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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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2
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Bai G, Yuan Q, Guo Q, Duan Y. Identification and phylogenetic analysis in Pterorhinuschinensis (Aves, Passeriformes, Leiothrichidae) based on complete mitogenome. Zookeys 2023; 1172:15-30. [PMID: 38312436 PMCID: PMC10838554 DOI: 10.3897/zookeys.1172.107098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/05/2023] [Indexed: 02/06/2024] Open
Abstract
The Black-throated Laughingthrush (Pterorhinuschinensis) is a bird belonging to the order Passeriformes and the family Leiothrichidae, and is found in Cambodia, China, Laos, Myanmar, Thailand and Vietnam. Pterorhinuschinensis was once classified as belonging to the genus Garrulax. However, recent research has reclassified it in the genus Pterorhinus. In this study, we sequenced and characterized the complete mitogenome of P.chinensis. The complete mitochondrial genome of P.chinensis is 17,827 bp in length. It consists of 13 PCGs, 22 tRNAs, two rRNAs, and two control regions. All genes are coded on the H-strand, except for one PCG (nad6) and eight tRNAs. All PCGs are initiated with ATG and stopped by five types of stop codons. Our comparative analyses show irregular gene rearrangement between trnT and trnP genes with another similar control region emerging between trnE and trnF genes compared with the ancestral mitochondrial gene order, called "duplicate CR gene order". The phylogenetic position of P.chinensis and phylogenetic relationships among members of Leiothrichidae are assessed based on complete mitogenomes. Phylogenetic relationships based on Bayesian inference and maximum likelihood methods showed that Garrulax and (Pterorhinus + Ianthocincla) formed a clade. Leiothrix and Liocichla also formed a clade. Our study provides support for the transfer of P.chinensis from Garrulax to Pterorhinus. Our results provide mitochondrial genome data to further understand the mitochondrial genome characteristics and taxonomic status of Leiothrichidae.
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Affiliation(s)
- Guirong Bai
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Qiang Guo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
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3
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Pham LD, Giang TTN, Nguyen VB, Pham TPM, Tran TTT, Nguyen TQC, Van Nguyen K, Do DN. The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam. Genes (Basel) 2023; 14:genes14051088. [PMID: 37239448 DOI: 10.3390/genes14051088] [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: 03/24/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken.
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Affiliation(s)
- Lan Doan Pham
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Thi Thanh Nhan Giang
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Van Ba Nguyen
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Thi Phuong Mai Pham
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Thi Thu Thuy Tran
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Thi Quynh Chau Nguyen
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Khanh Van Nguyen
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Thuyphuong, Bac Tuliem, Hanoi 100000, Vietnam
| | - Duy Ngoc Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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4
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Yuan Q, Guo Q, Cao J, Luo X, Duan Y. Description of the Three Complete Mitochondrial Genomes of Sitta (S. himalayensis, S. nagaensis, and S. yunnanensis) and Phylogenetic Relationship (Aves: Sittidae). Genes (Basel) 2023; 14:genes14030589. [PMID: 36980861 PMCID: PMC10047972 DOI: 10.3390/genes14030589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis, S. nagaensis, and S. yunnanensis), which were 16,822–16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister group of Troglodytidae, and the genus Sitta can be divided into three major clades. We demonstrated the phylogenetic relationships within the genus Sitta (S. carolinensis + ((S. villosa + S. yunnanensis) + (S. himalayensis + (S. europaea + S. nagaensis)))).
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Affiliation(s)
- Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Qiang Guo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jing Cao
- Administration of Zixi Mountain Provincial Nature Reserve, Chuxiong 675000, China
| | - Xu Luo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Correspondence: authors: (X.L.); (Y.D.)
| | - Yubao Duan
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
- Correspondence: authors: (X.L.); (Y.D.)
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5
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Complete mitogenome of common myna (Acridotheres tristis) – characterization and phylogenetic implications. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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6
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Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications. Animals (Basel) 2022; 13:ani13010096. [PMID: 36611705 PMCID: PMC9817927 DOI: 10.3390/ani13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.
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7
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Yang N, Tang C, Azimu W, Wang H, Tuersuntuoheti T, Yalimaimaiti Y, Kelimu N, Li HS, Wumaier A, Sun XY, Hao CS, Muhatai G. Phenotypic and genetic diversity of the Anjian chicken in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1003615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Anjian chicken is a local breed in Hotan, Xinjiang, China. Herein, we studied the morphological characteristics and genetic diversity of the Anjian chicken population. The findings of this study could inform the genetic improvement strategy of this breed. Phenotypic characteristics investigated included the diversity in the general appearance, feather color, and crowing length of the Anjian cocks. The population structure of the Anjian chicken and its relationship with other chicken breeds were also assessed based on mitochondrial DNA (mtDNA) D-loop sequence analysis. Phenotypically, the feather color of the Anjian chicken varied considerably. The sequence diversity analysis revealed the following: nucleotide diversity (Pi) was 0.00618, haplotype diversity (Hd) was 0.776, the average number of nucleotide differences (k) was 7.631, and Tajima’s (D) was −0.00407, indicating that Anjian chicken is moderately genetically diverse. Further phylogenetic analysis revealed that the Anjian chicken breed has 10 haplotypes clustered into two branches. Genetic distance and median network analysis showed that the mtDNA D-loop sequence of the Anjian chicken was distributed in many different clusters of the tree. These data demonstrate that even though the Anjian chicken mainly originated from red jungle fowl, it has multiple maternal origins. In conclusion, the Anjian chicken is highly genetically diverse.
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8
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Jia Y, Qiu G, Cao C, Wang X, Jiang L, Zhang T, Geng Z, Jin S. Mitochondrial genome and phylogenetic analysis of Chaohu duck. Gene 2022; 851:147018. [DOI: 10.1016/j.gene.2022.147018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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9
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Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, Prada CF. Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class. Sci Rep 2022; 12:5479. [PMID: 35361853 PMCID: PMC8971445 DOI: 10.1038/s41598-022-09512-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.
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Affiliation(s)
- Paula Montaña-Lozano
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Manuela Moreno-Carmona
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Mauricio Ochoa-Capera
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Natalia S Medina
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia.
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Kanakachari M, Rahman H, Chatterjee RN, Bhattacharya TK. Signature of Indian native chicken breeds: a perspective. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2026201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - H. Rahman
- Molecular Genetics and Breeding Unit, South Asia Regional Office, New Delhi, International Livestock Research Institute (ILRI), Nairobi, Kenya
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11
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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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12
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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13
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Kundu S, Alam I, Maheswaran G, Tyagi K, Kumar V. Complete Mitochondrial Genome of Great Frigatebird (Fregata minor): Phylogenetic Position and Gene Rearrangement. Biochem Genet 2021; 60:1177-1188. [PMID: 34800202 DOI: 10.1007/s10528-021-10156-6] [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: 09/06/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022]
Abstract
The complete mitogenome sequence of the Great Frigatebird, Fregata minor was sequenced for the first time in this study. The mitogenome (16,899 bp) comprises of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The mitogenome was AT-rich (55.60%) with 11 overlapping and 18 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. A maximum-likelihood phylogeny of concatenated PCGs resulted in a well-resolved phylogeny of all the species of Suliformes and illuminates the sister relationship of F. minor with F. magnificens. The present mitogenome-based phylogeny clearly enlightens the evolutionary position of Suliformes and Pelecaniformes species. Unique tandem repeats were identified in both F. minor and F. magnificens, which can be employed as a species-specific marker. To illuminate the population structure of this migratory seabirds, the present study advocate more sampling and the generation of additional molecular data to clarify their genetic diversity. The present study also rejects an earlier hypothesis on the mitochondrial gene order of Suliformes and corroborated the typical avian gene order in frigatebirds.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India
| | - Imran Alam
- Bird Section, Zoological Survey of India, Kolkata, 700053, India
| | | | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India.
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14
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Urantówka AD, Kroczak A, Strzała T, Zaniewicz G, Kurkowski M, Mackiewicz P. Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration. Genome Biol Evol 2021; 13:6357707. [PMID: 34432018 PMCID: PMC8435663 DOI: 10.1093/gbe/evab193] [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] [Accepted: 08/15/2021] [Indexed: 11/25/2022] Open
Abstract
The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland.,Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| | - Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Grzegorz Zaniewicz
- Department of Vertebrate Ecology and Zoology, Avian Ecophysiology Unit, University of Gdańsk, Poland
| | - Marcin Kurkowski
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
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15
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Thintip J, Ahmad SF, Singchat W, Laopichienpong N, Suntronpong A, Panthum T, Ho My Nguyen D, Ariyaraphong N, Muangmai N, Suksawet W, Duengkae P, Srikulnath K. Mitochondrial genome of bronze-winged jacana ( Metopidius indicus, Latham 1790). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2251-2253. [PMID: 34377794 PMCID: PMC8330700 DOI: 10.1080/23802359.2021.1945971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We reported the mitochondrial genome (mitogenome) of bronze-winged jacana (Metopidius indicus, Latham 1790). The circular mitogenome was 17,208 base pairs (bp) in length, containing 13 protein-coding genes, two rRNAs, 22 tRNAs, and a non-coding control region. A DNA spacer 109 bp long was also detected between ND5 and Cytb. Phylogenetic analysis indicated that M. indicus was more closely related with the genera Himantopus, Jacana and Hydrophasianus. This annotated mitogenome reference can be utilized as a data resource for comparative mitogenomics of waders or shorebirds, with possible use in ecological and evolutionary studies.
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Affiliation(s)
- Jitmat Thintip
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Dung Ho My Nguyen
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Nattakan Ariyaraphong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Warong Suksawet
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand (CAST NAR, NRU-KU, Thailand).,Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, Thailand
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16
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Altgilbers S, Klein S, Dierks C, Weigend S, Kues WA. Cultivation and characterization of primordial germ cells from blue layer hybrids (Araucana crossbreeds) and generation of germline chimeric chickens. Sci Rep 2021; 11:12923. [PMID: 34155221 PMCID: PMC8217269 DOI: 10.1038/s41598-021-91490-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/21/2021] [Indexed: 11/29/2022] Open
Abstract
The chicken (Gallus gallus) is one of the most common and widespread domestic species, with an estimated total population of 25 billion birds worldwide. The vast majority of chickens in agriculture originate from hybrid breeding programs and is concentrated on few commercially used high performance lines, whereas numerous local and indigenous breeds are at risk to become extinct. To preserve the genomic resources of rare and endangered chicken breeds innovative methods are necessary. Here, we established a solid workflow for the derivation and biobanking of chicken primordial germ cells (PGCs) from blue layer hybrids. To achieve this, embryos of a cross of heterozygous blue egg layers were sampled to obtain blood derived and gonadal male as well as female PGCs of different genotypes (homozygous, heterozygous and nullizygous blue-allele bearing). The total efficiency of established PGC lines was 45% (47/104) within an average of 49 days until they reached sufficient numbers of cells for cryopreservation. The stem-cell character of the cultivated PGCs was confirmed by SSEA-1 immunostaining, and RT-PCR amplification of the pluripotency- and PGC-specific genes cPOUV, cNANOG, cDAZL and CVH. The Sleeping Beauty transposon system allowed to generate a stable integration of a Venus fluorophore reporter into the chicken genome. Finally, we demonstrated that, after re-transfer into chicken embryos, Venus-positive PGCs migrated and colonized the forming gonads. Semen samples of 13 raised cell chimeric roosters were analyzed by flow cytometry for the efficiency of germline colonization by the transferred PGCs carrying the Venus reporter and their proper differentiation into vital spermatids. Thus, we provide a proof-of-concept study for the potential use of PGCs for the cryobanking of rare breeds or rare alleles.
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Affiliation(s)
- Stefanie Altgilbers
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Sabine Klein
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Claudia Dierks
- Department of Genetic Ressources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Steffen Weigend
- Department of Genetic Ressources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Wilfried A Kues
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany.
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17
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Dey P, Sharma SK, Sarkar I, Ray SD, Pramod P, Kochiganti VHS, Quadros G, Rathore SS, Singh V, Singh RP. Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis. PLoS One 2021; 16:e0241098. [PMID: 33836001 PMCID: PMC8034733 DOI: 10.1371/journal.pone.0241098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/01/2021] [Indexed: 11/19/2022] Open
Abstract
Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.
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Affiliation(s)
- Prateek Dey
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | - Sanjeev Kumar Sharma
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | - Indrani Sarkar
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | - Swapna Devi Ray
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | - Padmanabhan Pramod
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | | | - Goldin Quadros
- Wetland Ecology Division, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
| | | | - Vikram Singh
- Central University of Himachal Pradesh, Dharamshala, India
| | - Ram Pratap Singh
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, Tamil Nadu, India
- Department of Life Science, Central University of South Bihar, Gaya, India
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18
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Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens. Animals (Basel) 2021; 11:ani11030825. [PMID: 33804055 PMCID: PMC8001891 DOI: 10.3390/ani11030825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/06/2022] Open
Abstract
Simple Summary Mitochondria are commonly known as “the powerhouse of the cell”, influencing the fitness, lifespan and metabolism of eukaryotic organisms. In our study we examined mitochondrial and nuclear genomic diversity in two high yielding strains of laying hens. We tested if the mitochondrial genome affects functional traits such as body weight and phosphorus utilization. We discovered a surprisingly low mitochondrial genetic diversity and an unequal distribution of the haplotypes among both strains, leading to limitations of robust links to phenotypic traits. In contrast, we found similar levels of nuclear genome diversity in both strains. Our study explores the potential influence of the mitochondrial genome on phenotypic traits and thus contributes to a better understanding of the function of this organelle in laying hens. Further, we focus on its usefulness as a genetic marker, which is often underestimated in breeding approaches, given the different inheritance mechanism compared to the nuclear genome. Abstract Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.
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19
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Barzegar S, Swick RA, Kheravii SK, Choct M, Wu SB. Peroxisome proliferator-activated receptor gamma upregulation and dietary fat levels in laying hens. Poult Sci 2021; 100:101049. [PMID: 33744616 PMCID: PMC8005814 DOI: 10.1016/j.psj.2021.101049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/28/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
The present study was conducted to investigate the effect of feeding the different levels of the dietary fat on the expression of genes encoding proteins involving energy metabolism, oxidative phosphorylation, and lipid synthesis including peroxisome proliferator-activated receptor gamma (PPARγ) of laying hens in the intestine. Birds fed diets with 3 levels of fat, that is, low (LF), medium (MF), and high fat (HF) were reared from 22 to 42 wk of age. Jejunum tissue was collected at week 42 for gene expression analysis. Dietary fat content as ether extract, net energy to AME ratio, and CP content of 3 treatment groups were as follows: LF: 25, 0.735, 187 (g/kg, DM); MF: 61, 0.739, 185 (g/kg, DM); HF: 73, 0.752, 181 (g/kg, DM). The BW, fat pad weight (g), fat pad–to–BW ratio (%) was the same for all the treatments (P > 0·05). Birds fed a diet containing HF increased the AME daily intake per metabolic BW (BW0.75) (P < 0.05). The expression of jejunal PPARγ was increased in the birds fed MF than that fed LF (P < 0.05). Dietary fat level did not affect the expression of other genes: protein kinase AMP-activated noncatalytic subunit gamma 2, NADH dehydrogenase subunit 2, succinate dehydrogenase complex flavoprotein subunit A, ubiquinol-cytochrome c reductase Rieske iron-sulfur polypeptide 1, cytochrome c oxidase subunit III, ATP synthase subunit alpha, avian adenine nucleotide translocator, and acetyl-CoA carboxylase alpha (P > 0·05). The mitochondrial count per cell showed no difference among the 3 groups with different dietary treatments (P > 0·05). The results suggest that PPARγ may be important to the energy expenditure during nutrient absorption, digestion, and metabolism, and respiratory chain complexes, and other genes involving mitochondrial energy metabolism and lipogenesis may be less responsive to dietary treatment.
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Affiliation(s)
- Shahram Barzegar
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Robert A Swick
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Sarbast K Kheravii
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Mingan Choct
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Shu-Biao Wu
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia.
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20
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Peng SY, Lu MX, Wang M, Wang L, Wang CQ, Wang JR, Zhang YF, Zhang HJ, Li J. The complete mitochondrial genome of Huainan partridge chicken ( Gallus gallus). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:99-101. [PMID: 33537415 PMCID: PMC7832493 DOI: 10.1080/23802359.2020.1847616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Huainan Partridge chicken is one of the indigenous chicken breeds in China. In this study, the first complete mitochondrial DNA (mtDNA) sequence of Huainan Partridge chicken had been obtained using PCR amplification, sequencing and assembling. The mitogenome of Huainan Partridge chicken is 16785 bp in length, including a control region (D-loop), 13 protein-coding genes, 22 transfer genes and 2 ribosomal genes. The base composition of the complete mtDNA sequence is 30.27% for A, 23.73% for T, 13.50%for G, 32.50% for C. This study will provide reference for the phylogenetic analysis of Huainan Partridge chicken.
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Affiliation(s)
- Shu-Ying Peng
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Ming-Xin Lu
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Min Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Ling Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Cheng-Qiao Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Jing-Ru Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Yun-Fang Zhang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Hai-Jun Zhang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Jun Li
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, P.R. China
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21
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Jia X, Lu J, Tang X, Fan Y, Ge Q, Gao Y. Characterization and phylogenetic evolution of mitochondrial genome in Tibetan chicken. Anim Biotechnol 2020; 33:1371-1377. [PMID: 33347342 DOI: 10.1080/10495398.2020.1858846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The objective of this study was to characterize mitochondrial genome and investigate phylogenetic evolution in Tibetan chicken. In this study, four haplotypes were identified based on D-loop sequencing in Tibetan chicken (n = 40), and each representative of four haplotypes was selected for total mitochondrial genome sequencing and analyzed together with published mitochondrial genome data of red jungle fowl. Four haplotypes belonged to three previously published clades, i.e., Clade A, clade B and clade E. Based on D-loop sequencing data, the average haplotype diversity and nucleotide diversity were 0.658 ± 0.065 and 0.00442 ± 0.00094, respectively. The mitochondrial genome of Tibetan chicken is 16,785 bp in size, consisting of 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein-coding genes and one non-coding control region (CR). Compared with the mitochondrial genome, a phylogenetic tree based on the D-loop sequence had a messy distribution, and no breed cluster pattern was observed in Tibetan chicken. The results indicate that Tibetan chicken populations in our study have relatively low nucleotide and haplotype diversity and likely share multiple maternal lineages. The D-loop sequence has limited power for the resolution of phylogenetic relationships in comparison with the complete mitochondrial genome.
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Affiliation(s)
- Xiaoxu Jia
- Jiangsu Institute of Poultry Science, Yangzhou, PR China
| | - Junxian Lu
- Jiangsu Institute of Poultry Science, Yangzhou, PR China
| | - Xiujun Tang
- Jiangsu Institute of Poultry Science, Yangzhou, PR China.,Nanjing Agricultural University, Nanjing, PR China
| | - Yanfeng Fan
- Jiangsu Institute of Poultry Science, Yangzhou, PR China
| | - Qinglian Ge
- Jiangsu Institute of Poultry Science, Yangzhou, PR China
| | - Yushi Gao
- Jiangsu Institute of Poultry Science, Yangzhou, PR China
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22
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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23
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Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H. Sequence and organisation of the mitochondrial genome of Japanese Grosbeak ( Eophona personata), and the phylogenetic relationships of Fringillidae. Zookeys 2020; 995:67-80. [PMID: 33281468 PMCID: PMC7688617 DOI: 10.3897/zookeys.995.34432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial DNA is a useful molecular marker for phylogenetic and evolutionary analysis. In the current study, we determined the complete mitochondrial genome of Eophona personata, the Japanese Grosbeak, and the phylogenetic relationships of E. personata and 16 other species of the family Fringillidae based on the sequences of 12 mitochondrial protein-coding genes. The mitochondrial genome of E. personata consists of 16,771 base pairs, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region. Analysis of the base composition revealed an A+T bias, a positive AT skew and a negative GC skew. The mitochondrial gene order and arrangement in E. personata was similar to the typical avian mitochondrial gene arrangement. Phylogenetic analysis of 17 species of Fringillidae, based on Bayesian inference and Maximum Likelihood (ML) estimation, showed that the genera Coccothraustes and Hesperiphona are closely related to the genus Eophona, and further showed a sister-group relationship of E. personata and E. migratoria.
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Affiliation(s)
- Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Shi Feng
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
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24
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Improving read alignment through the generation of alternative reference via iterative strategy. Sci Rep 2020; 10:18712. [PMID: 33127969 PMCID: PMC7599232 DOI: 10.1038/s41598-020-74526-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/30/2020] [Indexed: 11/08/2022] Open
Abstract
There is generally one standard reference sequence for each species. When extensive variations exist in other breeds of the species, it can lead to ambiguous alignment and inaccurate variant calling and, in turn, compromise the accuracy of downstream analysis. Here, with the help of the FPGA hardware platform, we present a method that generates an alternative reference via an iterative strategy to improve the read alignment for breeds that are genetically distant to the reference breed. Compared to the published reference genomes, by using the alternative reference sequences we built, the mapping rates of Chinese indigenous pigs and chickens were improved by 0.61-1.68% and 0.09-0.45%, respectively. These sequences also enable researchers to recover highly variable regions that could be missed using public reference sequences. We also determined that the optimal number of iterations needed to generate alternative reference sequences were seven and five for pigs and chickens, respectively. Our results show that, for genetically distant breeds, generating an alternative reference sequence can facilitate read alignment and variant calling and improve the accuracy of downstream analyses.
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25
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Jing M, Yang H, Li K, Huang L. Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics. Genet Mol Biol 2020; 43:e20190392. [PMID: 33026411 PMCID: PMC7539371 DOI: 10.1590/1678-4685-gmb-2019-0392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/13/2020] [Indexed: 12/04/2022] Open
Abstract
Coraciiformes contains more than 200 species with great differences on external
morphology and life-style. The evolutionary relationships within Coraciiformes
and the phylogenetic placement of Coraciiformes in Aves are still questioned.
Mitochondrial genome (mitogenome) sequences are popular markers in molecular
phylogenetic studies of birds. This study presented the genome characteristics
of three new mitogenomes in Coraciiformes and explored the phylogenetic
relationships among Coraciiformes and other five related orders with mitogenome
data of 30 species. The sizes of three mitogenomes were 17,383 bp
(Alcedo atthis), 17,892 bp (Halcyon
smyrnensis) and 17,223 bp (Megaceryle lugubris).
Each mitogenome contained one control region and 37 genes that were common in
vertebrate mitogenomes. The organization of three mitogenomes was identical to
the putative ancestral gene order in Aves. Among 13 available Coraciiform
mitogenomes, 12 protein coding genes showed indications of negative selection,
while the MT-ND6 presented sign of positive selection or relaxed purifying
selection. The phylogenetic results supported that Upupidae and Bucerotidae
should be separated from Coraciiformes, and that Coraciiformes is more closely
related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our
study provide valuable data for further phylogenetic investigation of
Coraciiformes.
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Affiliation(s)
- Meidong Jing
- Nantong University, School of Life Sciences, Nantong, Jiangsu, P. R. China
| | - Huanhuan Yang
- Ludong University, School of Life Sciences, Yantai, Shandong, P. R. China
| | - Kai Li
- Nantong Xingdong International Airport, Nantong, Jiangsu, P. R. China
| | - Ling Huang
- Nantong University, School of Life Sciences, Nantong, Jiangsu, P. R. China
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26
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Cicero C, Mason NA, Benedict L, Rising JD. Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows ( Aimophila and Peucaea, Passerellidae). PeerJ 2020; 8:e9249. [PMID: 32596039 PMCID: PMC7307569 DOI: 10.7717/peerj.9249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Nicholas A Mason
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America.,Current affiliation: Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Lauryn Benedict
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States of America
| | - James D Rising
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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27
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Wang E, Zhang D, Braun MS, Hotz-Wagenblatt A, Pärt T, Arlt D, Schmaljohann H, Bairlein F, Lei F, Wink M. Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds? Sci Rep 2020; 10:9290. [PMID: 32518318 PMCID: PMC7283232 DOI: 10.1038/s41598-020-66287-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm’s Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.
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Affiliation(s)
- Erjia Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Dezhi Zhang
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China
| | - Markus Santhosh Braun
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management Core Facility, German Cancer Research Center, Heidelberg University, Heidelberg, Germany
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Debora Arlt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Heiko Schmaljohann
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,Institute for Biology und Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Franz Bairlein
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany
| | - Fumin Lei
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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28
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Kumar A, Dewan S, Lochan R, Sharma DK. Spatial genetic structure of black francolin ( Francolinus francolinus asiae) in the North-Western Himalayan region based on mitochondrial control region. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:163-170. [PMID: 32340511 DOI: 10.1080/24701394.2020.1757664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Due to specific habitat preferences and behavioural limitations, black francolin is not uniformly distributed across the northwestern Himalayan landscape, rather is confined to certain land mosaic. The habitable zones are further reduced due to several manmade threats as logging and forest fire leading to sparse distribution. Overall 54 samples were used for partial sequence analysis of mitochondrial control region. A well evident divergence pattern was observed as individuals collected from low altitude, terrai region significantly distanced from high altitude sampled individuals. Also, the individuals at lower elevation sites exhibited higher genetic diversity in comparison to the samples collected at higher elevations. This indicates that patchy distribution and low dispersal rate have resulted in fine-scale patterns of genetic diversity among the black francolin population. Further, habitat loss and forest fragmentation could lead to more small and isolated populations that could suffer from reduced genetic diversity and may be higher extinction rates.
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Affiliation(s)
- Anand Kumar
- Department of Zoology, HNB Garhwal University, Badshahithaul, New Tehri, India
| | - Saurabh Dewan
- Department of Zoology and Biotechnology, HNB Garhwal University, Srinagar, India
| | - Rajeev Lochan
- Department of Zoology and Biotechnology, HNB Garhwal University, Srinagar, India
| | - Dinesh K Sharma
- Department of Zoology, HNB Garhwal University, Badshahithaul, New Tehri, India
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29
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Perktaş U, Groth JG, Barrowclough GF. Phylogeography, Species Limits, Phylogeny, and Classification of the Turacos (Aves: Musophagidae) Based on Mitochondrial and Nuclear DNA Sequences. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3949.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Utku Perktaş
- Division of Vertebrate Zoology (Ornithology), American Museum of Natural History
| | - Jeff G. Groth
- Division of Vertebrate Zoology (Ornithology), American Museum of Natural History
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30
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Li H, Hu B, Luo Q, Hu S, Luo Y, Zhao B, Gan Y, Li Y, Shi M, Nie Q, Zhang D, Zhang X. Runting and Stunting Syndrome Is Associated With Mitochondrial Dysfunction in Sex-Linked Dwarf Chicken. Front Genet 2020; 10:1337. [PMID: 32010193 PMCID: PMC6978286 DOI: 10.3389/fgene.2019.01337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 12/09/2019] [Indexed: 11/13/2022] Open
Abstract
Runting and stunting syndrome (RSS) in chicken are commonly known as “frozen chicken.” The disease is characterized by lower body weight and slow growth and the incidence rate is widely 5%–20% in sex-linked dwarf (SLD) chickens. However, the etiology of RSS in chickens has plagued researchers for several decades. In this study, histopathology studies demonstrated that the hepatocytes of the RSS chickens contain many mitochondria with damaged and outer and inner membrane along with vacuolar hydropic degeneration. No mtDNA mutation was detected, but our microarray data showed that RSS chickens exhibited abnormal expression of genes, many of which are involved in oxidative phosphorylation (OXPHOS) and fatty acid metabolism. In particular, nuclear gene IGF2BP3 was upregulated in RSS chickens' liver cells. The abnormal expression of these genes is likely to impair the OXPHOS, resulting in reduced ATP synthesis in the hepatocytes of the RSS chickens, which may in turn leads to poor weight gain and retarded growth or stunting of chicks. Our findings suggest that mitochondria dysfunction rather than chronic inflammation is responsible for the reduced growth and RSS in SLD chickens. Mutations in GHR have been shown to compromise mitochondrial function in SLD chickens. Since the mitochondrial damage in the RSS chicken is more severe, we suggest that extra genes are likely to be affected to exacerbate the phenotype.
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Affiliation(s)
- Hongmei Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Bowen Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qingbin Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shuang Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yabiao Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Bojing Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yanmin Gan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ying Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Meiqing Shi
- Division of Immunology, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, College Park, MD, United States
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Dexiang Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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31
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Do SQ, Nguyen LTP, Nguyen TH, Nguyen TQ. Genomic characterization of three Vietnamese indigenous chicken varieties using mitochondrial D-loop sequences. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2019-0025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of three Vietnamese indigenous chicken varieties, including Mong Tien Phong, To, and Sau Ngon, were analyzed to access genetic diversity and the maternal lineages of origin. A 525 bp fragment of the mtDNA D-loop region was sequenced from a total of 61 chickens of the three varieties. A neighbor-joining phylogenetic tree was assembled from the haplotypes obtained and reference sequences of mtDNA D-loop sequences of Red Junglefowl and domestic chickens from National Center for Biotechnology Information database. Genetic diversity indices and analysis of molecular variance were performed. Evaluation of genetic relationships between the three varieties was carried out with pairwise fixation index (FST). In total, 16 haplotypes were identified in the chickens studied. These haplotypes were classified in three haplogroups (A, B, and E) with the majority grouped in haplogroup B and haplogroup E. All three chicken varieties studied were distributed into 2–3 haplogroups and all three haplogroups found in this study are also represented by Red Junglefowl. In conclusion, all three Vietnamese indigenous chicken varieties have likely originated from multiple maternal lineages and potentially descended from the Red Junglefowl.
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Affiliation(s)
- Son Quang Do
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi 12406, Vietnam
| | - Lan Thi Phuong Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi 12406, Vietnam
| | - Thinh Hoang Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi 12406, Vietnam
| | - Trung Quoc Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi 12406, Vietnam
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32
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Sha Y, Gao C, Liu M, Zhao S. Evaluation of the genetic diversity of six Chinese indigenous chickens. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:1566-1572. [PMID: 32054196 PMCID: PMC7463083 DOI: 10.5713/ajas.19.0606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/30/2019] [Indexed: 11/27/2022]
Abstract
Objective The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China. Methods In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds. Results Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious. Conclusion The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.
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Affiliation(s)
- Yuzhu Sha
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Meimei Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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33
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Huang Y, Lu W, Ji J, Zhang X, Zhang P, Chen W. Heteroplasmy in the complete chicken mitochondrial genome. PLoS One 2019; 14:e0224677. [PMID: 31703075 PMCID: PMC6839896 DOI: 10.1371/journal.pone.0224677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/19/2019] [Indexed: 12/16/2022] Open
Abstract
Chicken mitochondrial DNA is a circular molecule comprising ~16.8 kb. In this study, we used next-generation sequencing to investigate mitochondrial heteroplasmy in the whole chicken mitochondrial genome. Based on heteroplasmic detection thresholds at the 0.5% level, 178 cases of heteroplasmy were identified in the chicken mitochondrial genome, where 83% were due to nucleotide transitions. D-loop regionwas hot spot region for mtDNA heteroplasmy in the chicken since 130 cases of heteroplasmy were located in these regions. Heteroplasmy varied among intraindividual tissues with allele-specific, position-specific, and tissue-specific features. Skeletal muscle had the highest abundance of heteroplasmy. Cases of heteroplasmy at mt.G8682A and mt.G16121A were validated by PCR-restriction fragment length polymorphism analysis, which showed that both had low ratios of heteroplasmy occurrence in five natural breeds. Polymorphic sites were easy to distinguish. Based on NGS data for crureus tissues, mitochondrial mutation/heteroplasmy exhibited clear maternal inheritance features at the whole mitochondrial genomic level. Further investigations of the heterogeneity of the mt.A5694T and mt.T5718G transitions between generations using pyrosequencing based on pedigree information indicated that the degree of heteroplasmy and the occurrence ratio of heteroplasmy decreased greatly from the F0 to F1 generations in the mt.A5694T and mt.T5718G site. Thus, the intergenerational transmission of heteroplasmy in chicken mtDNA exhibited a rapid shift toward homoplasmy within a single generation. Our findings indicate that heteroplasmy is a widespread phenomenon in chicken mitochondrial genome, in which most sites exhibit low heteroplasmy and the allele frequency at heteroplasmic sites changes significantly during transmission events. It suggests that heteroplasmy may be under negative selection to some degree in the chicken.
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Affiliation(s)
- Yanqun Huang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Weiwei Lu
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiefei Ji
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangli Zhang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Pengfei Zhang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wen Chen
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail:
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34
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Wang M, Wang L, Wang CQ, Wan SH, Wang H, Sun JY, Tang JQ, Zhang XC, Zhang HJ, Li J, Peng SY. Complete mitochondrial genome of the Partridge Shank chicken (Galliformes: Phasianidae). Mitochondrial DNA B Resour 2019; 4:3298-3300. [PMID: 33365964 PMCID: PMC7707235 DOI: 10.1080/23802359.2019.1673232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Affiliation(s)
- Min Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Ling Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Cheng-Qiao Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Sheng-Hao Wan
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Hu Wang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Jie-Yu Sun
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Jian-Qiang Tang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Xiao-Chun Zhang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Hai-Jun Zhang
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Jun Li
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
| | - Shu-Ying Peng
- Human and Animal Genetics Laboratory, School of Life Science, Huaibei Normal University, Huaibei, Anhui, People’s Republic of China
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35
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Characterization of the complete mitochondrial genome of Rhinogobius leavelli (Perciformes: Gobiidae: Gobionellinae) and its phylogenetic analysis for Gobionellinae. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-018-00189-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Mol Phylogenet Evol 2019; 130:132-142. [DOI: 10.1016/j.ympev.2018.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/11/2018] [Accepted: 10/09/2018] [Indexed: 11/23/2022]
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37
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Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, Mackiewicz P. New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region. Mol Biol Evol 2018; 35:2989-3009. [PMID: 30304531 PMCID: PMC6278868 DOI: 10.1093/molbev/msy189] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
| | | | | | | | - Julie Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Barry Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
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Thakur M, Fernandes M, Sathyakumar S, Singh SK, Vijh RK, Han J, Wu DD, Zhang YP. Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India. PLoS One 2018; 13:e0204351. [PMID: 30307994 PMCID: PMC6188471 DOI: 10.1371/journal.pone.0204351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022] Open
Abstract
Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are
believed to be in genetic endangerment due to introgression of domestic genes
through opportunistic matings with domestic or feral chickens. Previous studies
from India reported rare hybridization of RJFs in the wild. However, RJF
population genetic structure, pattern of gene flow and their admixture with DC
populations are poorly understood at the landscape level. We conducted this
study with a large sample size, covering the predicted natural distribution
range of RJFs in India. We documented strong evidence of directional gene flow
from DCs to free-ranging wild RJFs, with the Northeastern RJF population
exhibiting the most genetic variants in their nuclear and mitochondrial genomes,
indicating it to be the ancestral population from which early radiation may have
occurred. The results provide evidence that landscape features do not act as a
barrier to gene flow and the distribution pattern could not be explored due to
physical sharing or exchange of wild birds in the past when forests were
continuous across RJF range in India.
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Affiliation(s)
- Mukesh Thakur
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
- * E-mail: (MT); (SS)
| | - Merwyn Fernandes
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Sambandam Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- * E-mail: (MT); (SS)
| | - Sujeet K. Singh
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), G.T. Road Bye
Pass, Near Basant Vihar, Karnal, Haryana, India
| | - Jianlin Han
- CAAS—ILRI Joint Laboratory on Livestock and Forage Genetic Resources,
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS),
Beijing, P.R. China
- International Livestock Research Institute (ILRI), Nairobi,
Kenya
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
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39
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Zhang T, Liu H, Yang LK, Yin YJ, Lu HZ, Wang L. The complete mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken. Br Poult Sci 2018; 59:618-623. [PMID: 30130415 DOI: 10.1080/00071668.2018.1514581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
1. The objectives of the current study were to investigate the mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken, and provide molecule base to preserve and explore the specific chicken strain. 2. Based on sequencing and clustering, the complete mitochondrial DNA map and sequences of Lueyang black-bone chicken were revealed, and two phylogenetic trees of Lueyang black-bone chickens based on D-loop sequences and the mitochondrial genome were constructed. 3. The results showed that the complete mitochondrial genome of Lueyang black-bone chickens is 16,784bp in size, consisting of 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and one non-coding control region. The base composition of the complete mtDNA sequence is 30.28% for A, 23.78% for T, 32.42% for C, 13.52% for G. Additionally, 10 haplotypes of D-loop sequences in 32 Lueyang black-bone chickens were detected, which were distributed into 4 clades (A, B, C and E). 4. It was concluded that genetic diversity is wide in Lueyang black-bone chickens, and this strain has multiple maternal origins from different regions in China and neighbouring regions.
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Affiliation(s)
- T Zhang
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
| | - H Liu
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
| | - L-K Yang
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
| | - Y-J Yin
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
| | - H-Z Lu
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
| | - L Wang
- a School of Biological Science and Engineering , Shaanxi University of Technology , Hanzhong , China
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40
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Lima NCB, Soares AER, Almeida LGDP, Costa IRD, Sato FM, Schneider P, Aleixo A, Schneider MP, Santos FR, Mello CV, Miyaki C, Vasconcelos ATR, Prosdocimi F. Comparative mitogenomic analyses of Amazona parrots and Psittaciformes. Genet Mol Biol 2018; 41:593-604. [PMID: 30235395 PMCID: PMC6136379 DOI: 10.1590/1678-4685-gmb-2017-0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.
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Affiliation(s)
- Nicholas Costa Barroso Lima
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.,Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | | | - Igor Rodrigues da Costa
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Midori Sato
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Patricia Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Belém, PA, Brazil
| | - Maria Paula Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fabrício R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Cristina Miyaki
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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41
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Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations. J Genet 2018; 96:959-968. [PMID: 29321355 DOI: 10.1007/s12041-017-0860-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and four commercial egg line strains (two Anak titan, one Giriraja and one Yaffa) as out-groups were analysed. Thirty-one haplotypes (28 from Nigerian chickens and three from commercial strains) and 34 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.39 ± 0.05 and 0.02 ± 0.02, respectively. Majority of Nigerian chicken haplotypes observed were grouped into haplogroup D which originated from Indian subcontinent, suggesting a single maternal lineage. Genetic variation within and between populations accounted for 97.30 and 2.70% of the total genetic variation, respectively, which is in agreement with a recent and maternal founding effect. High number (4) of negatively selected sites observed based on single likelihood ancestral counting (SLAC) model indicated that the sampled Nigerian chicken populations were undergoing purifying selection. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably paveway for further evaluation studies, preservation and improvement of Nigerian chickens as genetic resources towards ensuring food security.
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42
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Poulsen JY, Miller MJ, Sado T, Hanel R, Tsukamoto K, Miya M. Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders. PLoS One 2018; 13:e0199982. [PMID: 30044814 PMCID: PMC6059418 DOI: 10.1371/journal.pone.0199982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 11/24/2022] Open
Abstract
Deep-sea midwater "saccopharyngiform" eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the general anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as "Leptocephalus holti", which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial gene orders.
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Affiliation(s)
- Jan Y. Poulsen
- Department of Fish and Shellfish, Greenland Institute of Natural Resources, Kivioq, Nuuk, Greenland
- Fish Section, Australian Museum, Sydney NSW, Australia
| | - Michael J. Miller
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | | | - Katsumi Tsukamoto
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Masaki Miya
- Thunen-Institute of Fisheries Ecology, Hamburg, Germany
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43
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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44
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The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes. Genes Genomics 2018; 40:151-165. [PMID: 29892923 DOI: 10.1007/s13258-017-0617-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772 bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.
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45
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Dong Y, Li B, Zhou L. A new insight into the classification of dusky thrush complex: bearings on the phylogenetic relationships within the Turdidae. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1245-1252. [PMID: 29457530 DOI: 10.1080/24701394.2018.1439026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp. The mtDNAs are circular molecules, containing the 37 typical genes, with an identical gene order and arrangement as those of other Turdidae. The ATG and TAA, respectively, are observed the most commonly start and stop codon. Most of the tRNA could be folded into the canonical cloverleaf secondary structure except for tRNASer (AGY) and tRNALeu (CUN), which lose 'DHU' arm. The control region presented a higher A + T content than the average value for the whole mitogenome. The phylogenetic trees reconstructed by the concatenated nucleotide sequences of mtDNA genes (Cyt b, ND2 and COI) indicate the Dusky thrush complex cannot be divided into two species, but the relationships between Dusky thrush subspecies still need additional study. This study improves our understanding of mitogenomic structure and evolution of the Dusky thrush complex, which can provide further insights into our understanding of phylogeny and taxonomy in Turdidae.
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Affiliation(s)
- Yuanqiu Dong
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
| | - Bo Li
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
| | - Lizhi Zhou
- a School of Resources and Envirodnmental Engineering , Anhui University , Hefei , China.,b Anhui Biodiversity Information Center , Hefei , Anhui , China
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46
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Caparroz R, Rocha AV, Cabanne GS, Tubaro P, Aleixo A, Lemmon EM, Lemmon AR. Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes. Mol Biol Rep 2018; 45:279-285. [PMID: 29455315 DOI: 10.1007/s11033-018-4160-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/06/2018] [Indexed: 11/27/2022]
Abstract
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.
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Affiliation(s)
- Renato Caparroz
- Departamento de Genética e Morfologia, Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal, CEP 70910-900, Brazil.
| | - Amanda V Rocha
- Departamento de Genética e Morfologia, Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal, CEP 70910-900, Brazil
| | - Gustavo S Cabanne
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Ciudad de Buenos Aires, Argentina
| | - Pablo Tubaro
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Ciudad de Buenos Aires, Argentina
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4102, USA
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Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis. Genes Genomics 2018; 40:1137-1148. [PMID: 30315517 DOI: 10.1007/s13258-018-0669-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/07/2018] [Indexed: 10/18/2022]
Abstract
Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A + T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.
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48
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Molecular identification of species and production origins of edible bird's nest using FINS and SYBR green I based real-time PCR. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.07.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Seligmann H, Raoult D. Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA. Front Microbiol 2018; 9:101. [PMID: 29449833 PMCID: PMC5799277 DOI: 10.3389/fmicb.2018.00101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/16/2018] [Indexed: 12/31/2022] Open
Abstract
We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5' UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing).
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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50
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Goldberg NR, Mason NA. Species Identification of Vagrant Empidonax Flycatchers in Northeastern North America Via Non-Invasive DNA Sequencing. Northeast Nat (Steuben) 2017. [DOI: 10.1656/045.024.0408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Nathan R. Goldberg
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850
| | - Nicholas A. Mason
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850
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