Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae)
This study aims to elucidate the characteristics of the mitogenome of <i>Lysmata lipkei</i> and investigate its phylogenetic relationships. Using both the Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park,...
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MDPI AG
2025-04-01
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| author | Xixi Zhang Zhihuang Zhu Jianxin Wang Ge Shi Qi Lin |
| author_facet | Xixi Zhang Zhihuang Zhu Jianxin Wang Ge Shi Qi Lin |
| author_sort | Xixi Zhang |
| collection | DOAJ |
| description | This study aims to elucidate the characteristics of the mitogenome of <i>Lysmata lipkei</i> and investigate its phylogenetic relationships. Using both the Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park, CA, USA) platforms, the complete mitogenome sequence of <i>L. lipkei</i> was determined. The mitogenome of <i>L. lipkei</i> was annotated, measuring 17,497 bp in length and comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). The nucleotide composition of the genome exhibited an AT bias of 63.4%. Among the PCGs, the most frequently used codon was UUA. All tRNAs, except for <i>trnD</i>, which lacks the TψC loop, were capable of forming the typical cloverleaf structure. Phylogenetic trees for Caridea were constructed using Bayesian Inference (BI) and Maximum Likelihood (ML) methods based on the nucleotide sequences of the 13 PCGs. Both methods yielded consistent topological structures, with <i>L. lipkei</i> showing the closest phylogenetic relationship to <i>L. kuekenthali</i>. Additionally, Lysmatidae, Thoridae, and Hippolytidae formed a monophyletic clade. This research not only filled the gap in mitogenome data for Lysmatidae but also provided novel molecular insights into Caridean phylogenetics. |
| format | Article |
| id | doaj-art-9470cdc0ee9148e5baf9be9d18218c50 |
| institution | OA Journals |
| issn | 2410-3888 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
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| series | Fishes |
| spelling | doaj-art-9470cdc0ee9148e5baf9be9d18218c502025-08-20T02:28:14ZengMDPI AGFishes2410-38882025-04-0110417710.3390/fishes10040177Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae)Xixi Zhang0Zhihuang Zhu1Jianxin Wang2Ge Shi3Qi Lin4Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaFisheries Research Institute of Fujian, Xiamen 361013, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaFisheries Research Institute of Fujian, Xiamen 361013, ChinaThis study aims to elucidate the characteristics of the mitogenome of <i>Lysmata lipkei</i> and investigate its phylogenetic relationships. Using both the Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park, CA, USA) platforms, the complete mitogenome sequence of <i>L. lipkei</i> was determined. The mitogenome of <i>L. lipkei</i> was annotated, measuring 17,497 bp in length and comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). The nucleotide composition of the genome exhibited an AT bias of 63.4%. Among the PCGs, the most frequently used codon was UUA. All tRNAs, except for <i>trnD</i>, which lacks the TψC loop, were capable of forming the typical cloverleaf structure. Phylogenetic trees for Caridea were constructed using Bayesian Inference (BI) and Maximum Likelihood (ML) methods based on the nucleotide sequences of the 13 PCGs. Both methods yielded consistent topological structures, with <i>L. lipkei</i> showing the closest phylogenetic relationship to <i>L. kuekenthali</i>. Additionally, Lysmatidae, Thoridae, and Hippolytidae formed a monophyletic clade. This research not only filled the gap in mitogenome data for Lysmatidae but also provided novel molecular insights into Caridean phylogenetics.https://www.mdpi.com/2410-3888/10/4/177shrimpmitogenomephylogeny |
| spellingShingle | Xixi Zhang Zhihuang Zhu Jianxin Wang Ge Shi Qi Lin Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) Fishes shrimp mitogenome phylogeny |
| title | Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) |
| title_full | Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) |
| title_fullStr | Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) |
| title_full_unstemmed | Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) |
| title_short | Mitogenomic and Phylogenetic Analyses of <i>Lysmata lipkei</i> (Crustacea: Decapoda: Lysmatidae) |
| title_sort | mitogenomic and phylogenetic analyses of i lysmata lipkei i crustacea decapoda lysmatidae |
| topic | shrimp mitogenome phylogeny |
| url | https://www.mdpi.com/2410-3888/10/4/177 |
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