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Jiang C, Kang H, Zhou Y, Zhu W, Zhao X, Mohamed N, Li B. Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes). Life (Basel) 2024; 14:881. [PMID: 39063634 PMCID: PMC11278119 DOI: 10.3390/life14070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.
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Affiliation(s)
- Chuan Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Hui Kang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Yang Zhou
- BGI Research, Shenzhen 518083, China;
- BGI Research, Wuhan 430074, China
| | - Wenwen Zhu
- School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Xilong Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Nassoro Mohamed
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Bo Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin 150040, China
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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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Zhang S, Zheng X, Zhou C, Zhu M, Wu Y. The complete mitochondrial genome and the phylogenetic position of Alauda gulgula (Aves: Passeriformes). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1367-1368. [PMID: 33889752 PMCID: PMC8043529 DOI: 10.1080/23802359.2021.1909438] [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: 12/05/2022]
Abstract
The Oriental Skylark (Alauda gulgula) is a small songbird in the Alaudidae. Here we assembled the complete mitochondrial genome of Alauda gulgula which is 17,055 bp in length and consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA, 22 transfer RNA, and 2 extensive heteroplasmic control regions. The overall A + T content of the mitogenome is 52.3%The maximum-likelihood (ML) tree based on the complete mitochondrial genome of A. gulgula revealed the close genetic relationship between A. gulgula and A. arvensis, but separate from A. cheleensis.
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Affiliation(s)
- Shangmingyu Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaofeng Zheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuang Zhou
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Min Zhu
- The General Work Station of Protected Area of Sichuan Province, Chengdu, China
| | - Yongjie Wu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon. DIVERSITY 2020. [DOI: 10.3390/d12110428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
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Sun CH, Liu HY, Lu CH. Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses. Int J Biol Macromol 2020; 146:638-647. [DOI: 10.1016/j.ijbiomac.2019.12.253] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 12/28/2019] [Indexed: 11/30/2022]
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7
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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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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Zeng Z, Lu J, Yang M, Kang H, Li B. Complete mitochondrial genome of the Mongolian lark, Melanocorypha mongolica (Aves: Passeriformes). Mitochondrial DNA B Resour 2017; 2:266-267. [PMID: 33473794 PMCID: PMC7800670 DOI: 10.1080/23802359.2017.1325340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We sequenced the entire mitochondrial genome of Melanocorypha mongolica for the first time. The mitogenome is 17,358 bp in length, which includes 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA (rRNA) genes, the control region (CR1), and the control region 2 (CR2). Gene order follows a pattern similar to those of Eurasian Skylark. Using mitochondrial genomes of Melanocorypha mongolica and other seven reference birds in Sylvioidea, we preformed Bayesian analysis based on concatenated protein-coding genes. The results reveal that Alaudidae and Acroccphalidae are clustered together, which is sister to the branches included Sylviidae and Leiothrichidae. Further sequencing of mitochondrial genomes in Alaudidae is useful to advance phylogenetic relationship of species in the family.
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Affiliation(s)
- Zan Zeng
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Jinyao Lu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Mengli Yang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Hui Kang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
- State Forestry Administration Detecting Center of Wildlife, Harbin, China
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Li X, Lin L, Cui A, Bai J, Wang X, Xin C, Zhang Z, Yang C, Gao R, Huang Y, Lei F. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments. Mol Phylogenet Evol 2016; 104:14-20. [DOI: 10.1016/j.ympev.2016.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/20/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022]
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11
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Zhao Q, Xu HL, Li B, Xie M, Li DY, Ni QY, Zhang MW, Yao YF. Characterization of the complete mitochondrial genome and phylogenetic relationship of Pomatorhinus ruficollis (Passeriformes, Timaliinae). Mitochondrial DNA B Resour 2016; 1:142-143. [PMID: 33473438 PMCID: PMC7800912 DOI: 10.1080/23802359.2016.1144100] [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: 10/27/2022] Open
Affiliation(s)
- Qin Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huai-liang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Bo Li
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Di-yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing-yong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ming-wang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong-fang Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
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Huan Z, Yao Y, Zhou Y, Qi Y, Wang Q, Li D, Xie M, Ni Q, Zhang M, Xu H. Complete mitochondrial genome sequence of Garrulax formosus (Aves, Passeriformes, Timaliidae) and its phylogenetic analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2858-9. [PMID: 26190081 DOI: 10.3109/19401736.2015.1053128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Garrulax formosus was obtained for the first time, which is 17 869 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA, 22 tRNA genes and 2 different control regions. All genes are distributed in plus strand, with the exceptions of one PCG (ND6) and eight tRNA genes. All PCGs are initiated with ATG, except for COX1, which is initiated with GTG, while stopped by five types of stop codons. All tRNA genes have the potential to fold into typical clover-leaf structure except tRNA(Ser)(GCT). According to the phylogenetic tree, we can infer that it is reasonable to divide Garrulax formosus into the genus Garrulax.
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Affiliation(s)
- Zongjin Huan
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China .,b Chengdu Zoo , Chengdu , Sichuan , China , and
| | - Yongfang Yao
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Yanyan Zhou
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Yu Qi
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Qiang Wang
- b Chengdu Zoo , Chengdu , Sichuan , China , and
| | - Diyan Li
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Meng Xie
- c College of Life Science, Sichuan Agricultural University , Ya'an, Sichuan , China
| | - Qingyong Ni
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Mingwang Zhang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Huailiang Xu
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
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Zhou Y, Qi Y, Xu H, Huan Z, Li D, Xie M, Ni Q, Zhang M, Yao Y. The complete mitochondrial genome sequence of Garrulax ocellatus (Aves, Passeriformes, Timaliidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2689-90. [PMID: 26152349 DOI: 10.3109/19401736.2015.1043736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Timaliidae, generally known as the babblers, includes about 275 species in 50 genera. We sequenced the complete mitochondrial genome of Garrulax ocellatus, and it was determined to be 17,828 bp in length, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNAsfer (tRNA) genes, and 2 control regions. The complete mitochondrial genome contained 15.24% G, 23.02% T, 33.13% C, and 28.61% A, which was similar to other Passeriformes mitochondrial genomes. There are eight tRNA genes and one PCG (ND6) encoded on the L-strand, and other PCGs were encoded on the H-strand. All genes were closely assembled and only 17 intergenic spacers were observed. In total, the spacers were 99 bp in length, and there were seven pairs of genes overlapping sequences of 30 bp in length. Phylogenetic relationship could provide useful information for the further study on the species taxonomic.
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Affiliation(s)
- Yanyan Zhou
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Yu Qi
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Huailiang Xu
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Zongjin Huan
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China .,b Chengdu Zoo , Chengdu, Sichuan , China , and
| | - Diyan Li
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Meng Xie
- c College of Life Science, Sichuan Agricultural University , Ya'an , China
| | - Qingyong Ni
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Mingwang Zhang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Yongfang Yao
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
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Kan X, Ren Q, Wang P, Jiang L, Zhang L, Wang Y, Zhang Q. Complete mitochondrial genome of the Eurasian siskin, Spinus spinus (Passeriformes: Fringillidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1833-5. [PMID: 25319308 DOI: 10.3109/19401736.2014.971247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Eurasian siskin (Spinus spinus), also called the European siskin, common siskin or just siskin, is found throughout Europe and Asia. In this study, the complete mitochondrial genome of S. spinus was determined to be 16,828 bp. The size of protein-coding genes (PCGs) in the S. spinus mitochondrial genome was 11,400 bp. The longest PCG of S. spinus mtDNA was nad5 (1818 bp), whereas the shortest is atp8 (168 bp). The nad6 gene of S. spinus mitogenome had strong skews of T versus A (-0.54), and G versus C (0.64). According to the distribution of the conserved motifs in other avian CRs, the CR of S. spinus can be divided into three domains: ETAS domain I, central conserved domain II, and CSB domain III.
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Affiliation(s)
- Xianzhao Kan
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and.,b The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Qiongqiong Ren
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and.,b The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Ping Wang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Lan Jiang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Liqin Zhang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Ying Wang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Qin Zhang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
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Keith Barker F. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Mol Phylogenet Evol 2014; 79:313-24. [DOI: 10.1016/j.ympev.2014.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/31/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
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16
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Ren Q, Qian C, Yuan J, Jiang L, Wang P, Kan X. Characterization of the complete mitochondrial genome of Collared Finchbill, Spizixos semitorques (Passeriformes: Pycnonotidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:700-2. [PMID: 24810073 DOI: 10.3109/19401736.2014.913150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The complete mitochondrial genome of Spizixos semitorques is 17,045 bp long with an A+T content of 55.52%, which composed of 13 typical protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 extensive heteroplasmic control regions (CR1 and CR2). Genome organization of S. semitorques is similar to that of other birds. All of the PCGs started with ATG, except for cox1, which began with GTG. Six types of termination codons were used, canonical TAA and TAG termination codons are found in seven protein-coding genes, while AGA for nad1 and nad5, AGG for cox1, and the remaining genes (nad2, cox3, nad4) have incomplete termination codons (TA- or T- -). All tRNA genes have a typical clover-leaf structure. Furthermore, a minisatellite of 24 nucleotides (5'-CACAAAAATCAAACAAAAATACAA-3') with 2.9 tandem repeats at the end of CR2 were detected.
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Affiliation(s)
- Qiongqiong Ren
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and.,b The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
| | - Chaoju Qian
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Jian Yuan
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Lan Jiang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Ping Wang
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and
| | - Xianzhao Kan
- a The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui , Wuhu , People's Republic of China and.,b The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University , Wuhu , People's Republic of China
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