuxent Environmental and Aquatic Research Laboratory, Morgan State University, St. Leonard, MD, United StatesKey Laboratory of Disease Control in Mariculture, Marine Science Research Institute of Shandong Province, Qingdao, ChinaPatuxent Environmental and Aquatic Research Laboratory, Morgan State University, St. Leonard, MD, United StatesPatuxent Environmental and Aquatic Research Laboratory, Morgan State University, St. Leonard, MD, United StatesFishery College, Guangdong Ocean University, Zhanjiang, ChinaKey Laboratory of Disease Control in Mariculture, Marine Science Research Institute of Shandong Province, Qingdao, ChinaKey Laboratory of Disease Control in Mariculture, Marine Science Research Institute of Shandong Province, Qingdao, ChinaKey Laboratory of Disease Control in Mariculture, Marine Science Research Institute of Shandong Province, Qingdao, ChinaIn this study we sequenced the genomes of three economically important swimming crabs Portunus trituberculatus, Charybdis japonica, and Callinectes sapidus using the next-generation sequencing approach and made a basic assembly. The genomes of the three species are characterized with high heterozygosity (>1.2%) and high repeat content (>50%). Genome comparative analysis revealed 40 long conserved fragments (>5,000 bp) among the three species, most of them are involved in cardiac-related biological process. Relative higher genome similarity was found between P. trituberculatus and C. japonica that are belong to different subfamilies, compared to that between P. trituberculatus and C. sapidus which are from the same subfamily. It is inconsistent with their phylogenetic evolutionary trees inferred from previous mitochondrial DNA coding fragments and a conserved ANK2 protein fragment from this study. We speculated that the high genome similarity between P. trituberculatus and C. japonica might be attributed to their same inhabit range in which the genome is subject to the same environment selection, and the inconsistence between genome similarity and phylogenetic relationship is caused by the different evolutionary rates of coding DNA and non-coding DNA under environment selection.https://www.frontiersin.org/articles/10.3389/fmars.2022.895119/fullPortunus trituberculatusCharybdis japonicaCallinectes sapidusgenome heterozygositygenome repeat sequencesgenome similarity |
| spellingShingle | Ming Liu Shanshan Ge Shivish Bhandari Chunlei Fan Yu Jiao Chunlei Gai Youhong Wang Hongjun Liu Genome characterization and comparative analysis among three swimming crab species Frontiers in Marine Science Portunus trituberculatus Charybdis japonica Callinectes sapidus genome heterozygosity genome repeat sequences genome similarity |
| title | Genome characterization and comparative analysis among three swimming crab species |
| title_full | Genome characterization and comparative analysis among three swimming crab species |
| title_fullStr | Genome characterization and comparative analysis among three swimming crab species |
| title_full_unstemmed | Genome characterization and comparative analysis among three swimming crab species |
| title_short | Genome characterization and comparative analysis among three swimming crab species |
| title_sort | genome characterization and comparative analysis among three swimming crab species |
| topic | Portunus trituberculatus Charybdis japonica Callinectes sapidus genome heterozygosity genome repeat sequences genome similarity |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.895119/full |
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