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Yang T, Tan C, Zhao L, Hu Z, Su C, Li F, Ma Y, Zhang W, Hao X, Zou W, Kang J, He Q. The Complete Mitochondrial Genome of the Luciocyprinus langsoni (Cypriniformes: Cyprinidae): Characterization, Phylogeny, and Genetic Diversity Analysis. Genes (Basel) 2024; 15:1621. [PMID: 39766888 PMCID: PMC11675621 DOI: 10.3390/genes15121621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 12/09/2024] [Accepted: 12/17/2024] [Indexed: 01/11/2025] Open
Abstract
Background: Luciocyprinus langsoni is a species belonging to the Cyprinidae family. The objective of this study is to gain a comprehensive understanding of its evolutionary history and genetic characteristics. Methods: The complete mitochondrial genome of L. langsoni was determined using overlapping PCR. A phylogenetic analysis was conducted based on 13 protein-coding genes from 48 species. A population genetic diversity analysis using the COI gene and a selection analysis of 13 protein-coding genes were also performed. Results: The mitogenome is 16,586 base pairs long and consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two control regions. It has a high adenine-thymine (A + T) content. The phylogenetic analysis confirms the placement of L. langsoni within the subfamily Cyprininae. The population genetic diversity analysis reveals low variability in the Hechi Longjiang population. The selection analysis shows that all 13 protein-coding genes have evolved under purifying selection with Ka/Ks ratios below 1. Conclusions: These results enhance our understanding of L. langsoni's evolutionary history and lay a genetic foundation for future studies in population genetics and phylogenetics.
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Affiliation(s)
- Tiezhu Yang
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Chenxi Tan
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Liangjie Zhao
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Zhiguo Hu
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Chaoqun Su
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Fan Li
- Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum, Shanghai 200041, China
| | - Yuanye Ma
- Xinyang Nanwan Reservoir Fishery Development Co., Ltd., Xinyang 464000, China;
| | - Wenchao Zhang
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Xiaoyu Hao
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Wenxu Zou
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Jiayin Kang
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
| | - Qingqing He
- School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China; (T.Y.); (C.T.); (L.Z.); (Z.H.); (W.Z.); (X.H.); (W.Z.); (J.K.); (Q.H.)
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
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Despabiladeras JB, Bautista MAM. Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths. INSECTS 2024; 15:220. [PMID: 38667350 PMCID: PMC11050083 DOI: 10.3390/insects15040220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.
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Affiliation(s)
| | - Ma. Anita M. Bautista
- Functional Genomics Laboratory, National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines-Diliman, Quezon City 1101, Philippines;
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Luis Molina-Quirós J, Hernández-Muñoz S, Antonio Baeza J. The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes. Gene 2022; 845:146847. [PMID: 36058495 DOI: 10.1016/j.gene.2022.146847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.
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Affiliation(s)
- José Luis Molina-Quirós
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica.
| | - Sebastián Hernández-Muñoz
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica; Sala de Colecciones, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, IV Región, Chile; Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
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