Complete mitochondrial genome and phylogenetic analysis of Huangshan Black chicken (<i>Gallus gallus</i>)

Jin, Sihua; Zang, He; He, Peigen; Pan, Shenqiang; Zhao, Geng

doi:10.1080/23802359.2020.1860694

Cited by 5 publications

(2 citation statements)

References 9 publications

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“…The complete mtDNA genome of To chicken was 16,874 bp in size and included 13 proteincoding genes, 22 tRNA genes, two rRNA genes, and one non-coding region (D-loop region) similar to the mitochondrial genome of other vertebrates. The overall A + T contents of To chicken mtDNA genomes was 53.98% with the percentage of each nucleotide composition being 32.51% for C, 30.26% for A, 23.72% for T, and 13.51% for G which were similar to those of some Chinese native breeds such as Wuhua three-yellow chickens, Longsheng Feng chickens, Luhua chickens, Piao chickens, Taoyan chickens, and Huangshan Black chickens [33][34][35][36][37][38]. Moreover, the overall composition of Indian local chickens is in the order G > A > T > C [39].…”

Section: Discussionmentioning

confidence: 56%

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam

Pham

Giang

Nguyen

et al. 2023

Genes

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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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Section: Discussionmentioning

confidence: 56%

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam

Pham

Giang

Nguyen

et al. 2023

Genes

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“…The presence of different types of stop codons is common in most vertebrates, and incomplete termination codon T--. is due to the 5' terminal of an adjacent gene (Mindell et al, 1998;Jin et al, 2021). All 22 tRNAs were distributed among the rRNAs and PCGs.…”

Section: Assembly Structure and Features Of The Complete Mitogenomementioning

confidence: 99%

High throughput sequencing data reveals the complete mitogenome, abundance, maternal phylogeny, and mitogenomic diversity of Alectoris chukar of Iraq

Yousif,

Taha

2023

Emir J Food Agric

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Alectoris chukar is a wild game bird found in the north of Iraq, near the center of domestication and diversity of species. The mitogenome is one of the most vital resources for comprehensive studies of genetic diversity and molecular evolutionary relationships among avian species. In this study, we used whole genome sequencing raw reads and bioinformatics analysis to sequence and assemble Alectoris chukar's complete mitogenome for the first time. We also studied the maternal lineage and phylogenetic position of Alectoris chukar, as well as some mitogenomic diversity parameters. As a result, the complete mitogenomes with a length ranging from 16686 bp to 16688 bp of four individuals of wild Alectoris chukar were sequenced and assembled. They have a typical avian mitogenome structure with 2 ribosomal RNA (rRNA), 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and one non-coding control region. Our findings from bioinformatics analysis remarkably demonstrated that copies of the mitogenome are more abundant in liver tissues than in blood and in the liver tissues of females than in males. The results of phylogenetic analysis clustered the studied mitogenomes with Alectoris chukar as a monophyletic clade. Moreover, in comparison to the different genera, Alectoris chukar showed a high level of mitogenomic similarities to the snowcock species of the genus Tetraogallus within the Phasianidae family. However, they were more distant from other partridges. Additionally, a high percentage of mitogenomic pairwise identities within Iraqi Alectoris chukar and high mitogenomic variations compared to Chinese populations were discovered. The number and location of polymorphic sites indicated that the majority of the mitogenome sequences were conserved, with the control region, ND5, and CYTB genes having the most polymorphic sites. Analyses of phylogenetic and mitogenomic diversity revealed that samples of Alectoris chukar from Iraq have a unique maternal lineage and mitogenomic diversity specific to their geographic distribution, suggesting an Alectoris chukar kurdestanica subspecies. The molecular findings presented here provide valuable knowledge and mitogenomic resources into the evolutionary relationships of Alectoris chukar from the Middle East to avian species in the Phasianidae family. Key words: DNA sequencing; Mitochondrial genome; Partridges; Phasianidae; Phylogeny

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Unraveling the genetic tapestry of Indian chicken: A comprehensive study of molecular variations and diversity

Goli,

Sukhija,

Rathi

et al. 2024

Ecological Genetics and Genomics

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Complete mitochondrial genome and phylogenetic analysis of Huangshan Black chicken (Gallus gallus)

Cited by 5 publications

References 9 publications

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam

High throughput sequencing data reveals the complete mitogenome, abundance, maternal phylogeny, and mitogenomic diversity of Alectoris chukar of Iraq

Unraveling the genetic tapestry of Indian chicken: A comprehensive study of molecular variations and diversity

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