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Zhang L, Xia T, Gao X, Yang X, Sun G, Zhao C, Liu G, Zhang H. Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila. Genes (Basel) 2023; 14:1205. [PMID: 37372385 DOI: 10.3390/genes14061205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. FST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Guangshuai Liu
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
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Mitochondrial genome of the critically endangered Baer's Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species. Sci Rep 2021; 11:24302. [PMID: 34934156 PMCID: PMC8692624 DOI: 10.1038/s41598-021-03868-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 11/27/2022] Open
Abstract
Historically, the diving duck, Baer’s Pochard (Aythya baeri) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of A. baeri has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between A. baeri and the other three Aythya mitochondrial genomes. Among 13 protein-coding genes of the four Aythya species, the fastest-evolving gene was ATP8 while the slowest-evolving gene was COII. Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows: Dendrocygna was an early diverging lineage that was fairly distant from the other ingroup taxa; Cygnus, Branta, and Anser were clustered into one branch that corresponded to the Anserinae subfamily; and Aythya, Asarcornis, Netta, Anas, Mareca, Mergus, Lophodytes, Bucephala, Tadorna, Cairina, and Aix were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other Aythya species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.
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Choi EH, Enkhtsetseg G, Baek SY, Hwang J, Park B, Jang KH, Ryu SH, Hwang UW. Complete mitochondrial genome of a hen harrier Circus cyaneus (Accipitriformes: Accipitridae) from South Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:185-186. [PMID: 33537437 PMCID: PMC7832496 DOI: 10.1080/23802359.2020.1860700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A hen harrier Circus cyaneus (Accipitriformes: Accipitridae), a migrant raptor having a wide breeding range from Europe to Northeast Asia, migrates to more southerly areas (Southern Europe, China, Korea and Japan) in winter. In this study, the complete mitochondrial genome of C. cyaneus was completely sequenced and characterized. It was 20,173 bp in length being composed of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. It has a base composition of A (32.2%), G (12.6%), C (30.5%) and T (24.7%). The phylogenetic tree reconstructed based on the maximum likelihood (ML) method confirms that C. cyaneus places within the clade of the family Accipitridae in the monophyletic avian order Accipitriformes.
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Affiliation(s)
- Eun Hwa Choi
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea.,Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
| | - Gankhuyag Enkhtsetseg
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Su Youn Baek
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Jihye Hwang
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Bia Park
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Kuem Hee Jang
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
| | - Shi Hyun Ryu
- Strategic Planning Department, Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Ui Wook Hwang
- Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea.,Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
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Chen YX, Sun CH, Li YK, Fei YL, Xue XM, Hou SL, Zhou YW, Jiang J, Guo HT. Complete mitogenome of Treron sphenurus (Aves, Columbiformes): the first representative from the genus Treron, genomic comparisons and phylogenetic analysis of Columbidae. Anim Biotechnol 2021; 33:1003-1013. [PMID: 33439093 DOI: 10.1080/10495398.2020.1862135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The wedge-tailed green pigeon (Treron sphenurus) has a protective value in the evolution of the family Columbidae. In this study, the complete mitogenome of T. sphenurus from Baise City, China, which represents the first sequenced species of the genus Treron in Tribe Treronini, is reported. This was accomplished using PCR-based methods and a primer-walking sequencing strategy with genus-specific primers. The mitogenome was found to be 18,919 bp in length comprising 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. In terms of structure and composition, many similarities were found between the T. sphenurus and Hemiphaga novaeseelandiae (New Zealand pigeon) mitogenomes. This was further supported by phylogenetic analysis showing that T. sphenurus has a close evolutionary relationship with H. novaeseelandiae. The complete mitogenome of T. sphenurus reported here is expected to provide valuable molecular information for further studies on the phylogeny of the genus Treron and for analyses of the taxonomic status of the family Columbidae.
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Affiliation(s)
- Yun-Xia Chen
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Cheng-He Sun
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yao-Kai Li
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yi-Ling Fei
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Xiao-Ming Xue
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Sen-Lin Hou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Yong-Wu Zhou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Jing Jiang
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Hai-Tao Guo
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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6
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Volkovsky DV, Fisenko PV, Zhuravlev YN. Variability of the mtDNA Control Region in the Bean Goose, Anser fabalis Latham 1787, in the Russian Far East. BIOL BULL+ 2020. [DOI: 10.1134/s1062359020070171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jing M, Yang H, Li K, Huang L. Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics. Genet Mol Biol 2020; 43:e20190392. [PMID: 33026411 PMCID: PMC7539371 DOI: 10.1590/1678-4685-gmb-2019-0392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/13/2020] [Indexed: 12/04/2022] Open
Abstract
Coraciiformes contains more than 200 species with great differences on external
morphology and life-style. The evolutionary relationships within Coraciiformes
and the phylogenetic placement of Coraciiformes in Aves are still questioned.
Mitochondrial genome (mitogenome) sequences are popular markers in molecular
phylogenetic studies of birds. This study presented the genome characteristics
of three new mitogenomes in Coraciiformes and explored the phylogenetic
relationships among Coraciiformes and other five related orders with mitogenome
data of 30 species. The sizes of three mitogenomes were 17,383 bp
(Alcedo atthis), 17,892 bp (Halcyon
smyrnensis) and 17,223 bp (Megaceryle lugubris).
Each mitogenome contained one control region and 37 genes that were common in
vertebrate mitogenomes. The organization of three mitogenomes was identical to
the putative ancestral gene order in Aves. Among 13 available Coraciiform
mitogenomes, 12 protein coding genes showed indications of negative selection,
while the MT-ND6 presented sign of positive selection or relaxed purifying
selection. The phylogenetic results supported that Upupidae and Bucerotidae
should be separated from Coraciiformes, and that Coraciiformes is more closely
related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our
study provide valuable data for further phylogenetic investigation of
Coraciiformes.
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Affiliation(s)
- Meidong Jing
- Nantong University, School of Life Sciences, Nantong, Jiangsu, P. R. China
| | - Huanhuan Yang
- Ludong University, School of Life Sciences, Yantai, Shandong, P. R. China
| | - Kai Li
- Nantong Xingdong International Airport, Nantong, Jiangsu, P. R. China
| | - Ling Huang
- Nantong University, School of Life Sciences, Nantong, Jiangsu, P. R. China
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8
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Liu HY, Sun CH, Zhu Y, Zhang QZ. Complete mitogenomic and phylogenetic characteristics of the speckled wood-pigeon (Columba hodgsonii). Mol Biol Rep 2020; 47:3567-3576. [PMID: 32307661 DOI: 10.1007/s11033-020-05448-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 10/24/2022]
Abstract
The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.
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Affiliation(s)
- Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610015, China
| | - Qing-Zheng Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
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9
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Zhang L, Zhou Z, Chen S, Li H, Zhang Y. Characterization of complete mitochondrial genome of a new identification of Gymnothorax minor (Temminck & Schlegel, 1846) in China. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1573112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Liyan Zhang
- Fujian Institute of Oceanography, Xiamen, P.R. China
- Fujian Provincial Key Laboratory of Coast and Island Management Technology Study, Xiamen, P.R. China
| | - Zhidong Zhou
- Fujian Institute of Oceanography, Xiamen, P.R. China
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen, P.R. China
| | - Shiquan Chen
- Hainan Academy of Ocean and Fisheries Science, Haikou, P.R. China
| | - Haiping Li
- Fujian Institute of Oceanography, Xiamen, P.R. China
- Fujian Provincial Key Laboratory of Coast and Island Management Technology Study, Xiamen, P.R. China
| | - Yueping Zhang
- Fujian Institute of Oceanography, Xiamen, P.R. China
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen, P.R. China
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10
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Yu Y, Zhang H, Yang CM, Chen X, Peng X, Qin S. Complete mitochondrial genome and the phylogenetic position of the thornback cowfish ( Lactoria fornasini). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Yue Yu
- Zhejiang Mariculture Research Institute, Wenzhou, P. R. China
| | - Huawei Zhang
- Zhejiang Mariculture Research Institute, Wenzhou, P. R. China
| | - Can-Ming Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, P. R. China
| | - Xin Peng
- Zhejiang Mariculture Research Institute, Wenzhou, P. R. China
| | - Song Qin
- Zhejiang Mariculture Research Institute, Wenzhou, P. R. China
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11
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Buckner JC, Ellingson R, Gold DA, Jones TL, Jacobs DK. Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck. Mol Phylogenet Evol 2018; 122:102-109. [DOI: 10.1016/j.ympev.2017.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/27/2017] [Accepted: 12/05/2017] [Indexed: 11/28/2022]
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Dong Y, Li B, Zhou L. A new insight into the classification of dusky thrush complex: bearings on the phylogenetic relationships within the Turdidae. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1245-1252. [PMID: 29457530 DOI: 10.1080/24701394.2018.1439026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp. The mtDNAs are circular molecules, containing the 37 typical genes, with an identical gene order and arrangement as those of other Turdidae. The ATG and TAA, respectively, are observed the most commonly start and stop codon. Most of the tRNA could be folded into the canonical cloverleaf secondary structure except for tRNASer (AGY) and tRNALeu (CUN), which lose 'DHU' arm. The control region presented a higher A + T content than the average value for the whole mitogenome. The phylogenetic trees reconstructed by the concatenated nucleotide sequences of mtDNA genes (Cyt b, ND2 and COI) indicate the Dusky thrush complex cannot be divided into two species, but the relationships between Dusky thrush subspecies still need additional study. This study improves our understanding of mitogenomic structure and evolution of the Dusky thrush complex, which can provide further insights into our understanding of phylogeny and taxonomy in Turdidae.
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Affiliation(s)
- Yuanqiu Dong
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
| | - Bo Li
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
| | - Lizhi Zhou
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
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13
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Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA. Landscape genomics: natural selection drives the evolution of mitogenome in penguins. BMC Genomics 2018; 19:53. [PMID: 29338715 PMCID: PMC5771141 DOI: 10.1186/s12864-017-4424-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species. Results We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation. Conclusions These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4424-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Ramos
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile.,Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Portugal 49, Santiago, Chile.,I+DEA Biotech, Av. Central 3413, Padre Hurtado, Santiago, Chile
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Patricia G Parker
- University of Missouri St Louis and Saint Louis Zoo, One University Blvd., St. Louis, MO, 63121-4400, USA
| | - Melanie Massaro
- School of Environmental Sciences and Institute for Land, Water and Society, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Av. Dom José Gaspar 500, Coração Eucarístico, Belo Horizonte, MG, Brazil
| | - Marcelo D Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile. .,Centro de Cambio Global UC, Santiago, Chile.
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14
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Trewick SA, Pilkington S, Shepherd LD, Gibb GC, Morgan-Richards M. Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response. Mol Ecol 2017; 26:5752-5772. [PMID: 28805283 DOI: 10.1111/mec.14323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/01/2022]
Abstract
The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island-South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.
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Affiliation(s)
- Steve A Trewick
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Stephen Pilkington
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Lara D Shepherd
- Te Papa Tongarewa Museum of New Zealand, Wellington, New Zealand
| | - Gillian C Gibb
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Mary Morgan-Richards
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
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15
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Sarker S, Das S, Frith S, Forwood JK, Helbig K, Raidal SR. Complete mitochondrial genome sequence of an Australian little penguin ( Eudyptula minor novaehollandia, J.R. Forster, 1781). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:428-429. [PMID: 33473850 PMCID: PMC7799458 DOI: 10.1080/23802359.2017.1357446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this paper, we report the complete mitochondrial genome of an Australian little penguin (Eudyptula minor novaehollandia). The mitogenome sequence has been found to be circular, and 17,608 bp in length. Similar to other Spheniscidae species, the genome encoded a typically conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, as well as all protein coding sequences started with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 977 bp and 1612 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of E. minor novaehollandia had slightly higher AT (55.5%) content than GC (45.5%). The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and conservation of E. minor novaehollandia.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
| | | | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
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16
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Characterization of complete mitochondrial genomes of Mastacembelus erythrotaenia and Mastacembelus armatus (Synbranchiformes: Mastacembelidae) and phylogenetic studies of Mastacembelidae. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0807-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Wang YC, Zou Y, Sun XM, Gong J, Huang L, Jing MD. The complete mitochondrial genome sequence of the little grebe (Tachybaptus ruficollis). Genes Genomics 2017. [DOI: 10.1007/s13258-016-0480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Si R, Ding W, Ai W, Chen X. Complete mitochondrial genome and the phylogenetic position of the Borneo leg skate Sinobatis borneensis (Rajiformes: Anacanthobatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:443-444. [PMID: 33473513 PMCID: PMC7799655 DOI: 10.1080/23802359.2016.1180560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
In this study, the complete mitochondrial genome of the Borneo leg skate Sinobatis borneensis (Rajiformes, Anacanthobatidae) was determined. It had circular molecules (16,701 bp), consisting of 37 genes with a typical gene order in vertebrate mitogenome. In the whole mitogenome, there were 28 bp short intergenic and 31 bp overlaps, respectively, located in 12 and 7 gene junctions. The nucleotide composition was 31.1% A, 26.0% C, 13.9% G and 29.1% T. Two start codons (GTG and ATG) and two stop codons (TAG, TAA/T) were used in the protein-coding genes. The 22 tRNA genes ranged from 66 bp (tRNA-Cys) to 75 bp (tRNA-Leu1 and tRNA-Lys). The phylogenetic result showed that S. borneensis was clustered with the Atlantoraja castelnaui and Pavoraja nitida.
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Affiliation(s)
- Ranran Si
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenyong Ding
- Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, China
| | - Weiming Ai
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
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19
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Si R, Ding W, Yu J, Chen X, Ai W. Complete mitochondrial genome and the phylogenetic position of the Jenkins whipray Himantura jenkinsii (Myliobatiformes, Dasyatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:297-298. [PMID: 33644364 PMCID: PMC7871659 DOI: 10.1080/23802359.2016.1166085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We determined the complete mitochondrial genome of the Jenkins whipray Himantura jenkinsii. The total length of the mitogenome was 17, 670 bp, consisted of 37 genes with typical gene order in vertebrate mitogenome. The nucleotide composition was: 30.5% A, 29.1% T, 26.5% C and 13.9% G. It had 70 bp short intergenic spaces and 22 bp overlaps. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The 22 tRNA genes were ranged from 67 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result showed that H. jenkinsii was clustered with the Hortle's whipray H. hortlei.
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Affiliation(s)
- Ranran Si
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Wenyong Ding
- Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, PR China
| | - Junqi Yu
- Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, PR China
| | - Xiao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Weiming Ai
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
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20
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Si R, Chen H, Ai W, Chen X, Chen S. Complete mitochondrial genome and the phylogenetic position of the Bowmouth guitarfish Rhina ancylostoma (Rajiformes, Rhinobatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:270-272. [PMID: 33537411 PMCID: PMC7831657 DOI: 10.1080/23802359.2016.1159935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, the complete mitochondrial genome of the Bowmouth guitarfish Rhina ancylostoma (Rajiformes, Rhinobatidae) was first determined. The total length of this circle DNA was 17 217 bp, consisted of 37 genes with a typical gene order in vertebrate mitogenome. It had 42 bp short intergenic spaces and 40 bp overlaps. The nucleotide composition in R. ancylostoma was as follows: A, 33.0%; C, 25.1%; G, 12.6% and T, 29.3%. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The 22 tRNA genes were ranged from 67 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result showed that R. ancylostoma was clustered with the Rhinobatos.
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Affiliation(s)
- Ranran Si
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Hao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Weiming Ai
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xiao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Shaobo Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China.,Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, PR China
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21
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Chen H, Yu J, Si R, Chen X, Ai W. Complete mitochondrial genome and the phylogenetic position of the graceful catshark Proscyllium habereri (Carcharhiniformes: Proscylliidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:268-269. [PMID: 33473469 PMCID: PMC7799998 DOI: 10.1080/23802359.2016.1159934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this study, the complete mitogenome of Proscyllium habereri (Carcharhiniformes: Proscylliidae) is first determined. It is 16,708 bp in length, containing 37 genes with typical order to that of most other vertebrates. Its overall base composition of the H-strand is A 30.9%; C 23.7%; G 14.2%; T 31.2%. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) are found in the protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Cys, tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result showed that P. habereri was clustered to Pseudotriakis microdon.
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Affiliation(s)
- Hao Chen
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Junqi Yu
- Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, PR China
| | - Ranran Si
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xiao Chen
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Weiming Ai
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
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22
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Volkovsky DV, Fisenko PV, Gerasimov YN, Zhuravlev YN. Variability of the mtDNA control region in goose Anser albifrons Scopoli, 1769. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Chen H, Chen X, Ai W, Wang J. Complete mitochondrial genome and the phylogenetic position of the zebra shark ( Stegostoma fasciatum). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:105-106. [PMID: 33473426 PMCID: PMC7799981 DOI: 10.1080/23802359.2015.1137846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete mitochondrial genome of the zebra shark (Stegostoma fasciatum) was first determined in this study. The total length of this circle DNA was 16 658 bp, consisted of 37 genes with typical gene order in vertebrate mitogenome. Its nucleotide content was 34.1% A, 25.9% C, 12.5% G and 27.5% T. This mitogenome had 23 bp short intergenic spaces located in 10 gene junctions and 54 bp overlaps located in 11 gene junctions. In the protein-coding genes, two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were found. The 22 tRNA genes ranged from 66 bp (tRNA-Cys) to 75 bp (tRNA-Leu1). The phylogenetic result showed that S. fasciatum was clustered with the whale shark Rhincodon typus.
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Affiliation(s)
- Hao Chen
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhu, Zhejiang, PR China
| | - Xiao Chen
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, PR China
| | - Weiming Ai
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhu, Zhejiang, PR China
| | - Junjie Wang
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhu, Zhejiang, PR China.,Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, PR China
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24
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Si R, Chen X, Chen H, Ai W. Complete mitochondrial genome and the phylogenetic position of the Leadhued skate Notoraja tobitukai (Rajiformes: Arhynchobatidae). Mitochondrial DNA B Resour 2016; 1:502-503. [PMID: 33473535 PMCID: PMC7800088 DOI: 10.1080/23802359.2016.1192506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In this study, the complete mitochondrial genome of the Leadhued skate Notoraja tobitukai (Rajiformes: Arhynchobatidae) was determined. It was a circular molecule (16, 799 bp), consisted of 37 genes with a typical gene order in vertebrate mitogenome. In the whole mitogenome, there were 24 bp short intergenic and 26 bp overlaps. The nucleotide composition was 32.3% A, 22.6% C, 13.1% G and 32.0% T. Two start codons (GTG and ATG) and two stop codons (TAG, TAA/T––) were used in the protein-coding genes. The 22 tRNA genes ranged from 65 bp (tRNA-Cys) to 75 bp (tRNA-Leu1). The phylogenetic result showed that N. tobitukai was clustered with the Pavoraja nitida.
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Affiliation(s)
- Ranran Si
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiao Chen
- College of Marine Science, South China Agriculture University, Guangzhou, Guangdong, China
| | - Hao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weiming Ai
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
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25
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Si R, Chen X, Chen H, Ai W. Complete mitochondrial genome and the phylogenetic position of the Leadhued skate Notoraja tobitukai (Rajiformes: Arhynchobatidae). Mitochondrial DNA B Resour 2016; 1:787-788. [PMID: 33490421 PMCID: PMC7800987 DOI: 10.1080/23802359.2016.1192514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this study, the complete mitochondrial genome of the Leadhued skate Notoraja tobitukai (Rajiformes: Arhynchobatidae) was determined. It was a circle molecular (16, 799 bp), consisted of 37 genes with a typical gene order in vertebrate mitogenome. In the whole mitogenome, there were 24 bp short intergenic and 26 bp overlaps. The nucleotide composition was 32.3% A, 22.6% C, 13.1% G and 32.0% T. Two start codons (GTG and ATG) and two stop codons (TAG, TAA/T) were used in the protein-coding genes. The 22 tRNA genes ranged from 65 bp (tRNA-Cys) to 75 bp (tRNA-Leu1). The phylogenetic result showed that N. tobitukai was clustered with the Pavoraja nitida.
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Affiliation(s)
- Ranran Si
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xiao Chen
- College of Marine Science, South China Agriculture University, Guangzhou, Guangdong, China
| | - Hao Chen
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Weiming Ai
- Department of Marine Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
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26
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Halley YA, Oldeschulte DL, Bhattarai EK, Hill J, Metz RP, Johnson CD, Presley SM, Ruzicka RE, Rollins D, Peterson MJ, Murphy WJ, Seabury CM. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS One 2015; 10:e0144913. [PMID: 26713762 PMCID: PMC4699210 DOI: 10.1371/journal.pone.0144913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.
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Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - David L. Oldeschulte
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Eric K. Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Joshua Hill
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Richard P. Metz
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Steven M. Presley
- Department of Environmental Toxicology, Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas, United States of America
| | - Rebekah E. Ruzicka
- Texas A&M AgriLife Extension Service, Dallas, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, 1262 U.S. Highway 180 W., Rotan, Texas, United States of America
| | - Markus J. Peterson
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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27
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Grosser S, Burridge CP, Peucker AJ, Waters JM. Coalescent Modelling Suggests Recent Secondary-Contact of Cryptic Penguin Species. PLoS One 2015; 10:e0144966. [PMID: 26675310 PMCID: PMC4682933 DOI: 10.1371/journal.pone.0144966] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Molecular genetic analyses present powerful tools for elucidating demographic and biogeographic histories of taxa. Here we present genetic evidence showing a dynamic history for two cryptic lineages within Eudyptula, the world's smallest penguin. Specifically, we use a suite of genetic markers to reveal that two congeneric taxa ('Australia' and 'New Zealand') co-occur in southern New Zealand, with only low levels of hybridization. Coalescent modelling suggests that the Australian little penguin only recently expanded into southern New Zealand. Analyses conducted under time-dependent molecular evolutionary rates lend support to the hypothesis of recent anthropogenic turnover, consistent with shifts detected in several other New Zealand coastal vertebrate taxa. This apparent turnover event highlights the dynamic nature of the region’s coastal ecosystem.
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Affiliation(s)
- Stefanie Grosser
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
- * E-mail:
| | | | - Amanda J. Peucker
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia
| | - Jonathan M. Waters
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
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28
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Han C, Li Q, Xu J, Li X, Huang J. Characterization of Clarias gariepinus mitochondrial genome sequence and a comparative analysis with other catfishes. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Eberhard JR, Wright TF. Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 2015; 94:34-46. [PMID: 26291569 DOI: 10.1016/j.ympev.2015.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.
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Affiliation(s)
- Jessica R Eberhard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Timothy F Wright
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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30
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Chen H, Lin L, Chen X, Ai W, Chen S. Complete mitochondrial genome and the phylogenetic position of the Blotchy swell shark Cephaloscyllium umbratile. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3045-7. [PMID: 26258506 DOI: 10.3109/19401736.2015.1063127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of the Blotchy swell shark Cephaloscyllium umbratile was determined. It was a circle molecular (16 698 bp), contained 37 genes with typical order to that of most other vertebrates. The nucleotide composition was 31.0% A, 24.0% C, 14.0% G, and 31.3% T. There were 26 bp short intergenic spaces located in 11 gene junctions and 28 bp overlaps located in 7 gene junctions in the whole mitogenome. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The phylogenetic result showed that C. umbratile was clustered with Scyliorhinus canicula and formed the Scyliorhinidae clade, which was the most basal clade within Carcharhiniformes, and Carcharhinidae is not monophyletic.
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Affiliation(s)
- Hao Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and
| | - Lingling Lin
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and
| | - Xiao Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
| | - Weiming Ai
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
| | - Shaobo Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
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Yoon KB, Cho CU, Park YC. The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes). Gene 2015; 572:227-36. [PMID: 26165451 DOI: 10.1016/j.gene.2015.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 06/20/2015] [Accepted: 07/07/2015] [Indexed: 01/22/2023]
Abstract
The complete mitogenome of Chroicocephalus saundersi was characterized and compared with the 6 published Charadriiformes mitogenomes. The mitogenome of C. saundersi is a closed circular molecule 16,739 bp in size, and contains 37 genes and a control region. The AT and GC skews are positive and negative, respectively, and in agreement with those of the other Charadriiformes mitogenomes. The mitogenome of C. saundersi contains 3 start codons (ATG, GTG, and ATT), 4 stop codons (TAA, TAG, AGG, and AGA), and an incomplete stop codon (T-) in 13 PCGs. A codon usage analysis of all available Charadriiformes mitogenomes showed that the ATG (78%) and TAA (50.5%) were the most common start codon and stop codon, respectively. An unusual start codon, ATT, is commonly found in the ND3s of Charadriiformes mitogenomes, whereas the more common start codons, ATC and ATA, are rarely found. In all the Laridae species, one extra cytosine was inserted at position 174 in ND3. The control region of C. saundersi is 1180-bp long, with a nucleotide composition of 30.2% A, 28.6% T, 27.3% C, and 14.0% G. Variable numbers of tandem repeats (VNTRs) with nine copies of the 10 bp repeat sequence (AACAACAAAC) are found within the CSB domain of the control region. The ML/BI analyses, based on the amino acids of the 13 mitochondrial PCGs, strongly support the monophyly of the order Charadriiformes, with the suborder Lari considered sister to the Scolopaci, which is in turn a sister group to the suborder Charadrii.
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Affiliation(s)
- Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chea Un Cho
- Species Restoration Technology Institute, Korea National Park Service, Inje 252-829, Republic of Korea
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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Liu CZ, Wei GH, Hu JH, Liu XY. Complete mitochondrial genome of the Swan Goose (Anser cygnoides L.) and its phylogenetic analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2427-8. [PMID: 25922959 DOI: 10.3109/19401736.2015.1030627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we undertook the first complete the Swan Goose (Anser cygnoides L.) mitochondrial genome. The total length of the mitogenome is 16,739 bp. It contains the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop region. The overall composition of the mitogenome is A (29.2%), G (15.8%), C (32.8%), and T (22.2%). Besides, the base preference of AT was not determined. Twenty-two kinds of tRNA were all typically cloverleaf structures. According to the phylogenetic analysis, A. cygnoides L. has a closer relationship with Anser anser.
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Affiliation(s)
- Chang Zhong Liu
- a College of Animal Science, Henan Institute of Science and Technology , Xinxiang , Henan Province , China
| | - Guang Hui Wei
- a College of Animal Science, Henan Institute of Science and Technology , Xinxiang , Henan Province , China
| | - Jian He Hu
- a College of Animal Science, Henan Institute of Science and Technology , Xinxiang , Henan Province , China
| | - Xing You Liu
- a College of Animal Science, Henan Institute of Science and Technology , Xinxiang , Henan Province , China
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Yan SQ, Guo PC, Li YM, Qi SM, Bai CY, Zhao ZH, Sun JH. Complete mitochondrial genome of the Spotted dove (Streptopelia chinensis). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3067-8. [PMID: 25600734 DOI: 10.3109/19401736.2014.1003912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Spotted dove (Streptopelia chinensis) is a member of the bird family Columbidae. In this study, we report the complete mitochondrial genome of this species. The mitochondrial genome of Spotted dove is a circular molecule of 16,966 bp in size and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition is 30.1% for A, 32.1% for C, 13.9% for G, and 23.9% for T. These data will be useful for the phylogenetic and population diversity analyses of birds, especially Columbidae species.
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Affiliation(s)
- Shou-Qing Yan
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Peng-Cheng Guo
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Yu-Mei Li
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Shun-Min Qi
- b College of Animal Science and Veterinary Medicine, Qingdao Agricultural University , Qingdao , PR China
| | - Chun-Yan Bai
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Zhi-Hui Zhao
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Jin-Hai Sun
- b College of Animal Science and Veterinary Medicine, Qingdao Agricultural University , Qingdao , PR China
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Morinha F, Clemente C, Cabral JA, Lewicka MM, Travassos P, Carvalho D, Dávila JA, Santos M, Blanco G, Bastos E. Next-generation sequencing and comparative analysis of Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus (Passeriformes: Corvidae) mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2278-81. [PMID: 25431821 DOI: 10.3109/19401736.2014.984179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genomes of Red-billed Chough (Pyrrhocorax pyrrhocorax) and Yellow-billed Chough (Pyrrhocorax graculus) were sequenced using the Ion Torrent PGM platform. These mitogenomes contain 16,889 bp (Red-billed Chough) and 16,905 bp (Yellow-billed Chough), including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (D-loop). The gene content, orientation, and structure are similar to a wide range of other vertebrate species and the nucleotide composition is very similar to other Passeriformes. All PCGs start with ATG, except for COX1 that starts with GTG, and four stop codons and one incomplete stop codon are used (TAA, TAG, AGG, AGA, and T-). The size of PCGs is the same in both mitogenomes, except for ND6 that has one codon less in the Yellow-billed Chough. All the tRNAs can fold into a typical cloverleaf secondary structure. These mitogenomic data can be of great value in complementing forthcoming approaches on molecular ecology, comparative and functional genomics.
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Affiliation(s)
- Francisco Morinha
- a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal .,b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Carla Clemente
- c STAB VIDA, Madan Parque, Rua dos Inventores , Caparica , Portugal
| | - João A Cabral
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | | | - Paulo Travassos
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Diogo Carvalho
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - José A Dávila
- d Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM) , Ciudad Real , Spain , and
| | - Mário Santos
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | | | - Estela Bastos
- a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal
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Urantowka AD. Complete mitochondrial genome of Red-bellied Macaw (Orthopsittaca manilata): its comparison with mitogenome of Blue-throated Macaw (Ara glaucogularis). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2110-1. [PMID: 25391028 DOI: 10.3109/19401736.2014.982580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Red-bellied Macaw (Orthopsittaca manilata) is a species of the monotypic genus Orthopsittaca. The genus is one of the six genera, which form morphologically diverse group termed as Macaws. Individuals of Orthopsittaca manilata species are found in extremely large Amazonian area of South America. In this study, full mitochondrial genome of considered species was sequenced. It is 16,985 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. Its comparison with published Blue-throated Macaw (Ara glaucogularis) mitogenome revealed their high degree of identity. Presented Orthopsittaca manilata mitogenome is the first complete genomic sequence of this genus. It will enrich the resource of molecular markers for future examination of evolutionary diversification of Macaws. It will be also indispensable to refine the phylogenetic relationships within the tribe Arini.
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Affiliation(s)
- Adam Dawid Urantowka
- a Department of Genetics , Wroclaw University of Environmental and Life Sciences , Wroclaw , Poland
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Liu G, Zhou L, Li B, Zhang L. The complete mitochondrial genome of Aix galericulata and Tadorna ferruginea: bearings on their phylogenetic position in the Anseriformes. PLoS One 2014; 9:e109701. [PMID: 25375111 PMCID: PMC4222781 DOI: 10.1371/journal.pone.0109701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/22/2014] [Indexed: 11/21/2022] Open
Abstract
Aix galericulata and Tadorna ferruginea are two Anatidae species representing different taxonomic groups of Anseriformes. We used a PCR-based method to determine the complete mtDNAs of both species, and estimated phylogenetic trees based on the complete mtDNA alignment of these and 14 other Anseriforme species, to clarify Anseriform phylogenetics. Phylogenetic trees were also estimated using a multiple sequence alignment of three mitochondrial genes (Cyt b, ND2, and COI) from 68 typical species in GenBank, to further clarify the phylogenetic relationships of several groups among the Anseriformes. The new mtDNAs are circular molecules, 16,651 bp (Aix galericulata) and 16,639 bp (Tadorna ferruginea) in length, containing the 37 typical genes, with an identical gene order and arrangement as those of other Anseriformes. Comparing the protein-coding genes among the mtDNAs of 16 Anseriforme species, ATG is generally the start codon, TAA is the most frequent stop codon, one of three, TAA, TAG, and T-, commonly observed. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN), which are missing the "DHU" arm.Phylogenetic relationships demonstrate that Aix galericula and Tadorna ferruginea are in the same group, the Tadorninae lineage, based on our analyses of complete mtDNAs and combined gene data. Molecular phylogenetic analysis suggests the 68 species of Anseriform birds be divided into three families: Anhimidae, Anatidae, and Anseranatidae. The results suggest Anatidae birds be divided into five subfamilies: Anatinae, Tadorninae, Anserinae, Oxyurinae, and Dendrocygninae. Oxyurinae and Dendrocygninae should not belong to Anserinae, but rather represent independent subfamilies. The Anatinae includes species from the tribes Mergini, Somaterini, Anatini, and Aythyini. The Anserinae includes species from the tribes Anserini and Cygnini.
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Affiliation(s)
- Gang Liu
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lizhi Zhou
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
- * E-mail:
| | - Bo Li
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lili Zhang
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
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Li W, Zhang XC, Zhao J, Shi Y, Zhu XP. Complete mitochondrial genome of Cuora trifasciata (Chinese three-striped box turtle), and a comparative analysis with other box turtles. Gene 2014; 555:169-77. [PMID: 25445281 DOI: 10.1016/j.gene.2014.10.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/22/2014] [Accepted: 10/31/2014] [Indexed: 11/26/2022]
Abstract
Cuora trifasciata has become one of the most critically endangered species in the world. The complete mitochondrial genome of C. trifasciata (Chinese three-striped box turtle) was determined in this study. Its mitochondrial genome is a 16,575-bp-long circular molecule that consists of 37 genes that are typically found in other vertebrates. And the basic characteristics of the C. trifasciata mitochondrial genome were also determined. Moreover, a comparison of C. trifasciata with Cuora cyclornata, Cuora pani and Cuora aurocapitata indicated that the four mitogenomics differed in length, codons, overlaps, 13 protein-coding genes (PCGs), ND3, rRNA genes, control region, and other aspects. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 12 protein-coding genes of the genus Cuora indicated the phylogenetic position of C. trifasciata within Cuora. The phylogenetic analysis also showed that C. trifasciata from Vietnam and China formed separate monophyletic clades with different Cuora species. The results of nucleotide base compositions, protein-coding genes and phylogenetic analysis showed that C. trifasciata from these two countries may represent different Cuora species.
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Affiliation(s)
- Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Xin-Cheng Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Jian Zhao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yan Shi
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Xin-Ping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China.
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Keith Barker F. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Mol Phylogenet Evol 2014; 79:313-24. [DOI: 10.1016/j.ympev.2014.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/31/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
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39
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Ma YG, Huang Y, Lei FM. Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2014; 35:81-91. [PMID: 24668650 DOI: 10.11813/j.issn.0254-5853.2014.2.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.
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Affiliation(s)
- Yong-Gui Ma
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huang
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Fu-Min Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Urantowka AD. Complete mitochondrial genome of Critically Endangered Blue-throated Macaw (Ara glaucogularis): its comparison with partial mitogenome of Scarlet Macaw (Ara macao). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:422-4. [PMID: 24621219 DOI: 10.3109/19401736.2014.898287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Blue-throated Macaw (Ara glaucogularis) is Critically Endangered species of parrot endemic to small Bolivian area. In this study, full mitochondrial genome of considered species was sequenced. It is 16,983 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. It`s comparison with published Ara macao mitogenome revealed their high degree of identity. On the other hand, analysis of both the genome compositions showed incompleteness of Ara macao CYTB gene. Hence, mitogenome of Ara macao species occurred only partial sequence. In consequence, Ara glaucogularis mitogenome is the first complete Macaw sequence, which will be indispensable to refine the phylogenetic relationships within the tribe Arini and will enrich the resource of markers for systematic, phylogenetic and population genetic studies.
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Affiliation(s)
- Adam Dawid Urantowka
- a Department of Genetics , Wroclaw University of Environmental and Life Sciences , Wroclaw , Poland
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41
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The complete sequence of the mitochondrial genome of the African Penguin (Spheniscus demersus). Gene 2014; 534:113-8. [DOI: 10.1016/j.gene.2013.09.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 11/23/2022]
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The complete mitochondrial genome of bean goose (Anser fabalis) and implications for anseriformes taxonomy. PLoS One 2013; 8:e63334. [PMID: 23717412 PMCID: PMC3662773 DOI: 10.1371/journal.pone.0063334] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/30/2013] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial DNA plays an important role in living organisms, and has been used as a powerful molecular marker in a variety of evolutionary studies. In this study, we determined the complete mtDNA of Bean goose (Anser fabalis), which is 16,688 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. The arrangement is similar to that of typical Anseriform species. All protein-coding genes, except for Cyt b, ND5, COI, and COII, start with an ATG codon. The ATG start codon is also generally observed in the 12 other Anseriform species, including 2 Anser species, with sequenced mitochondrial genomes. TAA is the most frequent stop codon, one of three–TAA, TAG, and T- –commonly observed in Anseriformes. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer(AGY) and tRNALeu(CUN), which are missing the dihydrouridine (DHU) arm. The control region of Bean goose mtDNA, with some conserved sequence boxes, such as F, E, D, and C, identified in its central domain. Phylogenetic analysis of complete mtDNA data for 13 Anseriform species supports the classification of them into four major branches: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Phylogenetic analyses were also conducted on 36 Anseriform birds using combined Cyt b, ND2, and COI sequences. The results clearly support the genus Somateria as an independent lineage classified in its own tribe, the Somaterini. Recovered topologies from both complete mtDNA and combined DNA sequences strongly indicate that Dendrocygninae is an independent subfamily within the family Anatidae and Anseranatidae represents an independent family. Based on the results of this study, we conclude that combining ND2, Cyt b, and COI sequence data is a workable solution at present for resolving phylogenetic relationships among Anseriform species in the absence of sufficient complete mtDNA data.
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Kan X, Yuan J, Zhang L, Li X, Yu L, Chen L, Guo Z, Yang J. Complete mitochondrial genome of the Tristram's Bunting,Emberiza tristrami(Aves: Passeriformes): The first representative of the family Emberizidae with six boxes in the central conserved domain II of control region. ACTA ACUST UNITED AC 2013; 24:648-50. [DOI: 10.3109/19401736.2013.772165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Li X, Ren Q, Kan X, Qian C, Li X, Qian M. Complete mitochondrial genome of the ring-necked pheasant,Phasianus colchicus(Galliformes: Phasianidae). ACTA ACUST UNITED AC 2012; 24:89-90. [DOI: 10.3109/19401736.2012.717939] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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45
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Tu J, Si F, Xing X, Yue Z, Yang F. Determination and analysis of complete mitochondrial genome sequence of mallard (Anas platyrhychos). ACTA ACUST UNITED AC 2012; 23:283-5. [PMID: 22708861 DOI: 10.3109/19401736.2012.674121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mtDNA) of mallard (Anas platyrhychos) was determined by long and accurate polymerase chain reaction and with primer walking sequence method. The entire genome was 16,606 bp in length. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and a non-coding region (D-loop). The characteristics of the mitochondrial genome were analyzed and discussed in detail.
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Affiliation(s)
- Jianfeng Tu
- State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Wild Economic Animal and Plant Science, Chinese Academy Agricultural Sciences, Jilin, PR China
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Liu G, Zhou LZ, Gu CM. Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (Mergus squamatus) and phylogeny of some Anatidae species. Mol Biol Rep 2011; 39:2139-45. [PMID: 21655953 DOI: 10.1007/s11033-011-0961-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
The scaly-sided merganser (Mergus squamatus) is an endangered bird species on the IUCN Red List with the estimated global population of less than 2,500 individuals at present. In the present study, we studied the complete mitochondrial genome (mtDNA) and the phylogenetic of M. squamatus by PCR amplification and GenBank data. The genome was 16,595 bp in length and contained 37 genes (13 protein coding genes, two rRNAs, and 22 tRNAs) and a non-coding control region (D-loop). All protein-coding genes of M. squamatus mtDNA start with a typical ATG codon, except ND1, COI, and COII uses GTG as their initial codon. TAA, T- and TAG as the terminate codon occurred very commonly in the sequence. All tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA(Ser) (AGY) and tRNA(Leu) (CUN), which lose ''DHU'' arm. The genome sequences had been deposited in GenBank under accession number HQ833701. Based on the concatenated nucleotide sequences of mtDNA genes (Cyt b and D-loop), we reconstructed phylogenetic trees and discussed the phylogenetic relationships among ten Anatidae species. The results are different from the present classification, and we support Lophodytes cucullatus and Mergullus albellus to be members of the genus Mergus.
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Affiliation(s)
- Gang Liu
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 Anhui, People's Republic of China
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Sammler S, Bleidorn C, Tiedemann R. Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination. BMC Genomics 2011; 12:35. [PMID: 21235758 PMCID: PMC3025957 DOI: 10.1186/1471-2164-12-35] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 01/14/2011] [Indexed: 01/07/2023] Open
Abstract
Background Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i.e., in every generation. Conclusions The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.
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Affiliation(s)
- Svenja Sammler
- University of Potsdam, Institute for Biology and Biochemistry, Unit of Evolutionary Biology/Systematic Zoology, Karl-Liebknecht-Str. 24-25, Haus 26, D-14476 Potsdam, Germany
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Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L. Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1234-49. [PMID: 20603809 DOI: 10.4238/vol9-2gmr853] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rock pigeon (Columba livia), or Rock dove, is a member of the bird family Columbidae. We mapped the complete mitochondrial genome of the Rock pigeon. The mitochondrial genome of this species is a circular molecule of 17,229 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus a putative control region, demonstrating a structure very similar to that of other birds. As found in other vertebrates, most of these genes are coded on the H-strand, except for NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). The AT skew and GC skew of the whole genome, protein-coding genes, tRNA, rRNA, and the control region were calculated for the complete mitochondrial genomes of 30 avian species, representing 29 orders. All protein-coding genes initiated with ATG, except for cox1 and nad5, which began with GTG. One extra nucleotide 'C' was present in NADH dehydrogenase subunit 3 (nad3). All tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Within the control region, conserved sequences were identified in three domains. Although the conserved blocks, such as ETAS1, ETAS2, CSB1, CSB1-like, and boxes C, D, E, and F, are readily identifiable in the C. livia control region, the typical origin of H-strand replication (O(H)), CSB2 and CSB3 could not be detected. These results provide basic information for phylogenetic analyses of birds, especially Columbiformes species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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Kan XZ, Li XF, Lei ZP, Wang M, Chen L, Gao H, Yang ZY. Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1204-16. [PMID: 20589618 DOI: 10.4238/vol9-2gmr820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cabot's tragopan, Tragopan caboti, is a globally threatened pheasant endemic to southeast China. The complete mitochondrial genome of Cabot's tragopan was sequenced. The circular genome contains 16,727 bp, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, a structure very similar to that of other Galliformes. As found in other vertebrates, most of these genes code on the H-strand, except for the NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). All protein-coding genes initiated with ATG, except for cox1, which began with GTG, and had a strong skew of C vs G (GC skew = -0.29 to -0.73). One extra 'C' nucleotide was found in the NADH dehydrogenase subunit 3 (nad3). All the tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Conserved sequences in three domains were identified within the control region (D-loop). These results provide basic information for phylogenetic analyses among Galliform birds, and especially Tragopan species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China.
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Ksepka DT, Clarke JA. The Basal Penguin (Aves: Sphenisciformes) Perudyptes devriesi and a Phylogenetic Evaluation of the Penguin Fossil Record. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2010. [DOI: 10.1206/653.1] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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