The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics
In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three puta...
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| description | In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species. |
| doi_str_mv | 10.1371/journal.pone.0255547 |
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The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0255547</identifier><identifier>PMID: 34735446</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Biological research ; Biology and life sciences ; Biology, Experimental ; Computer and Information Sciences ; Crustacea ; Crustaceans ; Decapoda ; Decapoda (Crustacea) ; Decapoda - genetics ; Evolution ; Evolution, Molecular ; Fisheries ; Gene Order ; Genes ; Genes, Mitochondrial ; Genetic aspects ; Genetic diversity ; Genetics ; Genetics, Population ; Genome, Mitochondrial ; Genomes ; Genomics ; Hippolytidae ; Laboratories ; Lysmata vittata ; Mitochondria ; Morphology ; Natural history ; Nucleotide sequence ; Nucleotides ; Phylogenetics ; Phylogeny ; Population genetics ; Population studies ; Ribonucleic acid ; RNA ; rRNA ; Species ; Stop codon ; Structure ; Transfer RNA ; Translocation ; tRNA</subject><ispartof>PloS one, 2021-11, Vol.16 (11), p.e0255547-e0255547</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Zhu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species.</description><subject>Animals</subject><subject>Biological research</subject><subject>Biology and life sciences</subject><subject>Biology, Experimental</subject><subject>Computer and Information Sciences</subject><subject>Crustacea</subject><subject>Crustaceans</subject><subject>Decapoda</subject><subject>Decapoda (Crustacea)</subject><subject>Decapoda - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Fisheries</subject><subject>Gene Order</subject><subject>Genes</subject><subject>Genes, Mitochondrial</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetics</subject><subject>Genetics, Population</subject><subject>Genome, Mitochondrial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hippolytidae</subject><subject>Laboratories</subject><subject>Lysmata vittata</subject><subject>Mitochondria</subject><subject>Morphology</subject><subject>Natural history</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Population genetics</subject><subject>Population studies</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>rRNA</subject><subject>Species</subject><subject>Stop codon</subject><subject>Structure</subject><subject>Transfer 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complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics</title><author>Zhu, Longqiang ; Zhu, Zhihuang ; Zhu, Leiyu ; Wang, Dingquan ; Wang, Jianxin ; Lin, Qi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-b987ff22d46c48211b610192dd8b6f97d3ef7c68cb4a79776b75038e568f45cc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Biological research</topic><topic>Biology and life sciences</topic><topic>Biology, Experimental</topic><topic>Computer and Information Sciences</topic><topic>Crustacea</topic><topic>Crustaceans</topic><topic>Decapoda</topic><topic>Decapoda (Crustacea)</topic><topic>Decapoda - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Fisheries</topic><topic>Gene Order</topic><topic>Genes</topic><topic>Genes, 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Tzen-Yuh</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-11-04</date><risdate>2021</risdate><volume>16</volume><issue>11</issue><spage>e0255547</spage><epage>e0255547</epage><pages>e0255547-e0255547</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34735446</pmid><doi>10.1371/journal.pone.0255547</doi><orcidid>https://orcid.org/0000-0003-1749-2630</orcidid><orcidid>https://orcid.org/0000-0002-2337-625X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Biological research Biology and life sciences Biology, Experimental Computer and Information Sciences Crustacea Crustaceans Decapoda Decapoda (Crustacea) Decapoda - genetics Evolution Evolution, Molecular Fisheries Gene Order Genes Genes, Mitochondrial Genetic aspects Genetic diversity Genetics Genetics, Population Genome, Mitochondrial Genomes Genomics Hippolytidae Laboratories Lysmata vittata Mitochondria Morphology Natural history Nucleotide sequence Nucleotides Phylogenetics Phylogeny Population genetics Population studies Ribonucleic acid RNA rRNA Species Stop codon Structure Transfer RNA Translocation tRNA |
| title | The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics |
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