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Sangster G, Luksenburg JA. Complete mitochondrial genome MK992912 of Great Knot ( Calidris tenuirostris) is a chimera with DNA from Pacific Golden Plover Pluvialis fulva (Aves: Charadriiformes). Mitochondrial DNA B Resour 2024; 9:532-535. [PMID: 38638190 PMCID: PMC11025405 DOI: 10.1080/23802359.2024.2342932] [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: 08/06/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
A complete mitochondrial genome of Great Knot (Calidris tenuirostris), MK992912, was published by He and colleagues in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both C. tenuirostris (15,567 bp, 92.8%) and Pacific Golden Plover (Pluvialis fulva, 1208 bp, 7.2%). Detecting such errors is possible before publication if each sequenced fragment is separately analyzed phylogenetically before assembling the fragments into a single mitogenome. This mitogenome has been re-used in at least four phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
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Affiliation(s)
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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Sangster G, Luksenburg JA. The published complete mitochondrial genome of Spotted Greenshank ( Tringa guttifer) is a chimera with DNA from Red-necked Stint ( Calidris ruficollis) (Aves: Charadriiformes). Mitochondrial DNA B Resour 2023; 8:1273-1275. [PMID: 38188446 PMCID: PMC10769514 DOI: 10.1080/23802359.2023.2282791] [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: 08/23/2023] [Accepted: 11/08/2023] [Indexed: 01/09/2024] Open
Abstract
A recently published complete mitochondrial genome of Spotted Greenshank (Tringa guttifer) was the first DNA sequence of this species (GenBank accession number MK905885, RefSeq number NC_044665; Liu et al. 2019, The complete mitochondrial genome of the Spotted Greenshank Tringa guttifer (Charadriiforemes [sic]: Charadriidae), Mitochondrial DNA Part B. 4:2353-2354). Here we show that this mitogenome is actually a chimera containing DNA fragments of both a Tringa sandpiper (presumably T. guttifer) and the Red-necked Stint (Calidris ruficollis). This mitogenome has been re-used in at least three phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
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Affiliation(s)
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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Sangster G, Luksenburg JA. The importance of voucher specimens: misidentification or previously unknown mtDNA diversity in Phalacrocorax capillatus (Aves: Phalacrocoracidae)? Mitochondrial DNA B Resour 2023; 8:1158-1160. [PMID: 38188423 PMCID: PMC10769515 DOI: 10.1080/23802359.2023.2274986] [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: 07/17/2023] [Accepted: 10/19/2023] [Indexed: 01/09/2024] Open
Abstract
A recently published complete mitochondrial genome of Japanese or Temminck's cormorant (Phalacrocorax capillatus) was the first of this species (GenBank accession number LC714913). Comparison of COI sequences shows that this mitogenome clustered with great cormorant (Phalacrocorax carbo) rather than with its sister taxon P. capillatus. This suggests that the mitogenome was either a misidentified P. carbo or represents previously unknown intraspecific diversity in P. capillatus overlapping with that of P. carbo. Unfortunately, no voucher specimen was retained so it remains impossible to distinguish between these alternatives. We suggest that great restraint should be exercised using this mitogenome as a reference for P. capillatus. We reiterate previous pleas to retain voucher specimens for mitogenome sequences to enable re-analysis of the identity of the material.
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Affiliation(s)
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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Zhang H, Dong Y, Sun G, Wang Q, Dong Y, Dou H, Wei Q. The complete mitochondrial genome of Turdus obscurus (Passeriformes: Turdidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3076-3077. [PMID: 34595341 PMCID: PMC8477923 DOI: 10.1080/23802359.2021.1981165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Eyebrowed Thrush (Turdus obscurus) is a highly migratory bird, which breeds in northeastern Asia and overwinters in southeastern Asia. We obtained the mitochondrial genome of T. obscurus by Sanger sequencing. The mitogenome was 16,739 bp in length, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Its composition is consistent with the species in genus Turdus. Phylogenetic analysis based on the whole mitochondrial genome showed that the relationship between T. obscurus and Turdus kessleri was relatively close. This study improves the understanding of phylogeny and genetics of Turdidae and Muscicapoidea.
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Affiliation(s)
- Huanqing Zhang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yuehuan Dong
- College of Life Science, Qufu Normal University, Qufu, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, China
| | - Qingqian Wang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yuntao Dong
- College of Life Science, Qufu Normal University, Qufu, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, China
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Sangster G, Luksenburg JA. Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies. Genome Biol Evol 2021; 13:evab210. [PMID: 34505894 PMCID: PMC8462277 DOI: 10.1093/gbe/evab210] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 02/06/2023] Open
Abstract
Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.
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Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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Sangster G, Luksenburg JA. The published complete mitochondrial genome of the milk shark ( Rhizoprionodon acutus) is a misidentified Pacific spadenose shark ( Scoliodon macrorhynchos) (Chondrichthyes: Carcharhiniformes). Mitochondrial DNA B Resour 2021; 6:828-830. [PMID: 33763593 PMCID: PMC7954409 DOI: 10.1080/23802359.2021.1884019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The recently published mitogenome of milk shark Rhizoprionodon acutus (MN602076/NC_046016) was fully resolved in an unexpected phylogenetic position in the original mitogenome announcement, which rendered the genus Scoliodon paraphyletic. Here, we show that this mitogenome is actually that of a misidentified Pacific spadenose shark (Scoliodon macrorhynchos). The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
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Affiliation(s)
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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Xiong F, Zhai D, Yu J, Chen Y, Wang Y, Liu H. The complete mitochondrial genome of the Chinese noodlefish Leucosoma chinensis and phylogenetic analysis of Salangidae (Osteichthyes: Osmeriformes). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:176-177. [PMID: 33553629 PMCID: PMC7850319 DOI: 10.1080/23802359.2020.1860720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the present study, we obtained the first complete mitochondrial genome sequence of Leucosoma (Salanx) chinensis. It was 16,595 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding control region. The nucleotide composition was A (23.1%), T (25.2%), G (20.0%) and C (31.8%), and the A + T content (48.3%) was a little lower than G + C content (51.80%). Phylogenetic analysis of 10 species of Salangidae identified three major clades. These results may facilitate the future genetic research of L. chinensis and Salangidae.
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Affiliation(s)
- Fei Xiong
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China.,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Dongdong Zhai
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China.,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Jixin Yu
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Yuanyuan Chen
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Ying Wang
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Hongyan Liu
- School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
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Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H. Sequence and organisation of the mitochondrial genome of Japanese Grosbeak ( Eophona personata), and the phylogenetic relationships of Fringillidae. Zookeys 2020; 995:67-80. [PMID: 33281468 PMCID: PMC7688617 DOI: 10.3897/zookeys.995.34432] [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: 03/12/2019] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial DNA is a useful molecular marker for phylogenetic and evolutionary analysis. In the current study, we determined the complete mitochondrial genome of Eophona personata, the Japanese Grosbeak, and the phylogenetic relationships of E. personata and 16 other species of the family Fringillidae based on the sequences of 12 mitochondrial protein-coding genes. The mitochondrial genome of E. personata consists of 16,771 base pairs, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region. Analysis of the base composition revealed an A+T bias, a positive AT skew and a negative GC skew. The mitochondrial gene order and arrangement in E. personata was similar to the typical avian mitochondrial gene arrangement. Phylogenetic analysis of 17 species of Fringillidae, based on Bayesian inference and Maximum Likelihood (ML) estimation, showed that the genera Coccothraustes and Hesperiphona are closely related to the genus Eophona, and further showed a sister-group relationship of E. personata and E. migratoria.
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Affiliation(s)
- Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Shi Feng
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
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