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Zhukova A, Zakharov G, Pavlova O, Saifitdinova A. Description of the complete rDNA repeat unit structure of Coturnixjaponica Temminck et Schlegel, 1849 (Aves). COMPARATIVE CYTOGENETICS 2024; 18:183-198. [PMID: 39363903 PMCID: PMC11447458 DOI: 10.3897/compcytogen.18.127373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/29/2024] [Indexed: 10/05/2024]
Abstract
Ribosomal RNA (18S, 5.8S, 28S) gene clusters in genomes form regions that consist of multiple tandem repeats. They are located on a single or several pairs of chromosomes and play an important role in the formation of the nucleolus responsible for the assembly of ribosome subunits. The rRNA gene cluster sequences are widely used for taxonomic studies, however at present, complete information on the avian rDNA repeat unit structure including intergenic spacer sequence is available only for the chicken (Gallusgallusdomesticus Linnaeus, 1758). The GC enrichment and high-order repeats peculiarities within the intergenic spacer described for the chicken rDNA cluster may be responsible for these failures. The karyotype of the Japanese quail (Coturnixjaponica Temminck et Schlegel, 1849) deserves close attention because, unlike most birds, it has three pairs of nucleolar organizer bearing chromosomes, two of which are microchromosomes enriched in repeating elements and heterochromatin that carry translocated terminal nucleolar organizers. Here we assembled and annotated the complete Japanese quail ribosomal gene cluster sequence of 21166 base pairs (GenBank under the registration tag BankIt2509210 CoturnixOK523374). This is the second deciphered avian rDNA cluster after the chicken. Despite the revealed high similarity with the chicken corresponding sequence, it has a number of specific features, which include a slightly lower degree of GC content and the presence of bendable elements in the content of both the transcribed spacer I and the non-transcribed intergenic spacer.
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Affiliation(s)
- Alina Zhukova
- Herzen State Pedagogical University of Russia, Saint Petersburg, RussiaHerzen State Pedagogical University of RussiaSaint PetersburgRussia
| | - Gennadii Zakharov
- Pavlov Institute of Physiology, Russian Academy of Sciences, Saint Petersburg, RussiaPavlov Institute of Physiology, Russian Academy of SciencesSaint PetersburgRussia
- EPAM Systems Inc., Saint Petersburg, RussiaEPAM Systems Inc.Saint PetersburgRussia
| | - Olga Pavlova
- International Centre for Reproductive Medicine, Saint Petersburg, RussiaInternational Centre for Reproductive MedicineSaint PetersburgRussia
- Beagle Ltd., Saint Petersburg, RussiaBeagle Ltd.Saint PetersburgRussia
| | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, Saint Petersburg, RussiaHerzen State Pedagogical University of RussiaSaint PetersburgRussia
- International Centre for Reproductive Medicine, Saint Petersburg, RussiaInternational Centre for Reproductive MedicineSaint PetersburgRussia
- Saint Petersburg State University, Saint Petersburg, RussiaSaint Petersburg State UniversitySaint PetersburgRussia
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2
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Dey P, Ray SD, Kochiganti VHS, Pukazhenthi BS, Koepfli KP, Singh RP. Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails. Genes (Basel) 2024; 15:742. [PMID: 38927678 PMCID: PMC11202683 DOI: 10.3390/genes15060742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau's geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
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Affiliation(s)
- Prateek Dey
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
- Bharathiar University, Coimbatore 641046, Tamil Nadu, India
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Swapna Devi Ray
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
| | | | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya 824236, Bihar, India
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Wood ML, Neumann R, Roy P, Nair V, Royle NJ. Characterization of integrated Marek's disease virus genomes supports a model of integration by homology-directed recombination and telomere-loop-driven excision. J Virol 2023; 97:e0071623. [PMID: 37737586 PMCID: PMC10617522 DOI: 10.1128/jvi.00716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/03/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Marek's disease virus (MDV) is a ubiquitous chicken pathogen that inflicts a large economic burden on the poultry industry, despite worldwide vaccination programs. MDV is only partially controlled by available vaccines, and the virus retains the ability to replicate and spread between vaccinated birds. Following an initial infection, MDV enters a latent state and integrates into host telomeres and this may be a prerequisite for malignant transformation, which is usually fatal. To understand the mechanism that underlies the dynamic relationship between integrated-latent and reactivated MDV, we have characterized integrated MDV (iMDV) genomes and their associated telomeres. This revealed a single orientation among iMDV genomes and the loss of some terminal sequences that is consistent with integration by homology-directed recombination and excision via a telomere-loop-mediated process.
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Affiliation(s)
- Michael L. Wood
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Rita Neumann
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Poornima Roy
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Venugopal Nair
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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4
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Wattanadilokcahtkun P, Chalermwong P, Singchat W, Wongloet W, Chaiyes A, Tanglertpaibul N, Budi T, Panthum T, Ariyaraphong N, Ahmad SF, Lisachov A, Muangmai N, Nunome M, Han K, Matsuda Y, Duengkae P, Srikulnath K. Genetic admixture and diversity in Thai domestic chickens revealed through analysis of Lao Pa Koi fighting cocks. PLoS One 2023; 18:e0289983. [PMID: 37792798 PMCID: PMC10550135 DOI: 10.1371/journal.pone.0289983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/28/2023] [Indexed: 10/06/2023] Open
Abstract
Lao Pa Koi (LPK) chicken is a popular fighting breed in Thailand, prized for (its unique characteristics acquired by selective breeding), and a valuable model for exploring the genetic diversity and admixture of red junglefowls and domestic chickens. In this study, genetic structure and diversity of LPK chicken were assessed using 28 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequences, and the findings were compared to a gene pool library from "The Siam Chicken Bioresource Project". High genetic variability was observed in LPK chickens using mtDNA D-loop haplotype analysis, and six haplotypes were identified. Microsatellite data revealed 182 alleles, with an average of 6.5 alleles per locus. These results confirmed the occurrence of genetic admixture of red junglefowl and Thai domestic chickens in LPK chicken breed. A maximum entropy modeling approach was used to analyze the spatial suitability and to assess the adaptive evolution of LPK chickens in diverse local environments. The model identified 82.52% of the area studied as unsuitable, and 9.34%, 7.11%, and 2.02% of the area indicated moderate, low, and high suitability, respectively. The highest contribution rate to land suitability for LPK chickens was found at an elevation of 100-250 m, suggesting the importance of elevation for their potential distribution. The results of this study provide valuable insights into the genetic origin of LPK chicken breed and identify resources for future genetic improvement.
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Affiliation(s)
- Pish Wattanadilokcahtkun
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
| | - Piangjai Chalermwong
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Sciences for Industry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Wongsathit Wongloet
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Pakkret Nonthaburi, Thailand
| | - Nivit Tanglertpaibul
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, Thailand
| | - Trifan Budi
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, Thailand
| | - Nattakan Ariyaraphong
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Department of Genetics, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, Thailand
| | - Artem Lisachov
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Fisheries, Department of Fishery Biology, Kasetsart University, Bangkok, Thailand
| | - Mitsuo Nunome
- Faculty of Science, Department of Zoology, Okayama University of Science, Okayama, Japan
| | - Kyudong Han
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Department of Microbiology, Dankook University, Cheonan, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, Korea
| | - Yoichi Matsuda
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Sciences for Industry, Kasetsart University, Bangkok, Thailand
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Department of Genetics, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Kasetsart University, Bangkok, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Nakhon Pathom, Thailand
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5
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Wongloet W, Singchat W, Chaiyes A, Ali H, Piangporntip S, Ariyaraphong N, Budi T, Thienpreecha W, Wannakan W, Mungmee A, Jaisamut K, Thong T, Panthum T, Ahmad SF, Lisachov A, Suksavate W, Muangmai N, Chuenka R, Nunome M, Chamchumroon W, Han K, Nuangmek A, Matsuda Y, Duengkae P, Srikulnath K. Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken. Animals (Basel) 2023; 13:1949. [PMID: 37370459 PMCID: PMC10295432 DOI: 10.3390/ani13121949] [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: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.
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Affiliation(s)
- Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand;
| | - Hina Ali
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Surachai Piangporntip
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Worawit Thienpreecha
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Wannapa Wannakan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Autchariyapron Mungmee
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Kittipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | | | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama 700-0005, Japan;
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Aniroot Nuangmek
- Mae Hong Son Provincial Livestock Office, Department of Livestock Development, Ministry of Agriculture and Cooperatives, Mae Hong Son 58000, Thailand;
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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6
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Compendio JDZ, Mantana JMNP, Nishibori M. Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia. J Poult Sci 2022; 59:305-315. [PMID: 36382062 PMCID: PMC9596289 DOI: 10.2141/jpsa.0210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/28/2022] [Indexed: 11/21/2022] Open
Abstract
Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800-3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines.
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Affiliation(s)
- Jade Dhapnee Z. Compendio
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
- Department of Animal Science, Visayas State University, Philippines
| | | | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
- Department of Animal Science, Visayas State University, Philippines
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7
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Godinez CJP, Layos JKN, Yamamoto Y, Kunieda T, Duangjinda M, Liao LM, Huang XH, Nishibori M. Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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Affiliation(s)
- Cyrill John P Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
| | - John King N Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- College of Agriculture and Forestry, Capiz State University, Burias, Mambusao, Capiz, 5807, Philippines
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Tetsuo Kunieda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lawrence M Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou, 514015, China
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
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8
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Red Junglefowl Resource Management Guide: Bioresource Reintroduction for Sustainable Food Security in Thailand. SUSTAINABILITY 2022. [DOI: 10.3390/su14137895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The domestication of wild animals represents a major milestone for human civilization. Chicken is the largest domesticated livestock species and used for both eggs and meat. Chicken originate from the red junglefowl (Gallus gallus). Its adaptability to diverse environments and ease of selective breeding provides a unique genetic resource to address the challenges of food security in a world impacted by climatic change and human population growth. Habitat loss has caused population declines of red junglefowl in Thailand. However, genetic diversity is likely to remain in captive stocks. We determine the genetic diversity using microsatellite genotyping and the mitochondrial D-loop sequencing of wild red junglefowl. We identified potential distribution areas in Thailand using maximum entropy models. Protected areas in the central and upper southern regions of Thailand are highly suitable habitats. The Bayesian clustering analysis of the microsatellite markers revealed high genetic diversity in red junglefowl populations in Thailand. Our model predicted that forest ranges are a highly suitable habitat that has enabled the persistence of a large gene pool with a nationwide natural distribution. Understanding the red junglefowl allows us to implement improved resource management, species reintroduction, and sustainable development to support food security objectives for local people.
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9
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Liu S, Chen H, Ouyang J, Huang M, Zhang H, Zheng S, Xi S, Tang H, Gao Y, Xiong Y, Cheng D, Chen K, Liu B, Li W, Ren J, Yan X, Mao H. A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. Gigascience 2022; 11:giac018. [PMID: 35383847 PMCID: PMC8985102 DOI: 10.1093/gigascience/giac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/15/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl. RESULTS A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl. CONCLUSIONS This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.
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Affiliation(s)
- Shaojuan Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Min Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hui Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sumei Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Suwang Xi
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongbo Tang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yuren Gao
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Di Cheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kaifeng Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bingbing Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen 361021, China
| | - Jun Ren
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
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10
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Ren T, Nunome M, Suzuki T, Matsuda Y. Genetic diversity and population genetic structure of Cambodian indigenous chickens. Anim Biosci 2022; 35:826-837. [PMID: 34991210 PMCID: PMC9066038 DOI: 10.5713/ab.21.0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.
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Affiliation(s)
- Theary Ren
- General Directorate of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh 12352, Cambodia.,Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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11
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Ogada S, Otecko NO, Moraa Kennedy G, Musina J, Agwanda B, Obanda V, Lichoti J, Peng M, Ommeh S. Demographic history and genetic diversity of wild African harlequin quail ( Coturnix delegorguei delegorguei) populations of Kenya. Ecol Evol 2021; 11:18562-18574. [PMID: 35003693 PMCID: PMC8717324 DOI: 10.1002/ece3.8458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mitochondrial DNA (mtDNA) control region fragment and 119,339 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS) data. Genetic diversity analyses revealed that the genetic variation in wild African harlequin quails was predominantly among individuals than populations. Demographic analyses indicated a signal of rapid demographic expansion, and the estimated time since population expansion was found to be 150,000-350,000 years ago, corresponding to around the Pliocene-Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. These results provide the first account of the genetic diversity of wild African harlequin quails of Siaya, thereby creating a helpful foundation in their biodiversity conservation.
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Affiliation(s)
- Stephen Ogada
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Newton O. Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Grace Moraa Kennedy
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - John Musina
- Department of ZoologyNational Museums of KenyaNairobiKenya
| | | | - Vincent Obanda
- Department of Veterinary ServicesKenya Wildlife ServiceNairobiKenya
| | - Jacqueline Lichoti
- Central Veterinary Laboratories KabeteState Department of LivestockMinistry of Agriculture, Livestock and FisheriesNairobiKenya
| | - Min‐Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Sheila Ommeh
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
- Department of ZoologyNational Museums of KenyaNairobiKenya
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12
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Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Mol Genet Genomics 2021; 296:1147-1159. [PMID: 34251529 DOI: 10.1007/s00438-021-01806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.
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13
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Osman SAM, Nishibori M, Yonezawa T. Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens. Anim Biosci 2021; 34:941-948. [PMID: 32299160 PMCID: PMC8100483 DOI: 10.5713/ajas.19.0932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/20/2020] [Accepted: 04/09/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan. METHODS Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences. RESULTS This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1. CONCLUSION The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.
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Grants
- 22580319 Ministry of Education, Culture, Sports, Science, and Technology
- 26292139 Ministry of Education, Culture, Sports, Science, and Technology
- 19H00534 Ministry of Education, Culture, Sports, Science, and Technology
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Affiliation(s)
- Sayed A.-M. Osman
- Laboratory of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
- Department of Genetics, Faculty of Agriculture, Minia University, El Minia, Eg-61517, Egypt
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan
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14
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Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail ( Coturnix japonica) Using Restriction-Site Associated DNA Sequencing. Genes (Basel) 2021; 12:genes12050735. [PMID: 34068239 PMCID: PMC8153160 DOI: 10.3390/genes12050735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023] Open
Abstract
This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.
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15
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Hata A, Nunome M, Suwanasopee T, Duengkae P, Chaiwatana S, Chamchumroon W, Suzuki T, Koonawootrittriron S, Matsuda Y, Srikulnath K. Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens. Sci Rep 2021; 11:2035. [PMID: 33479400 PMCID: PMC7820500 DOI: 10.1038/s41598-021-81589-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023] Open
Abstract
In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.
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Affiliation(s)
- Ayano Hata
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Soontorn Chaiwatana
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Wiyada Chamchumroon
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Takayuki Suzuki
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Yoichi Matsuda
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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Hata A, Takenouchi A, Kinoshita K, Hirokawa M, Igawa T, Nunome M, Suzuki T, Tsudzuki M. Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers. Animals (Basel) 2020; 10:E2074. [PMID: 33182330 PMCID: PMC7695345 DOI: 10.3390/ani10112074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 01/10/2023] Open
Abstract
Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A-E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.
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Affiliation(s)
- Ayano Hata
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Atsushi Takenouchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Momomi Hirokawa
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Takayuki Suzuki
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
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17
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Zhou C, Liu Y, Qiao L, Liu Y, Yang N, Meng Y, Yue B. The draft genome of the blood pheasant ( Ithaginis cruentus): Phylogeny and high-altitude adaptation. Ecol Evol 2020; 10:11440-11452. [PMID: 33144976 PMCID: PMC7593199 DOI: 10.1002/ece3.6782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 11/10/2022] Open
Abstract
The blood pheasant (Ithaginis cruentus), the only species in the genus Ithaginis, lives in an extremely inhospitable high-altitude environment, coping with hypoxia and ultraviolet (UV) radiation. To further investigate the phylogeny of Phasianidae species based on complete genomes and understand the molecular genetic mechanisms of the high-altitude adaptation of the blood pheasant, we de novo assembled and annotated the complete genome of the blood pheasant. The blood pheasant genome size is 1.04 Gb with scaffold N50 of 10.88 Mb. We identified 109.92 Mb (10.62%) repetitive elements, 279,037 perfect microsatellites, and 17,209 protein-coding genes. The phylogenetic tree of Phasianidae based on whole genomes revealed three highly supported major clades with the blood pheasant included in the "erectile clade." Comparative genomics analysis showed that many genes were positively selected in the blood pheasant, which was associated with response to hypoxia and/or UV radiation. More importantly, among these positively selected genes (PSGs) which were related to high-altitude adaptation, sixteen PSGs had blood pheasant-specific missense mutations. Our data and analysis lay solid foundation to the study of Phasianidae phylogeny and provided new insights into the potential adaptation mechanisms to the high altitude employed by the blood pheasant.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Lu Qiao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Yang Liu
- Chengdu Zoo/Chengdu Wildlife Research InstituteChengduChina
| | - Nan Yang
- Institute of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduChina
| | - Yang Meng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
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18
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Yonezawa T, Nishibori M. The complete mitochondrial genome of the Japanese rock ptarmigan ( Lagopus muta japonica Clark, 1907). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1746207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Funako, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University
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19
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20
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Islam MA, Osman SAM, Nishibori M. Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region. Br Poult Sci 2019; 60:628-637. [PMID: 31475858 DOI: 10.1080/00071668.2019.1655708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.
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Affiliation(s)
- M A Islam
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.,Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - S A M Osman
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, El Minia, Egypt
| | - M Nishibori
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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Kartout-Benmessaoud Y, Ladjali-Mohammedi K. Banding cytogenetics of chimeric hybrids Coturnixcoturnix × Coturnixjaponica and comparative analysis with the domestic fowl. COMPARATIVE CYTOGENETICS 2018; 12:445-470. [PMID: 30364889 PMCID: PMC6199345 DOI: 10.3897/compcytogen.v12i4.27341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The Common quail Coturnixcoturnix Linnaeus, 1758 is a wild migratory bird which is distributed in Eurasia and North Africa, everywhere with an accelerating decline in population size. This species is protected by the Bonn and Berne conventions (1979) and by annex II/1 of the Birds Directive (2009). In Algeria, its breeding took place at the hunting centre in the west of the country. Breeding errors caused uncontrolled crosses between the Common quail and Japanese quail Coturnixjaponica Temminck & Schlegel, 1849. In order to help to preserve the natural genetic heritage of the Common quail and to lift the ambiguity among the populations of quail raised in Algeria, it seemed essential to begin to describe the chromosomes of this species in the country since no cytogenetic study has been reported to date. Fibroblast cultures from embryo and adult animal were initiated. Double synchronization with excess thymidine allowed us to obtain high resolution chromosomes blocked at prometaphase stage. The karyotype and the idiogram in GTG morphological banding (G-bands obtained with trypsin and Giemsa) corresponding to larger chromosomes 1-12 and ZW pair were thus established. The diploid set of chromosomes was estimated as 2N=78. Cytogenetic analysis of expected hybrid animals revealed the presence of a genetic introgression and cellular chimerism. This technique is effective in distinguishing the two quail taxa. Furthermore, the comparative chromosomal analysis of the two quails and domestic chicken Gallusgallusdomesticus Linnaeus, 1758 has been conducted. Differences in morphology and/or GTG band motifs were observed on 1, 2, 4, 7, 8 and W chromosomes. Neocentromere occurrence was suggested for Common quail chromosome 1 and Chicken chromosomes 4 and W. Double pericentric inversion was observed on the Common quail chromosome 2 while pericentric inversion hypothesis was proposed for Chicken chromosome 8. A deletion on the short arm of the Common quail chromosome 7 was also found. These results suggest that Common quail would be a chromosomally intermediate species between Chicken and Japanese quail. The appearance of only a few intrachromosomal rearrangements that occurred during evolution suggests that the organization of the genome is highly conserved between these three galliform species.
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Affiliation(s)
- Yasmine Kartout-Benmessaoud
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
- University of Bejaia, Faculty of Nature and Life Sciences, Department of Physico-Chemical Biology, 06000, Bejaia, AlgeriaUniversity of BejaiaBejaiaAlgeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
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22
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Teinlek P, Siripattarapravat K, Tirawattanawanich C. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:804-811. [PMID: 29381905 PMCID: PMC5933977 DOI: 10.5713/ajas.17.0611] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/02/2017] [Accepted: 01/09/2018] [Indexed: 11/27/2022]
Abstract
Objective Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima’s D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index (FST) was conducted to evaluated genetic relationships between these varieties. Results Twenty-three identified haplotypes were classified in six haplogroups (A–E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima’s D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise FST, LK was most closely related to DA (FST = 0.00879) while DA was farthest from CH (FST = 0.24882). Conclusion All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.
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Affiliation(s)
- Piyanat Teinlek
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Kannika Siripattarapravat
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.,Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Chanin Tirawattanawanich
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.,Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
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23
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Liu G, Zhang Y. Next-generation resequencing the complete mitochondrial genome of Japanese quail ( Coturnix japonica). Mitochondrial DNA B Resour 2016; 1:937-938. [PMID: 33473684 PMCID: PMC7799783 DOI: 10.1080/23802359.2016.1258343] [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: 11/09/2022] Open
Abstract
As the development of the new generation of sequencing (NGS) technologies, it has been used for standard sequencing applications more and more popular. We used NGS technologies to resequence the complete mitochondrial genome of Japanese quail. The complete mitochondrial genome of Japanese quail is a 16,668 bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, 2 rRNAs, and 22 tRNAs) and a 1156 bp D-loop. Its gene arrangement pattern is identical with typical other Galliformes. All protein-coding genes start with an ATG codon except COI, which start with GTG. TAA is the most frequent stop codon, although ND2 end with TAG, and COI and ND6 end with AGG, COIII and ND4 end with TGC. The mtDNA sequence contains 12S rRNA and 16S rRNA of rRNA. Except for tRNASer(AGY) and tRNALeu(CUN) without the dihydrouridine (DHU) arm, all tRNAs could be folded into canonical cloverleaf secondary structures. Coturnix japonica has close relative with C. chinensis.
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Affiliation(s)
- Gang Liu
- Department of Biology, School of Life Science, Anhui Medical University, Hefei, P. R. China
| | - Yingyin Zhang
- Department of Biology, School of Life Science, Anhui Medical University, Hefei, P. R. China
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24
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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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25
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Sahu PK, Das B, Sahoo L, Senapati S, Nayak GD. Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2986-8. [PMID: 26162050 DOI: 10.3109/19401736.2015.1060474] [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 genetic information obtained from the mitochondrial DNA D-loop region has paramount importance in understanding the evolution of closely related individuals, and designing proper breeding or conservation plans. The present study was conducted using partial D-loop sequences of three local poultry populations from Odisha, India. The partial D-loop sequences were found to be highly polymorphic having 164 polymorphic sites with 89 singletons and 75 parsimony informative sites. Furthermore, 25 insertion and deletion sites were observed. High genetic diversity was observed within three local chicken populations. Highest genetic difference was observed between Gujuri and Kalua population (0.2230) followed by Gujuri and Hansli (0.199) and Kalua with Hansli (0.166). The pairwise mismatch distribution showed that all populations are of constant size over time. Phylogenetic tree analysis indicated that the said three populations were close to the referred population of China, Sri Lanka, Indonesia and Japan than Aseel and Kadaknath (Indian native breeds).
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Affiliation(s)
- P K Sahu
- a Department of Poultry Science , College of Veterinary Science and Animal Husbandry, Orissa University of Agriculture and Technology , Bhubaneswar , Odisha , India
| | - B Das
- b Institute of Life Sciences , Bhubaneswar , Odisha , India , and
| | - L Sahoo
- c Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India
| | - S Senapati
- b Institute of Life Sciences , Bhubaneswar , Odisha , India , and
| | - G D Nayak
- a Department of Poultry Science , College of Veterinary Science and Animal Husbandry, Orissa University of Agriculture and Technology , Bhubaneswar , Odisha , India
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Zhou T, Shen X, Irwin DM, Shen Y, Zhang Y. Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds. Mitochondrion 2014; 18:70-5. [PMID: 25110061 DOI: 10.1016/j.mito.2014.07.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 02/05/2023]
Abstract
Galliform birds inhabit very diverse habitats, including plateaus that are above 3000 m in altitude. At high altitude, lower temperature and hypoxia are two important factors influencing survival. Mitochondria, as the ultimate oxygen transductor, play an important role in aerobic respiration through oxidative phosphorylation (OXPHOS). We analyzed the mitochondrial genomes of six high-altitude phasianidae birds and sixteen low-altitude relatives in an attempt to determine the role of mitochondrial genes in high-altitude adaptation. We reconstructed the phylogenetic relationships of these phasianidae birds and relatives and found at least four lineages that independently occupied this high-altitude habitat. Selective analyses revealed significant evidence for positive selection in the genes ND2, ND4, and ATP6 in three of the high-altitude lineages. This result strongly suggests that adaptive evolution of mitochondrial genes played a critical role during the independent acclimatization to high altitude by galliform birds.
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Affiliation(s)
- Taicheng Zhou
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuejuan Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yongyi Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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27
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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Huang Z, Ke D. Structure and evolution of the Phasianidae mitochondrial DNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:350-4. [PMID: 24617466 DOI: 10.3109/19401736.2014.895987] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial DNA control region is an area of the mitochondrial genome which is non-coding DNA. To infer the structural and evolutionary characteristics of Phasianidae mitochondrial DNA control region, the entire control region sequences of 34 species were analyzed. The length of the control region sequences ranged from 1144 bp (Phasianus colchicus) to 1555 bp (Coturnix japonica) and can be separated into three domains. The average genetic distances among the species within the genera varied from 1.96% (Chrysolophus) to 12.05% (Coturnix). The average genetic distances showed significantly negative correlation with ts/tv. In most genera (except Coturnix), domain I is the most variable among the three domains. However, the first 150 nucleotides apparently evolved at unusually low rates. Four conserved sequence boxes in the domain II of Phasianidae sequences were identified. The alignment of the Phasianidae four boxes and CSB-1 sequences showed considerable sequence variation.
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Affiliation(s)
- Zuhao Huang
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , China
| | - Dianhua Ke
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , China
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Li B, Zhu C, Ding P, Bai S, Cui J. Complete mitochondrial genome of black grouse (Lyrurus tetrix). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:134-5. [PMID: 24450707 DOI: 10.3109/19401736.2013.878911] [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
We sequenced the entire mitochondrial genome of Lyrurus tetrix for the first time. The mitogenome was 16,677 bp in length, encoded with a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes plus a putative control region. Almost all genes were encoded on the H-strand except the ND6 and eight tRNA genes. All protein-coding genes initiated with ATG, except for COX1 and ND5 (GTG). An 18-bp-nucleotide deletion occurred in the ND6 of Lyrurus tetrix in contrast to other Galliformes. The total base composition of the mitogenome was 30.4% for A, 30.4% for C, 25.8% for T and 13.4% for G. These results provide basic information for phylogenetic analyses among Galliformes.
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Affiliation(s)
- Bo Li
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and.,b State Forestry Administration Detecting Center of Wildlife , Harbin , China
| | - Can Zhu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Peng Ding
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Suying Bai
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Jie Cui
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
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Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations. J Poult Sci 2014. [DOI: 10.2141/jpsa.0130190] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Phylogenetic Analysis of Native Chicken from Bangladesh and Neighboring Asian Countries Based on Complete Sequence of Mitochondrial DNA D-loop Region. J Poult Sci 2012. [DOI: 10.2141/jpsa.0120007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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Japanese Silkie Fowls are Widely Distributed in the Phylogenetic Tree Derived from Mitochondrial Complete D-loop Nucleotide Sequences. J Poult Sci 2011. [DOI: 10.2141/jpsa.011023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Wada K, Okumura K, Nishibori M, Kikkawa Y, Yokohama M. The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae. Anim Sci J 2010; 81:551-7. [PMID: 20887306 DOI: 10.1111/j.1740-0929.2010.00799.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16,357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group.
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Affiliation(s)
- Kenta Wada
- Faculty of Bioindustry, Department of Bioproduction Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
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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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Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP. A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 2010; 10:132. [PMID: 20444289 PMCID: PMC2880301 DOI: 10.1186/1471-2148-10-132] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 05/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. RESULTS We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). CONCLUSIONS The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.
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Affiliation(s)
- Yong-Yi Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100000, China
| | - Lu Liang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100000, China
| | - Yan-Bo Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100000, China
| | - Bi-Song Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
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Kan XZ, Yang JK, Li XF, Chen L, Lei ZP, Wang M, Qian CJ, Gao H, Yang ZY. Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. GENETICS AND MOLECULAR RESEARCH 2010; 9:1625-33. [DOI: 10.4238/vol9-3gmr898] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae. Mol Biol Rep 2009; 37:3001-15. [PMID: 19823953 DOI: 10.1007/s11033-009-9868-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Galloanserae is an ancient and diverse avian group, for which comprehensive molecular evidence relevant to phylogenetic analysis in the context of molecular chronology is lacking. In this study, we present two additional mitochondrial genome sequences of Galloanserae (the whistling duck, Dendrocygna javanica, and the black swan, Cygnus atratus) to broaden the scope of molecular phylogenetic reconstruction. The lengths of the whistling duck's and black swan's mitochondrial genomes are 16,753 and 16,748 bases, respectively. Phylogenetic analyses suggest that Dendrocygna is more likely to be in a basal position of the branch consisting of Anatinae and Anserinae, an affiliation that does not conform to its traditional classification. Bayesian approaches were employed to provide a rough timescale for Galloanserae evolution. In general, a narrow range of 95% confidence intervals gave younger estimates than those based on limited genes and estimated that at least two lineages originated before the Coniacian epoch around 90 MYA, well before the Cretaceous-Tertiary boundary. In addition, these results, which were compatible with estimates from fossil evidence, also imply that the origin of numerous genera in Anseriformes took place in the late Oligocene to early Miocene. Taken together, the results presented here provide a working framework for future research on Galloanserae evolution, and they underline the utility of whole mitochondrial genome sequences for the resolution of deep divergence.
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Seabrook-Davison M, Huynen L, Lambert DM, Brunton DH. Ancient DNA resolves identity and phylogeny of New Zealand's extinct and living quail (Coturnix sp.). PLoS One 2009; 4:e6400. [PMID: 19636374 PMCID: PMC2712072 DOI: 10.1371/journal.pone.0006400] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 06/23/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. METHODOLOGY/PRINCIPAL FINDINGS Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. CONCLUSION/SIGNIFICANCE Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.
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Affiliation(s)
- Mark Seabrook-Davison
- Ecology and Conservation Group, Institute of Natural Sciences, Massey University, Auckland, New Zealand.
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Shen YY, Shi P, Sun YB, Zhang YP. Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res 2009; 19:1760-5. [PMID: 19617397 DOI: 10.1101/gr.093138.109] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of flight is the most important feature of birds, and this ability has helped them become one of the most successful groups of vertebrates. However, some species have independently lost their ability to fly. The degeneration of flight ability is a long process, and some species remain transitional locomotive models. Most of the energy required for locomotion is supplied by mitochondria via oxidative phosphorylation. Thus, rapidly flying birds should require a more energy efficient metabolism than weakly flying or flightless species. Therefore, we speculated that evolutionary constraints acted on the mtDNA of birds with different locomotive abilities. To test this hypothesis, we compared 76 complete avian mitochondrial genomes. Weakly flying and flightless birds, compared to rapidly flying birds, accumulated more nonsynonymous nucleotide substitutions relative to synonymous substitutions. Even after controlling for mutation rate, this trend remained significant. This finding was further tested for its generality by examining 214 complete mammalian mitochondrial genomes. The same as birds, a negative correlation was also found for the K(a)/K(s) ratio and locomotive speed. Our results demonstrated that, in addition to the previously described role for effective population size, functional constraints due to locomotion play an important role in the evolution of mtDNA.
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Affiliation(s)
- Yong-Yi Shen
- Kunming Institute of Zoology, The Chinese Academy of Sciences, China
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42
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Evidence for introgressive hybridization of wild common quail (Coturnix coturnix) by domesticated Japanese quail (Coturnix japonica) in France. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9951-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ksepka DT. Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status forGallinuloides wyomingensisand rallid affinities forAmitabha urbsinterdictensis. Cladistics 2009; 25:173-197. [DOI: 10.1111/j.1096-0031.2009.00250.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Oka T, Ino Y, Nomura K, Kawashima S, Kuwayama T, Hanada H, Amano T, Takada M, Takahata N, Hayashi Y, Akishinonomiya F. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 2007; 38:287-93. [PMID: 17539973 DOI: 10.1111/j.1365-2052.2007.01604.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we analysed the mitochondrial DNA D-loop region of Japanese native chickens to clarify their phylogenetic relationships, possible maternal origin and routes of introduction into Japan. Seven haplogroups (Types A-G) were identified. Types A-C were observed in Jidori, Shokoku and related breeds. However, Type C was absent in Shokoku, which was introduced from China, while most Indonesian native chickens were included in the Type C haplogroup. Types D-G were observed in Shamo and related breeds. Type E had a close genetic relationship with Chinese native chickens. Our results indicate that some breeds were not introduced into Japan as suggested in conventional literature, based on low nucleotide diversity of certain chicken breeds. Sequences originating from China and Korea could be clearly distinguished from those originating from Southeast Asia. In each group, domestic chickens were divided into the Jidori-Shokoku and Shamo groups. These results indicate that Chinese and Korean chickens were derived from Southeast Asia. Following the domestication of red junglefowl, a non-game type chicken was developed, and it spread to China. A game type chicken was developed in each area. Both non-game and game chickens formed the foundation of Japanese native chickens.
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Affiliation(s)
- T Oka
- Department of Animal Science, Tokyo University of Agriculture, Kanagawa, Japan
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Wada K, Nishibori M, Yokohama M. The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer (Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2005.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, Hedderson TAJ, Randi E, Pereira SL, Wakeling J. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 2006; 22:495-532. [DOI: 10.1111/j.1096-0031.2006.00120.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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47
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Abstract
The nucleotide sequence of the mitochondrial genome of the Whistling Swan, Cygnus columbianus, is reported. Many of the features common to avian mitochondrial genomes are present in C. columbianus and are described here. The gene order is the same as in Gallus gallus. The sequence of this mitochondrial genome allows relationships within the family Anatidae (swans, geese and ducks) to be reconsidered in the light of a large suite of mitochondrial characters. Protein-coding gene sequences of C. columbianus were concatenated to form a supergene, which was analyzed phylogenetically with similar constructs from previously published avian genomes. Relationships within Anatidae and between the Anatidae and the galliform birds were addressed. Three independent phylogenetic methods confirmed traditional classifications and the existence of the Galloanseres clade.
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Affiliation(s)
- Julie Feinstein
- Ambrose Monell Collection for Molecular and Microbial Research, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA.
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48
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Lin G, Lo LC, Zhu ZY, Feng F, Chou R, Yue GH. The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:71-9. [PMID: 16228120 PMCID: PMC4273291 DOI: 10.1007/s10126-005-5051-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Accepted: 06/25/2005] [Indexed: 05/04/2023]
Abstract
We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.
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Affiliation(s)
- G. Lin
- />Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore
| | - L. C. Lo
- />Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Z. Y. Zhu
- />Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore
| | - F. Feng
- />Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore
| | - R. Chou
- />Agri-Food and Veterinary Authority of Singapore, Tower Block MND Complex, 069110 Singapore
| | - G. H. Yue
- />Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore
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49
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Shibusawa M, Nishibori M, Nishida-Umehara C, Tsudzuki M, Masabanda J, Griffin DK, Matsuda Y. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny. Cytogenet Genome Res 2004; 106:111-9. [PMID: 15218250 DOI: 10.1159/000078570] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Accepted: 01/07/2004] [Indexed: 11/19/2022] Open
Abstract
To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented.
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Affiliation(s)
- M Shibusawa
- Laboratory of Cytogenetics, Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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50
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van Tuinen M, Dyke GJ. Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol Phylogenet Evol 2004; 30:74-86. [PMID: 15022759 DOI: 10.1016/s1055-7903(03)00164-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
For more than a century, members of the traditional avian order Galliformes (i.e., pheasants, partridges, junglefowl, and relatives) have been among the most intensively studied birds, but still a comprehensive timeframe for their evolutionary history is lacking. Thanks to a number of recent cladistic interpretations for several galliform fossils, candidates now exist that can potentially be used as accurate internal calibrations for molecular clocks. Here, we describe a molecular timescale for Galliformes based on cytochrome b and ND2 using nine mostly internal fossil-based anchorpoints. Beyond application of calibrations spanning the entire evolutionary history of Galliformes, care was taken to investigate the effects of calibration choice, substitution saturation, and rate heterogeneity among lineages on divergence time estimation. Results show broad consistency in time estimation with five out of the nine total calibrations. Our divergence time estimates, based on these anchorpoints, indicate that the early history of Galliformes took place in the Cretaceous, including the origin of the basal-most megapode and perhaps cracid lineages, but that the remaining morphological diversification likely started in the earliest Tertiary. The multi-calibration/multi-genetic partition approach used here highlights the importance of understanding the genetic saturation, variation, and rate constancy spectra for the accurate calculation of divergence times by use of molecular clocks.
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Affiliation(s)
- Marcel van Tuinen
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.
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