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Liu F, Zhang X, Wei X, Li Y, Liu W, Gan G, Xiao L, Wang X, Luo H. Gonadal transcriptome analysis of paradise fish Macropodus opercularis to reveal sex-related genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101125. [PMID: 37666127 DOI: 10.1016/j.cbd.2023.101125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023]
Abstract
Macropodus opercularis is an ornamental fish species endemic to China, with obvious sexual dimorphism in phenotype. To obtain the gene expression profile of the gonads of M. opercularis and explore its sex-related genes, six cDNA libraries were constructed from the sexually mature M. opercularis, and RNA-seq analysis was performed. The sequenced clean data were assembled by de novo splicing to generate 171,415 unigenes, and differentially expressed genes (DEGs) screening revealed that there were 41,638 DEGs in the gonads of M. opercularis. By comparing those DEGS in the ovary with the testis, we found 29,870 DEGs were upregulated and 11,768 DEGs were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis showed that GO terms related to cell cycle and gamete formation were enriched, and pathway signals related to sex differences, such as FoxO signalling pathway and PI3K-Akt signalling pathway, were also detected. Reverse transcript fluorescence quantitative PCR (RT-qPCR) validation of 14 DEGs associated with sex differences showed that the RT-qPCR results were consistent with RNA-Seq analysis, and five genes, foxl2, sox3, foxo, zar1, cyp19a1, were significantly expressed in the ovaries. dmrt1, cyp11b, amh, sf1, sox9, gdf6, dmrt3, fstl1 and hsd11b2, a total of nine genes were significantly expressed in the testis. The results of this study provide a basis for the study of gonadal differentiation, developmental mechanisms and related functional genes in M. opercularis.
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Affiliation(s)
- Fan Liu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China. https://twitter.com/@FanLiu_
| | - Xueling Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Xiaokai Wei
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Yu Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Wei Liu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Guochen Gan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Lingling Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Xinyue Wang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Hui Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, College of Fisheries, Southwest University, Chongqing 402460, China.
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Wang J, Xu W, Liu Y, Bai Y, Liu H. Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae). Gene X 2023; 857:147186. [PMID: 36627090 DOI: 10.1016/j.gene.2023.147186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/25/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (OL) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.
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Affiliation(s)
- Jiachen Wang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yuyao Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yawen Bai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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Dong C, Jia Y, Han M, Chen W, Mou D, Feng C, Jia J, Liu X. Phylogenetic analysis of eight species of Anomopoda based on transcriptomic and mitochondrial DNA sequences. Gene 2021; 787:145639. [PMID: 33848576 DOI: 10.1016/j.gene.2021.145639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/10/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Anomopoda is the widespread planktonic microcrustacean, which plays a crucial role in aquatic ecosystem. There are few studies about the evolutionary relationships among various Anomopoda basing on molecular data. In the present study, phylogenetic analysis of eight Anomopoda was carried out. Firstly, the culture system was developed to breed cladocerans. By using this system, eight species (Daphnia magna, D. pulex, D. sinensis, Ceriodaphnia reticulata, Moina micrura, Scapholeberis kingi, Simocephalus vetulus and Eurycercus lamellatus) were purified and cultured stably in the laboratory. Then, transcriptomic sequences and partial mitochondrial DNA sequences were both used to reconstruct the phylogenetic tree among 8 species. Transcriptomic sequences were sequenced on Illumina Hiseq 2500 platform. After assembly and annotation, transcriptomic sequences were spliced together and aligned for phylogenetic analysis. Basing on the orthologous genes derived from transcriptomic sequences, the phylogenetic analysis showed that 4 genera of Daphniidae were clustered into one group, and among the 4 genera, Ceriodaphnia was closer to Daphnia than Simocephalus, while Scapholeberis was farthest from other species. In addition, Eurycercidae was closer to Daphniidae than Moinidae. The phylogenetic trees based on both 12S rRNA and 16S rRNA sequences were similar with that based on transcriptomic sequences. Meanwhile, the phylogenetic tree based on 16S rRNA sequences was more suitable than that based on 12S rRNA sequences. These results suggested that the phylogenetic analysis basing on the transcriptomic sequences was available in cladocerans, which will help us to effectively understand the phylogenetic relationships among various cladocerans.
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Affiliation(s)
- Chenchen Dong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyi Jia
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
| | - Mengqi Han
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenkai Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Dezhen Mou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Cui Feng
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyi Jia
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangjiang Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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6
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Li Z, Li M, Xu S, Liu L, Chen Z, Zou K. Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int J Mol Sci 2020; 21:E4685. [PMID: 32630142 PMCID: PMC7370159 DOI: 10.3390/ijms21134685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/31/2022] Open
Abstract
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.
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Affiliation(s)
- Zhenhai Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Min Li
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shannan Xu
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Zuozhi Chen
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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Liu H, Xu N, Zhang Q, Wang G, Xu H, Ruan H. Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora, Moniligastridae) and comparison with other Metagynophora species. Genomics 2020; 112:3056-3064. [PMID: 32454169 DOI: 10.1016/j.ygeno.2020.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/04/2020] [Accepted: 05/20/2020] [Indexed: 02/03/2023]
Abstract
Here, the complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species. The circular mitogenome was 14,648 bp in length and contained two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The types of constitutive genes and the direction of the coding strand that appeared in Drawida mitogenome were identical to those observed in other Metagynophora species, except for a missing lengthy non-coding region. The conservative relationships between Drawida species were supported by the overall analyses of 13 PCGs, two rRNAs, and 22 tRNAs. A comparison of the Metagynophora mitogenomes revealed that the ATP8 gene possessed the highest polymorphism among the 13 PCGs and two rRNAs. Phylogenetic analysis suggested that the Moniligastridae contained Drawida, which is a primitive Metagynophora group. Our study provides a step forward toward elucidating the evolutionary linkages within Drawida and even Metagynophora.
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Affiliation(s)
- Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Qingzheng Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Guobing Wang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hanmei Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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8
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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History. Int J Mol Sci 2020; 21:ijms21051874. [PMID: 32182936 PMCID: PMC7084342 DOI: 10.3390/ijms21051874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.
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Liu H, Xu N, Yang J, Zhang Q, Zuo K, Lv F. The complete mitogenome of Hong Kong paradise fish ( Macropodus hongkongensis), an endemic freshwater fish in South China. Mitochondrial DNA B Resour 2019; 4:2849-2850. [PMID: 33365757 PMCID: PMC7706895 DOI: 10.1080/23802359.2019.1660271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/01/2019] [Indexed: 11/26/2022] Open
Abstract
The first complete mitogenome of Hong Kong paradise fish (Macropodus hongkongensis) was determined in this study. The assembled mitogenome is 16,494 bp and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition of the complete mitogenome is 30.6% A, 24.8% C, 14.8% G, and 29.8% T, with an A + T bias of 60.4%. The maximum-likelihood tree based on 13 protein-coding genes showed that M. erythropterus was the closest related species to M. hongkongensis.
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Affiliation(s)
- Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jing Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qingzheng Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ke Zuo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Fangzhong Lv
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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10
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Yu P, Yang X, Zhou W, Yang W, Zhou L, Liu X, Wan Q, Zhang J. Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae). Genetica 2019; 147:165-176. [PMID: 30887216 DOI: 10.1007/s10709-019-00059-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.
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Affiliation(s)
- Peng Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Weishang Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wentao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xuan Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Quan Wan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Mingguang Modern Agricultural Science and Technology Cooperation Promotion Service Center, Mingguang, 239400, China.
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11
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Li R, Wang G, Wen ZY, Zou YC, Qin CJ, Luo Y, Wang J, Chen GH. Complete mitochondrial genome of a kind of snakehead fish Channa siamensis and its phylogenetic consideration. Genes Genomics 2018; 41:147-157. [PMID: 30242740 DOI: 10.1007/s13258-018-0746-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/18/2018] [Indexed: 12/28/2022]
Abstract
The snakehead fish, Channa siamensis, belongs to the genus of Channa (perciformes: Channidae) and was first reported by Günther in 1861. Despite it has been described approximately for 15 decades, the genetic information is limited and the taxon status of this kind of fish is still unclear. The primary objective of this study is to get more genomic data and calculate the taxon location of this kind of fish. The next generation sequencing method was used to obtain the whole mitochondrial DNA information, and bioinformatic analysis was performed to investigate the evolutionary status and taxon location of C. siamensis. The circular mitochondrial DNA was 16,570 bp in length, and which showed typical piscine structure and arrangement. The overall nucleotide composition was 29.28% A, 24.72% T, 30.71% C, 15.29% G, with 54.1% AT, respectively. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported C. siamensis belongs to the genus Channa and shows a close relationship with C. micropeltes. These data will provide more useful information for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Rui Li
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Gang Wang
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Zheng-Yong Wen
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China. .,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
| | - Yuan-Chao Zou
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Chuan-Jie Qin
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Yu Luo
- Institute of Aquaculture, Neijiang Academy of Agricultural Sciences, Neijiang, 641000, Sichuan, China
| | - Jun Wang
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Gui-Hong Chen
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
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Jiang L, Zhao L, Cheng D, Zhu L, Zhang M, Ruan Q, Chen W. The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications. Gene 2017; 626:367-375. [PMID: 28536079 DOI: 10.1016/j.gene.2017.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/30/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
Abstract
The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China; Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Li Zhao
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Dongmei Cheng
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Lilan Zhu
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
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13
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Characterization of the complete mitochondrial genome of the tidewater goby, Eucyclogobius newberryi (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0772-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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The complete mitochondrial genome of a threatened loach (Sinibotia reevesae) and its phylogeny. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0541-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Sun MH, Yue CW, Liu TT, Li L, Liu HY. The complete mitochondrial genome of Budorcas taxicolor bedfordi (Artiodactyla: Bovidae) and phylogenetic studies of Caprinae. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0693-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Villela LCV, Alves AL, Varela ES, Yamagishi MEB, Giachetto PF, da Silva NMA, Ponzetto JM, Paiva SR, Caetano AR. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 2017; 145:51-66. [DOI: 10.1007/s10709-016-9945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
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Zhang D, Wang F, Dong S, Lu Y. De novo assembly and transcriptome analysis of osmoregulation in Litopenaeus vannamei under three cultivated conditions with different salinities. Gene 2015; 578:185-93. [PMID: 26691500 DOI: 10.1016/j.gene.2015.12.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 01/13/2023]
Abstract
Litopenaeus vannamei, one of the most important euryhaline crustaceans, is cultured in seawater, brackish water, and freshwater worldwide. We performed Illumina RNA sequencing of L. vannamei gills, generating 124,914,870; 119,250,450; and 105,487,350 raw reads from the shrimps cultured in seawater, brackish water, and freshwater, respectively. From these reads, 466,293 transcripts were de novo assembled and annotated. Comparative genomic analysis showed that 1752 genes were significantly differentially expressed in the freshwater group compared with the seawater group, including 1242 upregulated and 510 downregulated genes. In addition, 1246 genes were differentially expressed in the brackish group vs. the seawater water group, including 659 upregulated and 587 downregulated genes. These differentially expressed genes were mainly involved in energy metabolism, substance metabolism, ion transport and signal transduction, and genetic process. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to analyze the functional significance of the differentially expressed genes, included those responding to salinity through diverse biological functions and processes and numerous potential genes associated with the osmotic response. L. vannamei responses to the three cultivated salinities were analyzed using next-generation sequencing. The transcriptional database established from the current research adds to the information available on L. vannamei and the findings expand our knowledge of the molecular basis of osmoregulation mechanisms in this species.
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Affiliation(s)
- Dan Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fang Wang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shuanglin Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yunliang Lu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Yang JP, Li XH, Li YF, Li J, Shuai FM, Zhu SL. Complete mitochondrial genome of Ochetobius elongatus (Cyprinidae, Leuciscinae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2695-7. [PMID: 26477619 DOI: 10.3109/19401736.2015.1089542] [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: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of Ochetobius elongatus was first sequenced and annotated. The entire mitogenome is 16 613 bp in length and has a typical vertebrate mitochondrial genetic trait, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. The overall nucleotide composition of O. elongatus mt genome is A: 30.96%, T: 25.38%, G: 16.26% and C: 27.40%, with the A + T content of 56.34%, showing an obvious anti-G bias. Phylogenetic analyses suggest that Leuciscinae formed a clade first and then clustered with Cultrinae. The complete mitochondrial genome of O. elongatus will benefit to a better understanding of population genetics, molecular systematics and stock evaluation, further serving the germplasm resources conservation and management of O. elongatus.
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Affiliation(s)
- Ji Ping Yang
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture , Guangzhou , People's Republic of China
| | - Xin Hui Li
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture , Guangzhou , People's Republic of China
| | - Yue Fei Li
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture , Guangzhou , People's Republic of China
| | - Jie Li
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture , Guangzhou , People's Republic of China
| | - Fang Min Shuai
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and.,b Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl River, Ministry of Agriculture , Guangzhou , People's Republic of China
| | - Shu Li Zhu
- a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , People's Republic of China and
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Mu X, Wang X, Liu Y, Song H, Liu C, Gu D, Wei H, Luo J, Hu Y. An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion. Gene 2015; 573:216-24. [PMID: 26187073 DOI: 10.1016/j.gene.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dangen Gu
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hui Wei
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jianren Luo
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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