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Chen W, Miao K, Wang J, Wang H, Sun W, Yuan S, Luo S, Hu C, Chang Q. Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris. PeerJ 2022; 10:e13268. [PMID: 35462767 PMCID: PMC9022639 DOI: 10.7717/peerj.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Background The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.
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Affiliation(s)
- Wan Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China,Jiangsu Open University (The City Vocational College of Jiangsu), College of Environment and Ecology, Nanjing, Jiangsu, China
| | - Keer Miao
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Junqi Wang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hao Wang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wan Sun
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Sijia Yuan
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Site Luo
- School of Life Science, Xiamen University, Xiamen, Guangdong, China
| | - Chaochao Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China,Nanjing Normal University, Analytical and Testing Center, Nanjing, Jiangsu, China
| | - Qing Chang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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Kundu S, Tyagi K, Alam I, Maheswaran G, Kumar V, Chandra K. Complete mitochondrial genome of Chroicocephalus brunnicephalus from India: phylogeny with other Larids. Mitochondrial DNA B Resour 2021; 6:339-343. [PMID: 33659671 PMCID: PMC7872550 DOI: 10.1080/23802359.2020.1866448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/13/2020] [Indexed: 11/14/2022] Open
Abstract
The complete mitogenome sequence of the brown-headed gull, Chroicocephalus brunnicephalus was determined in this study. The 16,771 bp genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The decoded mitogenome was AT-rich (54.77%) with nine overlapping and 17 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. Further, the usual termination codons (AGG, TAG, TAA, and AGA) were used by 11 PCGs except for cox3 and nad4. The concatenated PCGs based Bayesian phylogeny clearly discriminates all the Laridae species and reflects the sister relationship of C. brunnicephalus with C. ridibundus. The present mitogenome-based phylogeny was congruent with the earlier hypothesis and confirmed the evolutionary position of the brown-headed gull as masked species. The generated mitogenome of C. brunnicephalus is almost identical to the previously generated mitogenome from China except for two base pairs in CR. To visualize the population structure of this migratory species, we propose more sampling from different geographical locations and the generation of additional molecular data to clarify the reality.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Imran Alam
- Bird Section, Zoological Survey of India, Kolkata, India
| | | | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- Bird Section, Zoological Survey of India, Kolkata, India
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Chen W, Zhang C, Pan T, Liu W, Li K, Hu C, Chang Q. The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii. Genes Genomics 2018; 40:955-963. [PMID: 30155708 DOI: 10.1007/s13258-018-0703-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
Abstract
The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii's mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.
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Affiliation(s)
- Wan Chen
- College of Environment and Ecology, Jiangsu Open University (The City Vocational College of Jiangsu), Nanjing, 210036, Jiangsu, China.,Analytical and Testing Center, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, Jiangsu, People's Republic of China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230039, Anhui, People's Republic of China
| | - Wei Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Kexin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Chaochao Hu
- Analytical and Testing Center, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
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Hu C, Zhang C, Sun L, Zhang Y, Xie W, Zhang B, Chang Q. The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes. PLoS One 2017; 12:e0175244. [PMID: 28384231 PMCID: PMC5383286 DOI: 10.1371/journal.pone.0175244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/22/2017] [Indexed: 11/18/2022] Open
Abstract
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.
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Affiliation(s)
- Chaochao Hu
- Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Lei Sun
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, United States of America
| | - Yi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Wenli Xie
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui, People's Republic of China
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
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