1
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Willett E, Banta S. Synthetic NAD(P)(H) Cycle for ATP Regeneration. ACS Synth Biol 2023. [PMID: 37369039 DOI: 10.1021/acssynbio.3c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
ATP is the energy currency of the cell and new methods for ATP regeneration will benefit a range of emerging biotechnology applications including synthetic cells. We designed and assembled a membraneless ATP-regenerating enzymatic cascade by exploiting the substrate specificities of selected NAD(P)(H)-dependent oxidoreductases combined with substrate-specific kinases. The enzymes in the NAD(P)(H) cycle were selected to avoid cross-reactions, and the cascade was driven by irreversible fuel oxidation. As a proof-of-concept, formate oxidation was chosen as the fueling reaction. ATP regeneration was accomplished via the phosphorylation of NADH to NADPH and the subsequent transfer of the phosphate to ADP by a reversible NAD+ kinase. The cascade was able to regenerate ATP at a high rate (up to 0.74 mmol/L/h) for hours, and >90% conversion of ADP to ATP using monophosphate was also demonstrated. The cascade was used to regenerate ATP for use in cell free protein synthesis reactions, and the ATP production rate was further enhanced when powered by the multistep oxidation of methanol. The NAD(P)(H) cycle provides a simple cascade for the in vitro regeneration of ATP without the need for a pH-gradient or costly phosphate donors.
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Affiliation(s)
- Emma Willett
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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2
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Willett E, Jiang V, Koder RL, Banta S. NAD + Kinase Enzymes Are Reversible, and NAD + Product Inhibition Is Responsible for the Observed Irreversibility of the Human Enzyme. Biochemistry 2022; 61:1862-1873. [PMID: 35984481 DOI: 10.1021/acs.biochem.2c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NAD+ kinase (NADK) is the only known enzyme capable of phosphorylating NAD(H) to NADP(H) and therefore it plays a crucial role in maintaining NAD(P)(H) homeostasis. All domains of life contain at least one NADK gene, and the commonly investigated isoforms have been measured, or assumed, to be functionally irreversible. In 1977, the kinetics of native pigeon liver NADK were thoroughly investigated, and it was reported to exhibit reversible activity, such that ATP and NAD+ can be formed from ADP and NADP+. We hypothesized that the reverse activity of the pigeon enzyme may enable compensation of the high picolinic acid carboxylase (PC) activity present in pigeon livers, which inhibits NAD+ biosynthesis from dietary tryptophan. Here, we report the characterization of four recombinantly expressed NADKs and explore their reversible activities. Duck and cat livers have higher PC activity than pigeon livers, and the recombinant duck and cat NADKs exhibit high activity in the reverse direction. The human NADK has an affinity for NAD+ that is ∼600 times higher than the pigeon, duck, and cat isoforms, and we conclude that NAD+ serves as a potent product inhibitor for the reverse activity of the human NADK, which accounts for the observed irreversible behavior. These results demonstrate that while all four NADKs are reversible, the reverse activity of the human enzyme alone is impeded via product inhibition. This mechanism─the conversion of a reversible to a unidirectional reaction by product inhibition─may be valuable in future metabolic engineering applications.
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Affiliation(s)
- Emma Willett
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Virginia Jiang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York 10031, United States.,Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, New York 10016, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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3
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Yang C, Du X, Liu Y, Yuan H, Wang Q, Hou X, Gong H, Wang Y, Huang Y, Li X, Ye H. Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications. Zookeys 2022; 1109:49-65. [PMID: 36762344 PMCID: PMC9848870 DOI: 10.3897/zookeys.1109.81125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/21/2022] [Indexed: 11/12/2022] Open
Abstract
The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M.flava, M.cinerea, M.alba and Dendronanthusindicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M.flava and M.tschutschensis showed closer relationships, and M.cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.
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Affiliation(s)
- Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina,Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Xiaojuan Du
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Yuxin Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina,School of Basic Medical Sciences, Xi’an Medical University, Xi’an, ChinaXi’an Medical UniversityXi’anChina
| | - Qingxiong Wang
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Xiang Hou
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Huisheng Gong
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Yan Wang
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Haiyan Ye
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
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4
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Xu N, Ding J, Que Z, Xu W, Ye W, Liu H. The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus. Zookeys 2021; 1041:167-182. [PMID: 34149293 PMCID: PMC8190031 DOI: 10.3897/zookeys.1041.60150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/17/2021] [Indexed: 11/12/2022] Open
Abstract
Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T.curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rRNAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T.curvirostra + Hemiphaganovaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.
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Affiliation(s)
- Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Jiayu Ding
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Ziting Que
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wei Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wentao Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
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5
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Yang J, Gu J, Hu Y, Wang N, Gao J, Wang P. Molecular cloning and characterization of HSP60 gene in domestic pigeons (Columba livia) and differential expression patterns under temperature stress. Cell Stress Chaperones 2021; 26:115-127. [PMID: 32880058 PMCID: PMC7736444 DOI: 10.1007/s12192-020-01160-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/19/2020] [Accepted: 08/25/2020] [Indexed: 12/21/2022] Open
Abstract
Heat shock protein 60 (HSP60) is a well-recognized multifunctional protein, playing a substantial role in protecting organisms from environmental stress. The domestic pigeon (Columba livia) is a promising model organism, with important economic and ecological value, and its health is susceptible to temperature stress. To explore the molecular characteristics, tissue expression profile, and response to temperature stress for HSP60 of Columba livia (ClHSP60), we firstly cloned and characterized the complete cDNA sequence and investigated its expression profile under optimal conditions and acute temperature stress. The cDNA of ClHSP60 contained 2257 nucleotides, consisting of 12 exons with length ranging from 65 to 590 bp. The open reading frame (ORF) encoded 573 amino acids with calculated molecular weight of 60.97 kDa that contained a number of structurally prominent domains or motifs. Under optimal temperature conditions, levels of ClHSP60 expression differed between all the tested tissues (the highest was noted in liver and the lowest in pectoralis major muscle). Under acute temperature stress, five patterns of change were detected in the tested tissues, suggesting that different tissues in domestic pigeons differentially responded to various temperature stress conditions. Upregulation of ClHSP60 expression was highest in the lung and pectoralis major muscle, reflecting the crucial role of these two tissues in temperature regulation. However, the crop, cerebrum, and heart showed little change or decreased ClHSP60 expression. The results indicate that ClHSP60 may be sensitive to and play pivotal roles in responding to acute temperature stress.
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Affiliation(s)
- Jianke Yang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- Research laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, China
| | - Juan Gu
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of pharmacy, Wannan Medical College, Wuhu, 241001, China
| | - Yuqing Hu
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, 241001, China
| | - Nan Wang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, 241001, China
| | - Jiguang Gao
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China
- Research laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, China
| | - Ping Wang
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, China.
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6
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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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7
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Pan T, Miao JS, Zhang HB, Yan P, Lee PS, Jiang XY, Ouyang JH, Deng YP, Zhang BW, Wu XB. Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa074] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.
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Affiliation(s)
- Tao Pan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Shun Miao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua-Bin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ping-Shin Lee
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xin-Yue Jiang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Hui Ouyang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - You-Peng Deng
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Bao-Wei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiao-Bing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
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8
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Møller HD, Ramos-Madrigal J, Prada-Luengo I, Gilbert MTP, Regenberg B. Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome. Genome Biol Evol 2020; 12:3762-3777. [PMID: 31882998 PMCID: PMC6993614 DOI: 10.1093/gbe/evz281] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of repetitive elements within a genome, and/or animal physiology affect the number of eccDNAs. Here, we investigate the distribution and numbers of eccDNAs in a condensed and less repeat-rich genome compared with the human genome, using Columba livia domestica (domestic rock pigeon) as a model organism. By sequencing eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize 30,000 unique eccDNAs. We identify genomic regions that are likely hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find that although eccDNA counts do not correlate with the biological age in pigeons, the number of unique eccDNAs in a nonflying breed (king pigeons) is significantly higher (9-fold) than homing pigeons. Furthermore, a comparison between eccDNA from skeletal muscle in pigeons and humans reveals ∼9-10 times more unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions to genome content, that is, human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). Overall, our results support that eccDNAs are common in pigeons, that the amount of unique eccDNA types per nucleus can differ between species as well as subspecies, and suggest that eccDNAs from repeats are found in proportions relative to the content of repetitive elements in a genome.
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Affiliation(s)
- Henrik Devitt Møller
- Department of Biology, University of Copenhagen, Denmark.,Department of Biology, Institute of Biochemistry, ETH Zürich, Switzerland
| | | | | | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
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9
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Liu HY, Sun CH, Zhu Y, Zhang QZ. Complete mitogenomic and phylogenetic characteristics of the speckled wood-pigeon (Columba hodgsonii). Mol Biol Rep 2020; 47:3567-3576. [PMID: 32307661 DOI: 10.1007/s11033-020-05448-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 10/24/2022]
Abstract
The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.
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Affiliation(s)
- Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, 610015, China
| | - Qing-Zheng Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
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10
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Sun CH, Xu P, Lu CH, Han Q, Lin YF, Gao ZJ, Lu CH. Complete mitochondrial genome of the Grey thrush Turdus cardis (Aves, Turdidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1750996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Peng Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Cai-Hong Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qian Han
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuan-Feng Lin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Zi-Jing Gao
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chang-Hu Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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11
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Jiang L, Bi D, Ding H, Ren Q, Wang P, Kan X. Identification and comparative profiling of gonadal microRNAs in the adult pigeon ( Columba livia). Br Poult Sci 2019; 60:638-648. [PMID: 31343256 DOI: 10.1080/00071668.2019.1639140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.
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Affiliation(s)
- L Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - D Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - H Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Q Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - P Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - X Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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12
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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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13
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Waso M, Khan S, Khan W. Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:99-106. [PMID: 28963900 DOI: 10.1016/j.scitotenv.2017.09.229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/18/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters.
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Affiliation(s)
- M Waso
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - S Khan
- Faculty of Health and Applied Sciences, Namibia University of Science and Technology, 13 Storch Street, Private Bag 13388, Windhoek 9000, Namibia
| | - W Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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14
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Sun Z, Pan T, Hu C, Sun L, Ding H, Wang H, Zhang C, Jin H, Chang Q, Kan X, Zhang B. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses. PLoS One 2017; 12:e0184529. [PMID: 28892502 PMCID: PMC5593203 DOI: 10.1371/journal.pone.0184529] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/25/2017] [Indexed: 11/29/2022] Open
Abstract
The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chaochao Hu
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hengwu Ding
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, China
| | - Hong Jin
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Qing Chang
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xianzhao Kan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
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15
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Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes. Genetica 2017; 145:431-440. [PMID: 28791584 DOI: 10.1007/s10709-017-9978-6] [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] [Received: 01/17/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
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Shi Q, Wang J, Liu J, Jiang H, Nie L. The complete mitochondrial genome of Geochelone sulcata. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:463-464. [PMID: 33473863 PMCID: PMC7800827 DOI: 10.1080/23802359.2017.1357437] [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
The complete mitochondrial genome of Geochelone sulcata was determined using PCR, Long-PCR with length of 16,692 bp. The genome organization, gene order, and base composition was similar to typical vertebrate. Gene content included 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Otherwise, the lack of C, as same as in the other species of Testudinidae, was detected in arms of tRNALys gene in G. sulcata. In addition, an extra nucleotide A was discovered in ND3 gene in G. sulcata. The complete mitogenome of G. sulcata provides the basic data to research molecular systematics of Testudinidae.
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Affiliation(s)
- Qiong Shi
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jue Wang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jianjun Liu
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Hui Jiang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Liuwang Nie
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
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17
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Wang Y, Dai X, Wang M, Nie L. The complete mitochondrial genome of the Heosemys depressa (Testudines, Geoemydidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:437-438. [PMID: 33473854 PMCID: PMC7800218 DOI: 10.1080/23802359.2017.1357438] [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 complete mitochondrial genome of Heosemys depressa was obtained and characterized in this study. The mitochondrial genome is a circular molecule of 16,773bp in length, and harbours 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding D-loop region (control region). Its gene arrangement type is identical to the type of most vertebrate. Phylogenetic analysis suggests that H. depressa is closely related to H. annandalii than to the other species. Our data provide a useful resource for the phylogenetic studies of genus Heosemys.
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Affiliation(s)
- Yuqin Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xueting Dai
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Meng Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Liuwang Nie
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
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18
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Li J, Lu Y, Zan J, Nie L. Complete mitochondrial genome of the Cyclemys pulchristriata (Chelonia: Geoemydidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:403-404. [PMID: 33473841 PMCID: PMC7800075 DOI: 10.1080/23802359.2017.1347836] [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: 11/17/2022]
Abstract
In this study, we obtained complete mitochondrial genome sequence of Cyclemys pulchristriata. The mitochondrial genome reaches a length of 16,527 bp, containing 13 protein-coding genes (PCGs), 22tRNA genes, 2 rRNA genes and 1 control region. All protein-coding genes initiate with ATG as start codon, except for CO1 started with GTG. Most protein-coding genes ended by TAA as stop codon. Interestingly, there is an extra nucleotide A insertion in ND3 gene in C. pulchristriata. This study provides information on the genetic resources of C. pulchristriata that will contribute to protect this species.
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Affiliation(s)
- Jun Li
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Yuanhua Lu
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Jiawei Zan
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, China.,The Laboratory of Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
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19
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Looi QH, Amin H, Aini I, Zuki M, Omar AR. De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets. BMC Genomics 2017; 18:504. [PMID: 28673247 PMCID: PMC5496224 DOI: 10.1186/s12864-017-3861-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Edible bird's nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and medicinal benefits of EBN have been extensively studied, however, genomic and transcriptomic studies of the salivary glands of these birds have not been conducted. RESULTS The study described the transcriptomes of salivary glands from three swiftlet species (28 samples) generated by RNASeq. A total of 14,835 annotated genes and 428 unmapped genes were cataloged. The current study investigated the genes and pathways that are associated with the development of salivary gland and EBN composition. Differential expression and pathway enrichment analysis indicated that the expression of CREB3L2 and several signaling pathways involved in salivary gland development, namely, the EGFR, BMP, and MAPK signaling pathways, were up-regulated in swiftlets producing white EBN (Aerodramus fuciphagus) and black EBN (Aerodramus maximus) compared with non-EBN-producing swiftlets (Apus affinis). Furthermore, MGAT, an essential gene for the biosynthesis of N-acetylneuraminic acid (sialic acid), was highly expressed in both white- and black-nest swiftlets compared to non-EBN-producing swiftlets. Interspecies comparison between Aerodramus fuciphagus and Aerodramus maximus indicated that the genes involved in N-acetylneuraminic and fatty acid synthesis were up-regulated in Aerodramus fuciphagus, while alanine and aspartate synthesis pathways were up-regulated in Aerodramus maximus. Furthermore, gender-based analysis revealed that N-glycan trimming pathway was significantly up-regulated in male Aerodramus fuciphagus from its natural habitat (cave) compared to their female counterpart. CONCLUSIONS Transcriptomic analysis of salivary glands of different swiftlet species reveal differential expressions of candidate genes that are involved in salivary gland development and in the biosynthesis of various bioactive compounds found in EBN.
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Affiliation(s)
- Q H Looi
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - H Amin
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - I Aini
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M Zuki
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - A R Omar
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. .,Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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20
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Two mitogenomes in Gruiformes (Amaurornis akool/A. phoenicurus) and the phylogenetic placement of Rallidae. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Wang YC, Zou Y, Sun XM, Gong J, Huang L, Jing MD. The complete mitochondrial genome sequence of the little grebe (Tachybaptus ruficollis). Genes Genomics 2017. [DOI: 10.1007/s13258-016-0480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Soares AER, Novak BJ, Haile J, Heupink TH, Fjeldså J, Gilbert MTP, Poinar H, Church GM, Shapiro B. Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. BMC Evol Biol 2016; 16:230. [PMID: 27782796 PMCID: PMC5080718 DOI: 10.1186/s12862-016-0800-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. RESULTS We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. CONCLUSIONS Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.
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Affiliation(s)
- André E. R. Soares
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
| | - Ben J. Novak
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
- Revive & Restore, The Long Now Foundation, San Francisco, CA 94123 USA
| | - James Haile
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tim H. Heupink
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road QLD 4111, Nathan, Australia
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 L9 Canada
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115 USA
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
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23
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Huang Z, Tu F, Murphy RW. Analysis of the complete mitogenome of Oriental turtle dove (Streptopelia orientalis) and implications for species divergence. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Ren Q, Yuan J, Ren L, Zhang L, Zhang L, Jiang L, Chen D, Kan X, Zhang B. The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae), and phylogenetic relationships within the genus Emberiza. J Genet 2015; 93:699-707. [PMID: 25572228 DOI: 10.1007/s12041-014-0428-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mitochondrial genomes have proved to be powerful tools in resolving phylogenetic relationships. Emberiza chrysophrys (least concern species: IUCN 2013) is a passerine bird in the bunting family, Emberizidae. The complete mitochondrial genome of E. chrysophrys was sequenced. This circular mitochondrial genome was 16,803 bp in length, with an A+T content of 52.26%, containing 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a putative control region (CR). The CR of E. chrysophrys was divided into three conserved domains. Six conserved sequence boxes in the central conserved domain II were identified as F, E, D, C, b and B. An obvious positive AT-skew and negative GC-skew bias were found for all 28 genes encoded by the H strand, whereas it was the reverse in the remaining nine genes encoded by the L strand. Remarkable rate heterogeneity was present in the mitochondrial genome of E. chrysophrys. Notably, unusual slow rate of evolution in the mitochondrial CR of E. chrysophrys was detected, which is rarely seen in other birds. Phylogenetic analyses were carried out based on 13 PCGs that showed E. pusilla was the sister group of E. rustica, and the monophyly of Emberiza was established.
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Affiliation(s)
- Qiongqiong Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, People's Republic of China.
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Jiang L, Chen J, Wang P, Ren Q, Yuan J, Qian C, Hua X, Guo Z, Zhang L, Yang J, Wang Y, Zhang Q, Ding H, Bi D, Zhang Z, Wang Q, Chen D, Kan X. The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses. PLoS One 2015; 10:e0136297. [PMID: 26295156 PMCID: PMC4546579 DOI: 10.1371/journal.pone.0136297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/02/2015] [Indexed: 01/08/2023] Open
Abstract
The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide'C'is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes.
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Affiliation(s)
- Lan Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
| | - Juan Chen
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ping Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Qiongqiong Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jian Yuan
- The College of Life Sciences, Peking University, Beijing, China
| | - Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Xinghong Hua
- The Ningguo Museum of Natural History, Ningguo, Anhui, China
| | - Zhichun Guo
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Lei Zhang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jianke Yang
- The Department of Medical Biology, Wannan medical college, Wuhu, Anhui, China
| | - Ying Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Qin Zhang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - De Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Zongmeng Zhang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Qingqing Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Dongsheng Chen
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, Anhui, China
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26
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Eberhard JR, Wright TF. Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 2015; 94:34-46. [PMID: 26291569 DOI: 10.1016/j.ympev.2015.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.
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Affiliation(s)
- Jessica R Eberhard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Timothy F Wright
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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Li CH, Jin SG, Dong YL, Wang L, Shi WY. The complete mitochondrial genome of Rhodeus lighti (Cypriniformes: Cyprinidae): sequencing and analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2298-9. [PMID: 26065852 DOI: 10.3109/19401736.2015.1046167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Phylogenetic placement of Rhodeus lighti (R. lighti) remains unresolved. We determined the first complete mitochondrial genome of R. lighti (Cypriniformes: Cyprinidae). The genome is 16,597 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The gene composition and order were similar to most of the other vertebrates. The complete mitochondrial genome sequence of R. lighti should contribute towards clarifying the systematics of Rhodeus fishes. The phylogenetic relationships using partitioned Neighbor-Joining tree indicated that (((((Pseudorasbora, Rhodeus) Ctenopharyngodon) (Acheilognathus, Tanakia) Carassius)) Danio rerio). This study will contribute to confirm the phylogenetic status of Rhodeus within family Cyprinidae.
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Affiliation(s)
- Chun-Hong Li
- a Department of Animal Medicine , Hebei North University , Zhangjiakou , China and
| | - Shu-Gang Jin
- a Department of Animal Medicine , Hebei North University , Zhangjiakou , China and
| | - Yu-Long Dong
- a Department of Animal Medicine , Hebei North University , Zhangjiakou , China and
| | - Li Wang
- a Department of Animal Medicine , Hebei North University , Zhangjiakou , China and
| | - Wan-Yu Shi
- b College of Veterinary Medicine, Agricultural University of Hebei , Baoding , China
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Zou Y, Jing MD, Bi XX, Zhang T, Huang L. The complete mitochondrial genome sequence of the little egret (Egretta garzetta). Genet Mol Biol 2015; 38:162-72. [PMID: 26273219 PMCID: PMC4530654 DOI: 10.1590/s1415-4757382220140203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022] Open
Abstract
Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3' end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.
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Affiliation(s)
- Yi Zou
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Mei-Dong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Xiao-Xin Bi
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ting Zhang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ling Huang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
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Huang Z, Tu F, Liu X. Determination of the complete mitogenome of Spotted Dove, Spilopelia chinensis (Columbiformes: Columbidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4224-4225. [PMID: 25856515 DOI: 10.3109/19401736.2015.1022750] [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
The Spotted Dove Spilopelia chinensis (Columbiformes: Columbidae) is widely distributed in Southeast Asia. In the present study, we investigated the complete mitochondrial genome of S. chinensis and the mitogenome is 16,964 bp in length, consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region, with the base composition of A 31.1%, G 13.9%, T 23.9%, and C 32.1%. A single extra base "C" at position 174 is inserted in gene Nd3, similar to some other birds and turtles. The phylogenetic relationships using partitioned Bayesian inference based on the 12 concatenated PCGs indicated that ((((Spilopelia, Columba) Ectopistes) (Geotrygon (Leptotila, Zenaida))) Hemiphaga). While, more complete mitogenome sequences should be determined to confirm the phylogenetic status of Spilopelia within family Columbidae.
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Affiliation(s)
- Zuhao Huang
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , China and
| | - Feiyun Tu
- b Jiangxi Academy of Forestry , Nanchang , Jiangxi Province , China
| | - Xiaohua Liu
- b Jiangxi Academy of Forestry , Nanchang , Jiangxi Province , China
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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Zhang RH, He WX. The complete mitochondrial genome of the ice pigeon (Columba livia breed ice). MITOCHONDRIAL DNA 2015; 26:164-5. [PMID: 25722036 DOI: 10.3109/19401736.2015.1007308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The ice pigeon is a breed of fancy pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of ice pigeon for the first time. The total length of the mitogenome was 17,236 bp with the base composition of 30.2% for A, 24.0% for T, 31.9% for C, and 13.9% for G and an A-T (54.2 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of ice pigeon would serve as an important data set of the germplasm resources for further study.
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Affiliation(s)
- Rui-Hua Zhang
- Key Laboratory of Preventive Veterinary Medicine, Department of Veterinary Medicine, Animal Science College, Hebei North University , Zhangjiakou , PR China and
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32
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He WX, Jia JF. The complete mitochondrial genome of the Jacobin pigeon (Columba livia breed Jacobin). MITOCHONDRIAL DNA 2015; 26:493-4. [PMID: 25690052 DOI: 10.3109/19401736.2015.1007322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia. In the present work, we report the complete mitochondrial genome sequence of Jacobin pigeon for the first time. The total length of the mitogenome was 17,245 bp with the base composition of 30.18% for A, 23.98% for T, 31.88% for C, and 13.96% for G and an A-T (54.17 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region. The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of Jacobin pigeon would serve as an important data set of the germplasm resources for further study.
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Affiliation(s)
- Wen-Xiao He
- Artillery Training Base of General Staff , Xuanhua , PR China and
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Zhang RH, He WX, Xu T. Characterization of the complete mitochondrial genome of the king pigeon (Columba livia breed king). ACTA ACUST UNITED AC 2015; 26:491-2. [DOI: 10.3109/19401736.2014.1003906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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34
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Zhang RH, Xu MJ, Wang CL, Xu T, Wei D, Liu BJ, Wang GH. The complete mitochondrial genome of the Fancy Pigeon, Columba livia (Columbiformes: Columbidae). ACTA ACUST UNITED AC 2015; 26:162-3. [DOI: 10.3109/19401736.2014.1003851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Rui-Hua Zhang
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Ming-Ju Xu
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Cun-Lian Wang
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Tong Xu
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Dong Wei
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Bao-Jian Liu
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
| | - Guo-Hua Wang
- Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China
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Yan SQ, Guo PC, Li YM, Qi SM, Bai CY, Zhao ZH, Sun JH. Complete mitochondrial genome of the Spotted dove (Streptopelia chinensis). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3067-8. [PMID: 25600734 DOI: 10.3109/19401736.2014.1003912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Spotted dove (Streptopelia chinensis) is a member of the bird family Columbidae. In this study, we report the complete mitochondrial genome of this species. The mitochondrial genome of Spotted dove is a circular molecule of 16,966 bp in size and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition is 30.1% for A, 32.1% for C, 13.9% for G, and 23.9% for T. These data will be useful for the phylogenetic and population diversity analyses of birds, especially Columbidae species.
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Affiliation(s)
- Shou-Qing Yan
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Peng-Cheng Guo
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Yu-Mei Li
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Shun-Min Qi
- b College of Animal Science and Veterinary Medicine, Qingdao Agricultural University , Qingdao , PR China
| | - Chun-Yan Bai
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Zhi-Hui Zhao
- a Department of Animal Genetics and Breeding , College of Animal Science, Jilin University , Changchun , PR China and
| | - Jin-Hai Sun
- b College of Animal Science and Veterinary Medicine, Qingdao Agricultural University , Qingdao , PR China
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Jang KH, Ryu SH, Kang SG, Hwang UW. Complete mitochondrial genome of the Japanese wood pigeon, Columba janthina janthina (Columbiformes, Columbidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2165-6. [PMID: 25431823 DOI: 10.3109/19401736.2014.982608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Columba janthina janthina was sequenced and its total length was 17,469 bp, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 1 non-coding control region (D-loop). The A+T content of the overall base composition of H-strand were 54.46% (30.38% A, 24.08% T, 32.00% C and 13.54% G). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. Within the control region, conserved sequences were identified in three domains. These results provide basic information for phylogenetic analyses of pigeon, especially Columbiformes species.
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Affiliation(s)
- Kuem Hee Jang
- a Institute for Phylogenomics and Evolution, Kyungpook National University , Daegu , South Korea
| | - Shi Hyun Ryu
- a Institute for Phylogenomics and Evolution, Kyungpook National University , Daegu , South Korea
| | - Seung-Gu Kang
- b Animal Resources Division , National Institute of Biological Resources , Incheon , South Korea , and
| | - Ui Wook Hwang
- c Department of Biology , Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University , Daegu , South Korea
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Wu H, Liu BG, Hu GZ, Liu JH, Yuan L, Pan YS. The complete mitochondrial genome of Archangel pigeon. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:865-6. [PMID: 25007353 DOI: 10.3109/19401736.2014.919479] [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 Archangel pigeon mitochondrial DNA has 17,235 bp and its structural organization is conserved compared to those of other birds. In this study, we report the basic characteristics of the Archangel mitochondrial genome, including structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs. These features are applicable for the study of phylogenetic relationships in pigeons.
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Affiliation(s)
- Hua Wu
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and
| | - Bao-guang Liu
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and.,b Department of Animal Husbandry and Veterinary , Tibetan Vocational and Technical College , Lhasa , Tibet , PR China
| | - Gong-zheng Hu
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and
| | - Jian-hua Liu
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and
| | - Li Yuan
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and
| | - Yu-shan Pan
- a College of Animal Husbandry and Veterinary Science, Henan Agricultural University , Zhengzhou , PR China and
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Souto HM, Ruschi PA, Furtado C, Jennings WB, Prosdocimi F. The complete mitochondrial genome of the ruby-topaz hummingbird Chrysolampis mosquitus through Illumina sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:769-70. [PMID: 24841437 DOI: 10.3109/19401736.2014.915533] [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 the Ruby-Topaz Hummingbird, Chrysolampis mosquitus, was determined using 1/11 of an Illumina Hi-seq lane ran with a Nextera kit. We assembled the mitogenome in a two-step approach using both (i) de novo (SOAPdenovo-Trans) and (ii) reference-based (MITObim) genome assembly software. A circular molecule containing 17,767 bp was assembled. As expected for most vertebrates, the C. mosquitus mitogenome contained 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA genes, and 1 non-coding control region. We assembled the whole mitogenome using 0.45% of the total amount of reads and produced a high-coverage mitochondrial genome (>1000×). We deposited the assembled mitogenome into GenBank (accession number KJ619585).
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Affiliation(s)
- Helena Magarinos Souto
- a Genomics and Biodiversity Laboratory , Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Piero Angeli Ruschi
- b Molecular Laboratory of Biodiversity Research, Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil .,c Museu de Biologia Prof. Mello Leitão/MBML , Santa Teresa , Espírito Santo , Brazil , and
| | - Carolina Furtado
- d Division of Genetics , National Cancer Institute , Rio de Janeiro , Brazil
| | - W Bryan Jennings
- b Molecular Laboratory of Biodiversity Research, Departamento de Vertebrados , Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Francisco Prosdocimi
- a Genomics and Biodiversity Laboratory , Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
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Ren Q, Li X, Yuan J, Chen D, Zhang L, Guo W, Jiang L, Wang P, Kan X. Complete mitochondrial genome of the Blue Eared Pheasant,Crossoptilon auritum(Galliformes: Phasianidae). ACTA ACUST UNITED AC 2014; 27:615-7. [DOI: 10.3109/19401736.2014.908371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Ren Q, Yuan J, Zhu X, Wang P, Zhang L, Jiang L, Kan X. Complete mitochondrial genome of a Light-vented Bulbul subspecies,Pycnonotus sinensis hainanus(Passeriformes: Pycnonotidae). ACTA ACUST UNITED AC 2014; 27:375-7. [DOI: 10.3109/19401736.2014.895993] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Li CH, Liu F, Wang L. The complete mitochondrial genome of the Feral Rock Pigeon (Columba livia breed feral). MITOCHONDRIAL DNA 2014; 25:383-4. [PMID: 24438239 DOI: 10.3109/19401736.2013.873914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract In the present work, we report the complete mitochondrial genome sequence of feral rock pigeon for the first time. The total length of the mitogenome was 17,239 bp with the base composition of 30.3% for A, 24.0% for T, 31.9% for C, and 13.8% for G and an A-T (54.3 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of feral rock pigeon would serve as an important data set of the germplasm resources for further study.
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Affiliation(s)
- Chun-Hong Li
- Department of Animal Medicine, Hebei North University , Zhangjiakou , China and
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42
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Li CH, Shi W, Shi WY. Mitochondrial genome sequence of Egyptian swift Rock Pigeon (Columba liviabreed Egyptian swift). ACTA ACUST UNITED AC 2014; 26:479-80. [DOI: 10.3109/19401736.2013.873931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the complex phylogeny of the family Columbidae.
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Affiliation(s)
- Haseeb Ahmad Khan
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh , Saudi Arabia
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Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013; 8:e56301. [PMID: 23437111 PMCID: PMC3577829 DOI: 10.1371/journal.pone.0056301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022] Open
Abstract
The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum and Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chiou-Ju Yao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail:
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Qian C, Yan X, Guo Z, Wang Y, Li X, Yang J, Kan X. Characterization of the complete mitochondrial genome of the Grey-backed Shrike, Lanius tephronotus (Aves: Passeriformes): the first representative of the family Laniidae with a novel CAA stop codon at the end of cox2 gene. MITOCHONDRIAL DNA 2013; 24:359-61. [PMID: 23387995 DOI: 10.3109/19401736.2012.762577] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete Grey-backed Shrike mitochondrial genome has been sequenced to be 16,820 bp in length, consisting of 37 encode genes: 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. In addition, a single control region was also observed. Compared with other reported Passeriformes mtgenome sequences, three bases CAA were detected at the end of Lanius tephronotus cox2 gene with the downstream adjacent base T. The first base of CAA probably occurred C to U transcript editing event resulting in a normal stop codon UAA.
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Affiliation(s)
- Chaoju Qian
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, Republic of China
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Qian C, Wang Y, Guo Z, Yang J, Kan X. Complete mitochondrial genome of Skylark, Alauda arvensis (Aves: Passeriformes): the first representative of the family Alaudidae with two extensive heteroplasmic control regions. ACTA ACUST UNITED AC 2013; 24:246-8. [PMID: 23311453 DOI: 10.3109/19401736.2012.752481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The circular mitochondrial genome of Alauda arvensis is 17,018 bp in length, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and 2 extensive heteroplasmic control regions. All of the genes encoded on the H-strand, with the exceptions of one PCG (nad6) and eight tRNA genes (tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser(UCN)), tRNA(Pro), and tRNA(Glu)), as found in other birds' mitochondrial genomes. All of these PCGs are initiated with ATG, while stopped by six types of stop codons. All tRNA genes have the potential to fold into typical clover-leaf structure. Two extensive heteroplasmic control regions were found, and more interestingly, a minisatellite of 37 nucleotides (5'-TCAATCCCATTGATTTCATTATATTAGTATAAAGAAA-3') with 6 tandem repeats was detected at the end of CR2.
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Affiliation(s)
- Chaoju Qian
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, People's Republic of China
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Cooke GM, King AG, Johnson RN, Boles WE, Major RE. Rapid characterization of mitochondrial genome rearrangements in Australian songbirds using next-generation sequencing technology. J Hered 2012; 103:882-6. [PMID: 23125406 DOI: 10.1093/jhered/ess091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using next-generation sequencing technology, we describe the complete mitochondrial genomes for 5 Australian passerine birds (Epthianura albifrons, Petroica phoenicea, Petroica goodenovii, Petroica boodang, and Eopsaltria australis). We successfully assemble each mitogenome de novo using just 1/8th of a Roche GL FSX 454 pyrosequencing plate. From the assembled mitogenomes, we identify 2 different mitochondrial gene arrangements in the region spanning 5'-3' from Cytochrome B to 12s RNA. These gene arrangements represent 2 of the 4 known avian mitochondrial gene arrangements. Our results, together with other previously described avian mitogenomes, highlight that certain mitochondrial rearrangements appear to have arisen multiple times.
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Affiliation(s)
- Georgina M Cooke
- Australian Museum, 6 College Street, Sydney, NSW 2010, Australia
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Qian C, Ren Q, Kan X, Guo Z, Yang J, Li X, Yuan J, Qian M, Hu Q, Zhang L. Complete mitochondrial genome of the Red-billed Starling,Sturnus sericeus(Aves: Passeriformes): The first representative of the family Sturnidae with a single control region. ACTA ACUST UNITED AC 2012; 24:129-31. [DOI: 10.3109/19401736.2012.731407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Zhang L, Wang L, Gowda V, Wang M, Li X, Kan X. The mitochondrial genome of the Cinnamon Bittern, Ixobrychus cinnamomeus (Pelecaniformes: Ardeidae): sequence, structure and phylogenetic analysis. Mol Biol Rep 2012; 39:8315-26. [PMID: 22699875 DOI: 10.1007/s11033-012-1681-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 06/05/2012] [Indexed: 11/26/2022]
Abstract
Ixobrychus cinnamomeus is a member of the large wading bird family, known as Ardeidae. In the present study, we determined the complete mitochondrial genome of I. cinnamomeus for use in future phylogenetic analysis. This circular mitochondrial genome is 17,180 bp in length and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one putative control region. Three conserved domains and a minisatellite of 17 nucleotides with 22 tandem repeats were detected at the end of the control region. Phylogenetic relationships were reconstructed using the nucleotide and corresponding amino acid datasets of 12 concatenated protein-coding genes from the mitochondrial genome. Using maximum likelihood, maximum parsimony and Bayesian inference methods, the monophyly of Ciconiidae, Ardeidae and Threskiornithidae were confirmed; however, the monophyly of traditional Ciconiiformes and Pelecaniformes failed to be recovered. Although further studies are recommended to clarify relationships among and within the orders of Ciconiiformes, Pelecaniformes, Suliformes and Phaethontiformes, our results provide preliminary exploratory results that can be useful in the current understanding of avian phylogenetics.
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Affiliation(s)
- Liqin Zhang
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand. Ann Anat 2011; 194:36-51. [PMID: 21596537 DOI: 10.1016/j.aanat.2011.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/23/2022]
Abstract
The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.
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