Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris
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 Xiaoyangko...
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crpeerj:10.7717/peerj.13268 2024-09-15T18:17:50+00:00 Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris Chen, Wan Miao, Keer Wang, Junqi Wang, Hao Sun, Wan Yuan, Sijia Luo, Site Hu, Chaochao Chang, Qing Nature Science Fund of Jiangsu Province Jiangsu Higher Education Institutions of China Qing Lan Project of Jiangsu High School Jiangsu Open Laboratory of Major Scientific Instrument and Equipment, Nanjing Normal University 2022 http://dx.doi.org/10.7717/peerj.13268 https://peerj.com/articles/13268.pdf https://peerj.com/articles/13268.xml https://peerj.com/articles/13268.html en eng PeerJ https://creativecommons.org/licenses/by/4.0/ PeerJ volume 10, page e13268 ISSN 2167-8359 journal-article 2022 crpeerj https://doi.org/10.7717/peerj.13268 2024-07-23T04:08:29Z 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 ... Article in Journal/Newspaper Limicola falcinellus PeerJ Publishing PeerJ 10 e13268 |
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English |
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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 ... |
author2 |
Nature Science Fund of Jiangsu Province Jiangsu Higher Education Institutions of China Qing Lan Project of Jiangsu High School Jiangsu Open Laboratory of Major Scientific Instrument and Equipment, Nanjing Normal University |
format |
Article in Journal/Newspaper |
author |
Chen, Wan Miao, Keer Wang, Junqi Wang, Hao Sun, Wan Yuan, Sijia Luo, Site Hu, Chaochao Chang, Qing |
spellingShingle |
Chen, Wan Miao, Keer Wang, Junqi Wang, Hao Sun, Wan Yuan, Sijia Luo, Site Hu, Chaochao Chang, Qing Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
author_facet |
Chen, Wan Miao, Keer Wang, Junqi Wang, Hao Sun, Wan Yuan, Sijia Luo, Site Hu, Chaochao Chang, Qing |
author_sort |
Chen, Wan |
title |
Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
title_short |
Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
title_full |
Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
title_fullStr |
Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
title_full_unstemmed |
Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris |
title_sort |
five new mitogenomes sequences of calidridine sandpipers (aves: charadriiformes) and comparative mitogenomics of genus calidris |
publisher |
PeerJ |
publishDate |
2022 |
url |
http://dx.doi.org/10.7717/peerj.13268 https://peerj.com/articles/13268.pdf https://peerj.com/articles/13268.xml https://peerj.com/articles/13268.html |
genre |
Limicola falcinellus |
genre_facet |
Limicola falcinellus |
op_source |
PeerJ volume 10, page e13268 ISSN 2167-8359 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.7717/peerj.13268 |
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10 |
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e13268 |
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1810455939438870528 |