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Li Q, Jiang P, Li M, Du J, Sun J, Chen N, Wu Y, Chang Q, Hu C. Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae). Curr Issues Mol Biol 2024; 46:6186-6198. [PMID: 38921040 PMCID: PMC11202466 DOI: 10.3390/cimb46060369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
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Affiliation(s)
- Quanheng Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Peiyue Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Mingxuan Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jingjing Du
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jianxiang Sun
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Nuo Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Yu Wu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
- Analytical and Testing Center, Nanjing Normal University, Nanjing 210046, China
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He Y, Liu W, Wu Y, Chang Q. The complete mitochondrial genome of Calidris tenuirostris (Charadriiformes: Scolopacidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:178-179. [PMID: 33366475 PMCID: PMC7748780 DOI: 10.1080/23802359.2019.1698375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
There is a lack of genomic information on Calidris tenuirostris, which can provide valuable resource for genetic diversity and conservation biology. The complete mitogenome of C. tenuirostris was 16,775 bp in length and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 1 control region (D-loop). The overall nucleotide composition was 31.10% A, 24.9% T, 30.10% C and 13.9% G. The start codon (ATG) and end codon (TAA) were usual. Phylogenomic analysis using mitogenomes supports monophyly of Scolopacidae, and help us understand the evolutionary relationship in charadriiformes.
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Affiliation(s)
- Yuxiao He
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Jiangsu, People's Republic of China
| | - Wei Liu
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, People's Republic of China Nanjing
| | - Yanqing Wu
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Jiangsu, People's Republic of China
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, People's Republic of China Nanjing
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