| Five new mitogenomes sequences of Calidridine sandpipers (Ayes: Charadriiformes) and comparative mitogenomics of genus Calidris | |
| Chen, Wan1,2; Miao, Keer1; Wang, Junqi1; Wang, Hao1; Sun, Wan1; Yuan, Sijia1; Luo, Site3; Hu, Chaochao1,4; Chang, Qing1 | |
| 2022-04-18 | |
| 发表期刊 | PEERJ
 |
| ISSN | 2167-8359 |
| 卷号 | 10 |
| 摘要 | 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 x 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. |
| 关键词 | Comparative genomics RESOLVE PHYLOGENETIC-RELATIONSHIPS Phylogenetics TRANSFER-RNA GENES Mitogenome MITOCHONDRIAL GENOME Genomics ORGANIZATION Calidris DUPLICATION SHOREBIRDS SOFTWARE PATTERNS PROGRAM ORIGIN |
| DOI | 10.7717/peerj.13268 |
| 收录类别 | SCIE |
| 语种 | 英语 |
| WOS研究方向 | Science & Technology - Other Topics |
| WOS类目 | Multidisciplinary Sciences |
| WOS记录号 | WOS:000797917900007 |
| 出版者 | PEERJ INC |
| 原始文献类型 | Article |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.library.ouchn.edu.cn/handle/39V7QQFX/168505 |
| 专题 | 国家开放大学江苏分部 |
| 通讯作者 | Hu, Chaochao; Chang, Qing |
| 作者单位 | 1.Nanjing Normal Univ, Sch Life Sci, Nanjing, Jiangsu, Peoples R China; 2.Jiangsu Open Univ, Coll Environm & Ecol, City Vocat Coll Jiangsu, Nanjing, Jiangsu, Peoples R China; 3.Xiamen Univ, Sch Life Sci, Xiamen, Guangdong, Peoples R China; 4.Nanjing Normal Univ, Analyt & Testing Ctr, Nanjing, Jiangsu, Peoples R China |
| 第一作者单位 | 国家开放大学江苏分部 |
| 推荐引用方式 GB/T 7714 | Chen, Wan,Miao, Keer,Wang, Junqi,et al. Five new mitogenomes sequences of Calidridine sandpipers (Ayes: Charadriiformes) and comparative mitogenomics of genus Calidris[J]. PEERJ,2022,10. |
| APA | Chen, Wan.,Miao, Keer.,Wang, Junqi.,Wang, Hao.,Sun, Wan.,...&Chang, Qing.(2022).Five new mitogenomes sequences of Calidridine sandpipers (Ayes: Charadriiformes) and comparative mitogenomics of genus Calidris.PEERJ,10. |
| MLA | Chen, Wan,et al."Five new mitogenomes sequences of Calidridine sandpipers (Ayes: Charadriiformes) and comparative mitogenomics of genus Calidris".PEERJ 10(2022). |
| 条目包含的文件 | 条目无相关文件。 | |||||
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