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 Xiaoyangkou...
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ftpubmed:oai:pubmedcentral.nih.gov:9022639 2023-05-15T17:08:03+02:00 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 2022-04-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022639/ https://doi.org/10.7717/peerj.13268 en eng PeerJ Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022639/ http://dx.doi.org/10.7717/peerj.13268 © 2022 Chen et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. CC-BY PeerJ Evolutionary Studies Text 2022 ftpubmed https://doi.org/10.7717/peerj.13268 2022-04-24T00:52:32Z 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 ... Text Limicola falcinellus PubMed Central (PMC) PeerJ 10 e13268 |
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English |
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Evolutionary Studies |
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Evolutionary Studies 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 |
topic_facet |
Evolutionary Studies |
description |
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 ... |
format |
Text |
author |
Chen, Wan Miao, Keer Wang, Junqi Wang, Hao Sun, Wan Yuan, Sijia Luo, Site Hu, Chaochao Chang, Qing |
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 Inc. |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022639/ https://doi.org/10.7717/peerj.13268 |
genre |
Limicola falcinellus |
genre_facet |
Limicola falcinellus |
op_source |
PeerJ |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022639/ http://dx.doi.org/10.7717/peerj.13268 |
op_rights |
© 2022 Chen et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
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CC-BY |
op_doi |
https://doi.org/10.7717/peerj.13268 |
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PeerJ |
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10 |
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e13268 |
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1766063615417253888 |