1
|
Akhtar T, Ali G, Shafi N, Akhtar W, Khan AH, Latif Z, Wali A, Ain-ul-Batool S, Khan AR, Mumtaz S, Altaf SI, Khawaja S, Sadia, Khalid M, Rehman FU, Javid Q. Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5980135. [PMID: 33490246 PMCID: PMC7787735 DOI: 10.1155/2020/5980135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/29/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.
Collapse
Affiliation(s)
- Tasleem Akhtar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Wasim Akhtar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Hameed Khan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Latif
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Wali
- Faculty of Life Sciences & Informatics, BUITEMS, 87100 Quetta, Pakistan
| | - Syeda Ain-ul-Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Rehman Khan
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Mumtaz
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syed Iftikhar Altaf
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sundus Khawaja
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Madiha Khalid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Biotechnology, Women University Bagh, Pakistan
| | - Fazal Ur Rehman
- Department of Microbiology, University of Balochistan, Quetta 87300, Pakistan
| | - Qudir Javid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| |
Collapse
|
2
|
Development of four PCR-based methods to differentiate tilefish species (Branchiostegus japonicus and B. albus). Food Chem 2019; 271:1-8. [DOI: 10.1016/j.foodchem.2018.07.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/05/2018] [Accepted: 07/20/2018] [Indexed: 11/19/2022]
|
3
|
Niu Y, Li X, Zhang C, Wei Y. The phylogenetic placement of Odontobutis obscura base on complete mitochondrial DNA sequence. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:399-400. [PMID: 26730482 DOI: 10.3109/19401736.2015.1127363] [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
In our research, 16 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of Odontobutis obscura. The aim of our research was to provide some important genetic background information for conservational practice of these valuable fish species. The total length of the mitochondrial genome is 16 864 bp and deposited in the GenBank with accession numbers KT438552. The gene arrangement and transcriptional direction were similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNAs) and a major non-coding control region. The nucleotide skewness for the coding strands of O. obscura (GC-skew = -0.26) is biased toward G and the negative GC-skew ranges from -0.51(ND2) to -0.24(CO1). The phylogenetic analysis showed that the Gobiiformes could be divided into three groups, Eleotridae, Odontobutidae and Rhyacichthyidae. The O. Obscura and O. Potamophila are sister species and clustered together.
Collapse
Affiliation(s)
- Yandong Niu
- a Hunan Academy of Forestry , Changsha , China.,b Hunan Dongting Lake Wetland Ecosystem Research Station , Changsha , China
| | - Xiquan Li
- a Hunan Academy of Forestry , Changsha , China.,b Hunan Dongting Lake Wetland Ecosystem Research Station , Changsha , China
| | - Canming Zhang
- a Hunan Academy of Forestry , Changsha , China.,b Hunan Dongting Lake Wetland Ecosystem Research Station , Changsha , China.,c Hunan Cooperation Center of Water Resources Research and Development , Changsha , China
| | - Ying Wei
- d Forestry Department of Hunan Province , Changsha , China
| |
Collapse
|
4
|
Chen D, Chu W, He Y, Liang XF, Mai K. Characteristics and phylogenetic studies of complete mitochondrial DNA based on the ricefield eel (Monopterus albus) from four different areas. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2419-20. [PMID: 26258513 DOI: 10.3109/19401736.2015.1030623] [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
In this study, we cloned and sequenced the complete mitochondrial DNA of ricefield eel populations from four different areas (Guizhou province, Guangxi province, Hunan province, and Guangdong province) in China. The mitochondrial genome was 16,622 bp in length and deposited in the GenBank with accession numbers KP779622-KP779625. The organizations of the complete mitogenomes of the four ricefield eel were similar to those of other teleost species which contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, as well as a putative control region (CR). Most of these genes were encoded on the H-strand, except for the ND6 and eight tRNA genes, all other genes were encoded on the H-strand. Phylogenetic analyses using N-J computational algorithms showed that the ricefield eel was clustered with Mastacembelus armatus (KJ184553) and they belong to Synbranchiformes. The four ricefield eel populations could be divided into two groups: Guangxi province and the other population cluster together.
Collapse
Affiliation(s)
- Dunxue Chen
- a Key Lab of Freshwater Animal Breeding, Ministry of Education, College of Fisheries, Huazhong Agricultural University , Wuhan , Hubei , PR China and
| | - Wuying Chu
- a Key Lab of Freshwater Animal Breeding, Ministry of Education, College of Fisheries, Huazhong Agricultural University , Wuhan , Hubei , PR China and
| | - Yan He
- a Key Lab of Freshwater Animal Breeding, Ministry of Education, College of Fisheries, Huazhong Agricultural University , Wuhan , Hubei , PR China and
| | - Xu-Fang Liang
- a Key Lab of Freshwater Animal Breeding, Ministry of Education, College of Fisheries, Huazhong Agricultural University , Wuhan , Hubei , PR China and
| | - Kangsen Mai
- b College of Fisheries, Ocean University of China , Qingdao , PR China
| |
Collapse
|
5
|
Gong L, Shi W, Si LZ, Wang ZM, Kong XY. The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles. Mol Biol 2015. [DOI: 10.1134/s0026893315030061] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Song HY, Mabuchi K, Satoh TP, Moore JA, Yamanoue Y, Miya M, Nishida M. Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei). Gene 2014; 542:146-55. [PMID: 24680775 DOI: 10.1016/j.gene.2014.03.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 03/10/2014] [Accepted: 03/20/2014] [Indexed: 12/25/2022]
Abstract
Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families.
Collapse
Affiliation(s)
- Ha Yeun Song
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Takashi P Satoh
- National Museum of Nature and Science, Collection Center, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Jon A Moore
- Florida Atlantic University, Wilkes Honors College, Jupiter, FL 33458, USA & Harbor Branch Oceanographic Institution, Fort Pierce, FL 34946, USA
| | - Yusuke Yamanoue
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 2971-4 Bentenjima, Maisaka-cho, Nishi-ku, Hamamatsu 431-0214, Japan
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa 903-0213, Japan
| |
Collapse
|
8
|
Xincheng Z, Xinping Z, Kunci C, Jian Z, Qing L, Xiaoyou H. Comparison of the northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids (C. maculata ♀ × C. argus ♂ and C. argus ♀ × C. maculata ♂) based on complete mitochondrial DNA sequences. MITOCHONDRIAL DNA 2014; 26:805-6. [PMID: 24409853 DOI: 10.3109/19401736.2013.855902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial DNA of Channa argus, Channa maculata, C. maculate ♀ × C. argus ♂ and C. argus ♀ × C. maculata ♂ were sequenced to characterize and compare their mitochondrial genomes. The lengths were 16,558, 16,559, 16,558 and 16,559 bp respectively. Start codon of 13 protein-coding genes was ATG, except that COI was GTG. The control region of the mitogenome were 907, 908, 907 and 908 bp in C. argus, C. maculata and their reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculate ♀ × C. argus ♂), respectively.
Collapse
Affiliation(s)
- Zhang Xincheng
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b College of Life Science and Fisheries, Shanghai Ocean University , Shanghai , People's Republic of China
| | - Zhu Xinping
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b College of Life Science and Fisheries, Shanghai Ocean University , Shanghai , People's Republic of China
| | - Chen Kunci
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b College of Life Science and Fisheries, Shanghai Ocean University , Shanghai , People's Republic of China
| | - Zhao Jian
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b College of Life Science and Fisheries, Shanghai Ocean University , Shanghai , People's Republic of China
| | - Luo Qing
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and
| | - Hong Xiaoyou
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and
| |
Collapse
|
9
|
Cheng HL, Wu CY, Tsai KC, Liu AY, Chiu YW, Tseng DY. The complete mitochondrial genome sequence of Onychostoma alticorpus (Cypriniformes, Cyprinidae). ACTA ACUST UNITED AC 2013; 25:188-9. [PMID: 23992243 DOI: 10.3109/19401736.2013.792069] [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
We determined the complete mitochondrial genome (mitogenome) sequence of Onychostoma alticorpus, which is known as an endemic freshwater species in Taiwan, by using long polymerase chain reaction method. The total length of O. alticorpus mitogenome is 16,680 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The overall base composition of O. alticorpus is 30.88% for A, 23.57% for T, 16.56% for G and 28.99% for C, with a slight AT bias of 54.45%. Gene location and specific usage of distinct termination codon types characterize typically the vertebrate mitochondrial genome. The determination of O. alticorpus mitogenome would play an important role not only in the delineation of phylogeographic history and population genetic structure, but reflection of conservation efforts on the genetic diversity as well as population vitality.
Collapse
Affiliation(s)
- Hui-Ling Cheng
- Chia Nan University of Pharmacy and Science , Tainan City , Taiwan
| | | | | | | | | | | |
Collapse
|
10
|
Zhuang X, Qu M, Zhang X, Ding S. A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One 2013; 8:e73561. [PMID: 23951357 PMCID: PMC3739747 DOI: 10.1371/journal.pone.0073561] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.
Collapse
Affiliation(s)
- Xuan Zhuang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Meng Qu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Xiang Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| |
Collapse
|
11
|
Li SJ, Jing YJ, Song HM, Bai JJ, Ma D, Ye X. Complete mitochondrial genome of the green sunfish (Lepomis cyanellus). ACTA ACUST UNITED AC 2013; 25:42-3. [DOI: 10.3109/19401736.2013.782016] [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]
|
12
|
Chen DX, Li Y, Bin SY, Wang K, Chu WY, Zhang JS. The phylogenetic placement of Siniperca obscura base on complete mitochondrial DNA sequence. ACTA ACUST UNITED AC 2013; 25:218-9. [PMID: 23631364 DOI: 10.3109/19401736.2013.792075] [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
Abstract The extant freshwater sinipercids represent a group of 12 species and they are endemic to East Asia. In this study, we cloned and sequenced the complete mitochondrial DNA of Siniperca obscura from the Lijiang River. The size of the complete mitochondrial genome is 16,492 bp. The organization of the mitochondrial contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region as well as those reported sinipercid fishes. Among the 13 protein-coding genes, three reading-frame overlaps were found: ATP8 and ATP6 overlap by 10 nucleotides and ND4 and ND4L overlap by 7 nucleotides and ND5 and ND6 overlap by 5 nucleotides. Phylogenetic analyses using N-J and maximum parsimony (MP) computational algorithms showed that S. chuatsi and S. kneri are sister species, next joined by S. Obscura, based on combined 12 protein-coding genes (excluding DN6).
Collapse
Affiliation(s)
- Dun-Xue Chen
- Department of Bioengineering and Environmental Science, Changsha University , Hunan , P. R. China
| | | | | | | | | | | |
Collapse
|
13
|
Qiao H, Cheng Q, Chen Y. Complete mitochondrial genome sequence of Gymnocypris dobula (Cypriniformes: Cyprinidae). MITOCHONDRIAL DNA 2013; 25:21-2. [PMID: 23488926 DOI: 10.3109/19401736.2013.775270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Gymnocypris dobula is listed as Vulnerable (VU) status in the IUCN's Red List of Threatened Species. In this paper, complete mitochondrial DNA sequence of G. dobula was determined. The complete mitogenome is 16,720 bp in length, and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of G. dobula is conducive to futher studies on molecular systematics, stock evaluation and conservation genetics.
Collapse
Affiliation(s)
- Huiying Qiao
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai 200090 , China and
| | | | | |
Collapse
|
14
|
Wan Q, Chen Y, Cheng Q, Qiao H. The complete mitochondrial genome sequence of Ancherythroculter nigrocauda (Cypriniformes:Cyprinidae). ACTA ACUST UNITED AC 2013; 24:627-9. [PMID: 23452280 DOI: 10.3109/19401736.2013.772157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ancherythroculter nigrocauda is a fish endemic to the upper reaches of the Yangtze River in China. In this study, we determined and analyzed the complete mitochondrial DNA (mtDNA) sequence of this species. The mitogenome is 16,623 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). This mitogenome sequence data can contribute to elucidate the evolutionary mechanisms, molecular systematics, and biogeography of Ancherythroculter and is useful to conservation genetics and stock evaluation for A. nigrocauda.
Collapse
Affiliation(s)
- Quan Wan
- College of Animal Science and Technology, Anhui Agricultural University , Hefei 230036 , People's Republic of China
| | | | | | | |
Collapse
|
15
|
Chen Y, Cheng Q, Qiao H, Zhu Y, Chen W, Ren G. The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae). ACTA ACUST UNITED AC 2013; 24:353-5. [PMID: 23350526 DOI: 10.3109/19401736.2012.760556] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial DNA (mtDNA) sequence of Schizothorax wangchiachii has been determined. The mitogenome is 16,593 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The complete mtDNA sequence of S. wangchiachii can contribute to elucidate the evolutionary mechanisms and biogeography of Schizothorax and is useful to stock evaluation and conservation genetics for S. wangchiachii.
Collapse
Affiliation(s)
- Ying Chen
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, PR China
| | | | | | | | | | | |
Collapse
|
16
|
Chu W, Chen D, Wang K, Li Y, Du S, Zhang J. Analysis of the variable sites and phylogenetic studies of complete mitochondrial DNA based on the Siniperca scherzeri (Perciformes: Sinipercidae) from four different areas. MITOCHONDRIAL DNA 2012; 24:288-9. [PMID: 23245505 DOI: 10.3109/19401736.2012.748042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese mandarin fish, Siniperca scherzeri populations from four different areas of the Yangtze River and the Pearl River systems in China. In the Yangtze River system, fish samples were taken from three regions, Dongting Lake (DT), Poyang Lake (PL) and Xiangjiang River (XR). In the Pearl River system, fish samples were collected from the Lijiang River (LR). The sizes of their complete mitochondrial genome were 16,502 bp (LR), 16,508 bp (PL), 16,502 bp (XR) and 16,508 bp (DT), respectively. The organization of the S. scherzeri mitochondrial genomes was similar to those reported from other fish mitochondrial genomes. Phylogenetic analyses using N-J computational algorithms showed that the Sinipercidaes are monophyletic and can be divided into two genera, Siniperca and Coreoperca. The S. scherzeri could be divided into two groups along the Yangtze River system and the Pearl River.
Collapse
Affiliation(s)
- Wuying Chu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan, People's Republic of China
| | | | | | | | | | | |
Collapse
|
17
|
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.
Collapse
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
| | | | | | | | | | | |
Collapse
|
18
|
Chen DX, Chu WY, Liu XL, Nong XX, Li YL, Du SJ, Zhang JS. Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. ACTA ACUST UNITED AC 2012; 23:70-6. [PMID: 22409749 DOI: 10.3109/19401736.2011.653799] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.
Collapse
Affiliation(s)
- Dun-Xue Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
19
|
Li SJ, Bai JJ, Cai L, Ma DM, Du FF. The complete mitochondrial genomes of largemouth bass of the northern subspecies (Micropterus salmoides salmoides) and Florida subspecies (Micropterus salmoides floridanus) and their applications in the identification of largemouth bass species. ACTA ACUST UNITED AC 2012; 23:92-9. [PMID: 22409750 DOI: 10.3109/19401736.2012.660923] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The largemouth bass belongs to the family Centrarchidae, which includes two subspecies: the northern subspecies, Micropterus salmoides salmoides, and the Florida subspecies, Micropterus salmoides floridanus. In this study, the complete mitochondrial genomes of the two subspecies were sequenced, and their genetic differences were identified. The mitogenomes of M. s. salmoides and M. s. floridanus are 16,486 and 16,479 bp in length, respectively. The two subspecies consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA), which are typical for vertebrate mtDNA. Phylogenetic analysis provided statistical support for the monophyly of the family Centrarchidae. Comparison of the two subspecies' mitogenomes revealed a relatively high number (450) of single nucleotide polymorphisms (SNPs) in protein-coding genes. We characterized SNPs in the partial cytochrome c oxidase subunit 1 gene of different individuals from three cultured populations, one wild northern subspecies population, and one wild Florida subspecies population. Twenty-eight SNPs were fixed with alternative nucleotides in the two subspecies, which could be used for differentiating them. Based on this gene, phylogenetic tree and genetic distance analyses supported that cultured largemouth bass in China belongs to the northern subspecies.
Collapse
Affiliation(s)
- Sheng-Jie Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, P.R. China
| | | | | | | | | |
Collapse
|
20
|
Cheng J, Ma GQ, Song N, Gao TX. Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene 2011; 491:210-23. [PMID: 21989484 DOI: 10.1016/j.gene.2011.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 09/20/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus+Collichthys lucidus and Larimichthys crocea+Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.
Collapse
Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Yushan Road, 5, Qingdao 266003, China
| | | | | | | |
Collapse
|