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Kong D, Gan Z, Li X. Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes. Gene 2024; 896:148054. [PMID: 38042216 DOI: 10.1016/j.gene.2023.148054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023]
Abstract
The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.
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Affiliation(s)
- Deming Kong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhibin Gan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Xin ZZ, Tang S, Lu X, Zhang HB, Zhang DZ, Wang G, Tang BP, Liu QN. The analyses of the complete mitochondrial genomes of three crabs revealed novel gene rearrangements and phylogenetic relationships of Brachyura. Mol Biol Rep 2023; 50:10301-10313. [PMID: 37971570 DOI: 10.1007/s11033-023-08833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Brachyura crab is the largest branch of Decapoda crustacean. Phylogenetic relationships within Brachyura remain controversial to be investigated. The mitochondrial genome (mitogenome) is an important molecular marker for studying the phylogenetic relationships of Brachyura. METHODS AND RESULTS To understand the phylogeny of Brachyura, the three complete mitogenomes from Charybdis annulata, Leptodius exaratus, and Spider crab were sequenced and annotated. Their full length was 15,747, 15,716, and 16,608 bp long, respectively. The first two crabs both contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. However, Spider crab contained 13 PCGs, two rRNA genes, 25 tRNA genes and a control region. The mitogenomes of each of the three crabs exhibited high AT content (67.8%, 69.1%, and 70.8%), with negative AT skews (-0.014, - 0.028, and - 0.017) and GC skews (-0.269, - 0.286, and - 0.341). The gene order of C. annulata was identical to the ancestor of Brachyura. Compared with the ancestor of Brachyura, L. exaratus exhibited the gene rearrangements of Val (V)-rrnS-control region, and Spider crab had the four copies of Lys (K). Phylogenetic analyses indicated that C. annulata belonged to Portunidae family, Portunoidea superfamilies, L. exaratus belonged to Xanthidae family, Xanthoidea superfamilies, and Spider crab belonged to Mithracidae family, Majoidea superfamilies. Phylogenetic analyses showed that the two species (Somanniathelphusa boyangensis and Huananpotamon lichuanense) belonging to the Potamoidea were sister groups to the Thoracotremata, thus supporting the conclusion that Heterotremata is polyphyletic. CONCLUSION The results of this study enriched the crab mitogenome database and enabled us to better understand the phylogenetic relationships of Brachyura.
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Affiliation(s)
- Zhao-Zhe Xin
- The Laboratory of Aquatic Parasitology, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266237, Shandong, China
| | - Sheng Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China
| | - Xiang Lu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China.
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Jin X, Guo X, Chen J, Li J, Zhang S, Zheng S, Wang Y, Peng Y, Zhang K, Liu Y, Liu B. The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. Genes Genomics 2023; 45:377-391. [PMID: 36346542 DOI: 10.1007/s13258-022-01319-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed. OBJECTIVE The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. METHODS The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks. RESULTS This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution. CONCLUSION Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
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Affiliation(s)
- Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Xingle Guo
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jian Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China. .,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China.
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Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13112128. [DOI: 10.3390/genes13112128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.
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A novel gene order and remolded tRNAs revealed in the mitogenome of Asian gecarcinucid freshwater crabs (Brachyura, Gecarcinucidae). Gene 2021; 813:146102. [PMID: 34933078 DOI: 10.1016/j.gene.2021.146102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Here we report the first mitochondrial genomes (mitogenomes) of four species of gecarcinucid freshwater crabs (FWCs) in two genera, two from China (Somanniathelphusa hainanensis and S. yangshanensis), one from Laos (Esanthelphusa dugasti), and one from Myanmar (Esanthelphusa keyini). A novel gecarcinucid mitochondrial gene order (GMGO2) that was only found in E. dugasti that contains a total of 42 genes, including one pseudogene, two remolded tRNAs and two duplicated tRNAs. The GMGO2 of E. dugasti was compared with the brachyuran ground-pattern mitochondrial gene order (BMGO), revealing the rearrangements of the positions of 10 tRNAs, two PCGs, and one mNCR. The three other gecarcinucids in this study were all found to possess a previously reported gecarcinucid mitochondrial gene order (GMGO1). The phylogenetic tree reconstructed using the secondary structures of 22 tRNAs of the mitogenomes of 41 species of FWCs provides insights into the evolution of the mitogenome of E. dugasti (GMGO2) which includes remolded and duplicated tRNAs.
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Molecular characterization and phylogenetic analysis of crabs (Crustacea: Decapoda: Brachyura) based on mitochondrial COI and 16S rRNA genes. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Katneni VK, Shekhar MS, Jangam AK, Paran BC, Selvaraj A, Krishnan K, Kaikkolante N, Prabhudas SK, Gopalapillai G, Koyadan VK. Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato. Ecol Evol 2021; 11:2040-2049. [PMID: 33717440 PMCID: PMC7920775 DOI: 10.1002/ece3.7148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.
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Affiliation(s)
- Vinaya Kumar Katneni
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Mudagandur S. Shekhar
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | | | - Ashok Selvaraj
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Karthic Krishnan
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Nimisha Kaikkolante
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Sudheesh K. Prabhudas
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Gopikrishna Gopalapillai
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
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Tang YY, Tang BP, Xin ZZ, Li YT, Zha XH, Zhang DZ, Sun Y, Liu QN, Ma YF. Characterization of the complete mitochondrial genome of Helice latimera and its phylogenetic implications in Brachyura. Genomics 2020; 112:5180-5187. [DOI: 10.1016/j.ygeno.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/22/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
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Liu QN, Tang YY, Yang TT, Li YT, Yu XM. Phylogenetic relationships of Grapsoidea and insights into the higher phylogeny of Brachyuran. Genomics 2020; 113:429-439. [PMID: 32889043 DOI: 10.1016/j.ygeno.2020.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Abstract
Decapoda is one of the most diverse crustacean orders, and has become an important research subject. However, the phylogenetic relationships among the main lineages of Decapoda remain uncertain, especially in the order Brachyura. Herein, we sequenced the whole mitochondrial genome of V. litterata and constructed a phylogenetic tree to understand its phylogenetic relationships with other species. The results showed that the mitochondrial genome of V. litterata was generally similar to mitogenomes of Metazoa reported in the literature, with a size of 16,247 bp, 37 genes, and a control region. Both AT-skew and GC-skew were negative, indicating more abundant Cs and Ts than Gs and As. The gene arrangement of V. litterata is identical to those of Eriocheir hepuensis, Cyclograpsus granulosus, Hemigrapsus sanguineus, Helicana wuana, and Helice tientsinensis but differs from the pancrustacean ground pattern and typical arrangement of Brachyuran crabs. Phylogenetic reconstruction showed that V. litterata belongs to the Varunidae.
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Affiliation(s)
- Qiu-Ning Liu
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
| | - Ying-Yu Tang
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Ting-Ting Yang
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Yue-Tian Li
- School of Wetland, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Xiao-Min Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
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Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs. Genomics 2020; 112:10-19. [DOI: 10.1016/j.ygeno.2019.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 01/15/2023]
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Chen F, Wang K. Characterization of the innate immunity in the mud crab Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2019; 93:436-448. [PMID: 31362092 DOI: 10.1016/j.fsi.2019.07.076] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/20/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Mud crabs, Scylla paramamosain, are one of the most economical and nutritious crab species in China and South Asia. Inconsistent with the high development of commercial mud crab aquaculture, effective immunological methods to prevent frequently-occurring diseases have not yet been developed. Thus, high mortalities often occur throughout the different developmental stages of this species resulting in large economic losses. In recent years, numerous attempts have been made to use various advanced biological technologies to understand the innate immunity of S. paramamosain as well as to characterize specific immune components. This review summarizes these research advances regarding cellular and humoral responses of the mud crab during pathogen infection, highlighting hemocytes and gills defense, pattern recognition, immune-related signaling pathways (Toll, IMD, JAK/STAT, and prophenoloxidase (proPO) cascades), immune effectors (antimicrobial peptides), production of reactive oxygen species and the antioxidant system. Diseases affecting the development of mud crab aquaculture and potential disease control strategies are discussed.
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Affiliation(s)
- Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, China
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, Fujian, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, Fujian, China.
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Luo H, Li H, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Yu G, Zhang M. The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis. Genes (Basel) 2019; 10:E487. [PMID: 31252631 PMCID: PMC6678547 DOI: 10.3390/genes10070487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022] Open
Abstract
Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.
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Affiliation(s)
- Hongdi Luo
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Haijun Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - An Huang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qingyong Ni
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Bo Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ying Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, Hebei, China
| | - Guohua Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, Guangxi, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Mingwang Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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Li Y, Li R, Ye Y, Mu C, Wang C. 1H NMR metabolic profiling revealed characteristic metabolites in mud crab Scylla paramamosain for different geographical origins. JOURNAL OF APPLIED ANIMAL RESEARCH 2019. [DOI: 10.1080/09712119.2019.1623802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yongliang Li
- Key Laboratory of Applied Marine Biotechnology, Chinese Ministry of Education, Ningbo University, Ningbo, People’s Republic of China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, People’s Republic of China
| | - Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Chinese Ministry of Education, Ningbo University, Ningbo, People’s Republic of China
| | - Yangfang Ye
- Key Laboratory of Applied Marine Biotechnology, Chinese Ministry of Education, Ningbo University, Ningbo, People’s Republic of China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Chinese Ministry of Education, Ningbo University, Ningbo, People’s Republic of China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Chinese Ministry of Education, Ningbo University, Ningbo, People’s Republic of China
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Li JY, Zeng C, Yan GY, He LS. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep 2019; 9:2610. [PMID: 30796230 PMCID: PMC6385184 DOI: 10.1038/s41598-019-38735-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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Guan M, Tan H, Fazhan H, Xie Z, Shi X, Zhang Y, Lin F, Ikhwanuddin M, Ma H. The whole mitochondrial genome and phylogenetic analysis of Lupocycloporus gracilimanus (Stimpson, 1858) (Decapoda, portunidae). Mitochondrial DNA B Resour 2018; 3:1244-1245. [PMID: 33474478 PMCID: PMC7800190 DOI: 10.1080/23802359.2018.1532345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 08/31/2018] [Indexed: 11/25/2022] Open
Abstract
The mitochondrial genome plays an important role in studies on phylogeography and population genetic diversity. Here we report the complete mitochondrial genome of Lupocycloporus gracilimanus (Stimpson, 1858) which is the first mitochondrial genome reported in genus Lupocycloporus by now. The mitogenome is 15,990 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. The phylogenetic analysis showed that L. gracilimanus was closest to genus Scylla. The present research should provide valuable information for phylogenetic analysis and classification of Portunidae.
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Affiliation(s)
- Mengyun Guan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Zhuofang Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
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Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, Tan H, Ma H. The whole mitochondrial genome of the mangrove crab, Metopograpsus frontalis (Miers, 1880) (Decapoda, Grapsidae) and its phylogenetic relationship. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:368-369. [PMID: 33490509 PMCID: PMC7800978 DOI: 10.1080/23802359.2018.1450685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.
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Affiliation(s)
- Mengyun Guan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Xinming Liu
- Marine Resource and Environment Research Institute, Guangxi Academy of Oceanography, Nanning, China
| | - Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhuofang Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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Jia XN, Xu SX, Bai J, Wang YF, Nie ZH, Zhu CC, Wang Y, Cai YX, Zou JX, Zhou XM. The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa (Crustacea: Decapoda: Parathelphusidae). PLoS One 2018; 13:e0192601. [PMID: 29438407 PMCID: PMC5810993 DOI: 10.1371/journal.pone.0192601] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/28/2018] [Indexed: 11/18/2022] Open
Abstract
In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab. The authors established the phylogenetic relationships using the maximum likelihood and Bayesian inference methods. The phylogenetic relationship indicated that the molecular taxonomy of S. boyangensis is consistent with current morphological classification, and Parathelphusidae and Potamidae are derived within the freshwater clade or as part of it. In addition, the authors used the COX1 sequence of Somanniathelphusa in GenBank and the COX1 sequence of S. boyangensis to estimated the divergence time of this genus. The result displayed that the divergence time of Somanniathelphusa qiongshanensis is consistent with the separation of Hainan Island from mainland China in the Beibu Gulf, and the divergence time for Somanniathelphusa taiwanensis and Somanniathelphusa amoyensis is consistent with the separation of Taiwan Province from Mainland China at Fujian Province. These data indicate that geologic events influenced speciation of the genus Somanniathelphusa.
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Affiliation(s)
- Xin-nan Jia
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Shu-xin Xu
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Jun Bai
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yi-fan Wang
- Institute of Pathogen Biology, Jiangxi Academy of Medical Sciences, Nanchang, Jiangxi, PR China
| | - Zong-heng Nie
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Chun-chao Zhu
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yan Wang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yi-xiong Cai
- National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Jie-xin Zou
- Research lab of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, PR China
| | - Xian-min Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, Jiangxi, PR China
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Lin F, Tan H, Fazhan H, Xie Z, Guan M, Shi X, Ma H. The complete mitochondrial genome and phylogenetic analysis of Matuta planipes (Decapoda: Brachyura: Matutidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:157-158. [PMID: 33474103 PMCID: PMC7800499 DOI: 10.1080/23802359.2018.1437802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The complete mitochondrial genome of Matuta planipes was obtained using long and conventional PCR method. The circular genome was 15,760 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Of the 37 genes, 23 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with A + T bias (70.82%) and gene arrangement were largely identical to those observed in most arthropods, such as the mud crab (Scylla paramamosain). The phylogenetic analysis suggested that M. planipes was closest to Ashtoret lunaris. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Matutidae.
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Affiliation(s)
- Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhuofang Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Mengyun Guan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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Zhou YL, Gu WB, Tu DD, Zhu QH, Zhou ZK, Chen YY, Shu MA. Hemocytes of the mud crab Scylla paramamosain: Cytometric, morphological characterization and involvement in immune responses. FISH & SHELLFISH IMMUNOLOGY 2018; 72:459-469. [PMID: 29108971 DOI: 10.1016/j.fsi.2017.10.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/17/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Hemocytes play essential roles in the innate immune system of crustaceans. Characterization of hemocytes from estuary mud crab Scylla paramamosain was performed by flow cytometry and morphological studies such as cytochemical staining and electron microscopy. The hemocyte subsets were further separated using a modified Percoll density gradient centrifugation method. Based on the morphological characteristics of the cells, three distinct categories of hemocytes were identified: granulocytes with abundant large granularity representing 5.27 ± 0.42%, semigranulocytes with small or less granularity representing 76.03 ± 3.34%, and hyalinocytes (18.70 ± 3.92%) which were almost no granularity. The total hemocyte cell count and the percentage of hemocyte subsets varied after pathogen infection, including Vibrio alginolyticus and the viral double-stranded RNA analog Poly (I:C). The phagocytic process is of fundamental importance for crustaceans' cellular immune response as well as development and survival. The results of the in vitro phagocytosis assays analyzed by flow cytometry demonstrated that granulocytes and semigranulocytes had significantly higher phagocytic ability than hyalinocytes. A primary culture system, L-15 medium supplemented with 5-10% fetal bovine serum, was developed to further investigate the immune function of hemocytes. Furthermore, adenovirus can be utilized to effectively transfer GFP gene into hemocytes. Overall, three hemocyte sub-populations of S. paramamosain were successfully discriminated, moreover, their response to pathogen infections, phagocytic activity and adenovirus mediated transfection were also investigated for the first time. This study may contribute to a better understanding of the innate immune system of estuary crabs.
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Affiliation(s)
- Yi-Lian Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Bin Gu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dan-Dan Tu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi-Hui Zhu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Kai Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu-Yin Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Miao-An Shu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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Zhu KC, Liang YY, Wu N, Guo HY, Zhang N, Jiang SG, Zhang DC. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile). Sci Rep 2017; 7:15299. [PMID: 29127415 PMCID: PMC5681689 DOI: 10.1038/s41598-017-15702-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Yin-Yin Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Na Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, Guangdong Province, The People's Republic of China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China.
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
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Zhong S, Zhao Y, Wang X, Song Z, Zhang Q. The complete mitochondrial genome of Scylla paramamosain (Decapoda: Portunidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:789-790. [PMID: 33473981 PMCID: PMC7799674 DOI: 10.1080/23802359.2017.1398617] [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: 11/26/2022]
Abstract
The mud crab Scylla paramamosain (Decapoda:Portunidae) is a commercially important crustacean species in China, which is broadly distributed along the southeastern coastal regions of China. In previous studies, the population from Beibu Bay showed distinct genetic lineage. Here, we report the complete mitochondrial genome sequence of S. paramamosain from Beibu Bay. The mitogenome has 15,816 base pairs and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. The complete mitogenome in the Beibu Bay population was shorter than that in the Shenzhen population, because the non-coding region between tRNA-Glu and tRNA-His was shorter in the former, and there were 59 mutations sites between these two populations. This study adds a distinct mitogenomes of S. paramamosain and will provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable crab.
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Affiliation(s)
- Shengping Zhong
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yanfei Zhao
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Xianfeng Wang
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Zhifei Song
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Qing Zhang
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
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Chen X, Wang J, Huang L, Yue W, Zou J, Yuan C, Lu G, Wang C. Evolutionary relationship of three mitten crabs ( Eriocheir sp) revealed by mitogenome and 5S ribosomal DNA analysis. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tang BP, Liu Y, Xin ZZ, Zhang DZ, Wang ZF, Zhu XY, Wang Y, Zhang HB, Zhou CL, Chai XY, Liu QN. Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs. Genomics 2017; 110:S0888-7543(17)30099-X. [PMID: 28982639 DOI: 10.1016/j.ygeno.2017.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0.036) and GC-skew (-0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.
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Affiliation(s)
- Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
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25
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Xin ZZ, Yu-Liu, Zhang DZ, Wang ZF, Zhang HB, Tang BP, Zhou CL, Chai XY, Liu QN. Mitochondrial genome of Helice tientsinensis (Brachyura: Grapsoidea: Varunidae): Gene rearrangements and higher-level phylogeny of the Brachyura. Gene 2017. [DOI: 10.1016/j.gene.2017.06.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Qu L, Ma C, Ma H, Dong Y, Wang W, Ren G, Ma L. The complete mitochondrial genome of Stolephorus commersonii. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:573-574. [PMID: 33473904 PMCID: PMC7800927 DOI: 10.1080/23802359.2017.1372707] [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: 11/25/2022]
Abstract
In this study, the complete mitochondrial genome of Stolephorus commersonii is determined. It is 16,734 bp in length and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. Phylogenetic tree was constructed based on the complete mitogenome of S. commersonii and closely related 17 other species to assess its phylogenic relationship and evolution. The findings of the study will contribute to the phylogenetic classification and the genetic conservation management of S. commersonii.
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Affiliation(s)
- Liyan Qu
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Hongyu Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Yao Dong
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Guijing Ren
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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27
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Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura. Sci Rep 2017. [PMID: 28646134 PMCID: PMC5482888 DOI: 10.1038/s41598-017-04489-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.
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Tang BP, Xin ZZ, Liu Y, Zhang DZ, Wang ZF, Zhang HB, Chai XY, Zhou CL, Liu QN. The complete mitochondrial genome of Sesarmops sinensis reveals gene rearrangements and phylogenetic relationships in Brachyura. PLoS One 2017; 12:e0179800. [PMID: 28622362 PMCID: PMC5473591 DOI: 10.1371/journal.pone.0179800] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genome (mitogenome) is very important to understand molecular evolution and phylogenetics. Herein, in this study, the complete mitogenome of Sesarmops sinensis was reported. The mitogenome was 15,905 bp in size, and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew and the GC skew are both negative in the mitogenomes of S. sinensis. The nucleotide composition of the S. sinensis mitogenome was also biased toward A + T nucleotides (75.7%). All tRNA genes displayed a typical mitochondrial tRNA cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. S. sinensis exhibits a novel rearrangement compared with the Pancrustacean ground pattern and other Brachyura species. Based on the 13 PCGs, the phylogenetic analysis showed that S. sinensis and Sesarma neglectum were clustered on one branch with high nodal support values, indicating that S. sinensis and S. neglectum have a sister group relationship. The group (S. sinensis + S. neglectum) was sister to (Parasesarmops tripectinis + Metopaulias depressus), suggesting that S. sinensis belongs to Grapsoidea, Sesarmidae. Phylogenetic trees based on amino acid sequences and nucleotide sequences of mitochondrial 13 PCGs using BI and ML respectively indicate that section Eubrachyura consists of four groups clearly. The resulting phylogeny supports the establishment of a separate subsection Potamoida. These four groups correspond to four subsections of Raninoida, Heterotremata, Potamoida, and Thoracotremata.
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Affiliation(s)
- Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
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29
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Khan MF, Khattak MNK, He D, Rehman AU, Chen Y. Mitochondrial genome sequence and gene organization of Kunar Snow trout ( Schizothorax labiatus ) with phylogenetic consideration. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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31
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Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis. Gene 2016; 598:71-78. [PMID: 27816474 DOI: 10.1016/j.gene.2016.10.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/16/2016] [Accepted: 10/28/2016] [Indexed: 11/21/2022]
Abstract
To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.
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32
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Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Jing H, Yan P, Li W, Li X, Song Z. The complete mitochondrial genome of Triplophysa lixianensis (Teleostei: Cypriniformes: Balitoridae) with phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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34
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Meng Y, Ma H, Ma C, Wei H, Liu Y, Zhang F, Wang W, Chen W, Zhao M, Chen F, Ma L. The complete mitochondrial genome of Eleotris oxycephala (Perciformes: Eleotridae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3820-1. [PMID: 27158874 DOI: 10.3109/19401736.2015.1060469] [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 the present study, we obtained the complete mitochondrial genome sequence of Eleotris oxycephala, which was 16 527 bp in length. This genome consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Of the 37 genes, 28 were encoded by heavy strand, while nine were encoded by light strand. The overall base composition of this mitogenome was 28.21% for A, 16.81% for G, 24.75% for T, 30.23% for C, respectively, with a slight higher A + T content (52.96%). The phylogenetic analysis based on 13 concatenated protein-coding genes suggested that E. oxycephala as a sister species to Eleotris acanthopoma was clustered in family Eleotridae. This complete mitochondrial genome sequence of E. oxycephala should be helpful for the studies on population genetic structure, molecular evolution and phylogeny of E. oxycephala and related species.
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Affiliation(s)
- Yongyong Meng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Yuexing Liu
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Fengying Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Wang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Mengdi Zhao
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Fenfang Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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35
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Ma C, Ma H, Zhang H, Feng C, Wei H, Wang W, Chen W, Zhang F, Ma L. The complete mitochondrial genome sequence and gene organization of the rainbow runner (Elagatis bipinnulata) (Perciformes: Carangidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:5-6. [PMID: 26709669 DOI: 10.3109/19401736.2015.1106516] [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 complete mitochondrial genome information can play an important role in species identification, phylogeny, evolution research, genetic differentiation, and diversity. Here we determined the complete mitochondrial genome sequence of Elagatis bipinnulata (Perciformes: Carangidae). This circular genome was 16 542 bp in length, and included all 37 typical mitochondrial genes, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The gene order of E. bipinnulata was identical to that observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the other ones were encoded by light strand. According to the phylogenetic analysis based on 13 concatenated protein-coding genes, E. bipinnulata was genetically closer to the species of genus Seriola compared with any other species within Perciformes. This work can provide helpful data for further studies on population genetic diversity and molecular evolution.
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Affiliation(s)
- Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Heng Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Chunlei Feng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Wei Wang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Wei Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Fengying Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences , Shanghai , China
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36
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Wei H, Ma H, Ma C, Zhang H, Zhang F, Wang W, Chen W, Meng Y, Cheng J, Li S, Jiang Y, Ma L. Isolation and characterization of the complete mitochondrial genome of Taenioides anguillaris (Gobiidae: Amblyopinae) with phylogenetic consideration. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4681-4682. [PMID: 26642858 DOI: 10.3109/19401736.2015.1106500] [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
Here we first isolated and characterized the complete mitochondrial genome DNA of Taenioides anguillaris. It was 16 974 bp in length, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The structure and the gene arrangement of this genome were identical to those isolated from other Gobiidae fishes. Twenty-eight genes were encoded by heavy strand, while nine genes were encoded by light strand. The total nucleotide composition of this genome was 28.7% for A, 15.6% for G, 28.6% for C, and 27.1% for T, with a high A + T content of 55.8%. From the neighbor-joining (NJ) phylogenetic tree, we can find that T. anguillaris was genetically closest to species Odontamblyopus rubicundus among 20 species within suborder Gobioidei. This work should be helpful for the studies on population genetic diversity and molecular evolution in T. anguillaris and related fish species.
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Affiliation(s)
- Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Heng Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Fengying Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Wang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Yongyong Meng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Jiahua Cheng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Shengfa Li
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Yazhou Jiang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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Chen F, Ma H, Ma C, Ni Y, Zhang X, Wei H, Meng Y, Zhao M, Ma L. The complete mitochondrial genome sequence and gene organization of Amblychaeturichthys hexanema (Gobiidae: Amblychaeturichthys) with phylogenetic consideration. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4687-4688. [PMID: 26642097 DOI: 10.3109/19401736.2015.1106503] [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
We sequenced and characterized the complete mitochondrial genome of Amblychaeturichthys hexanema and uncovered its molecular phylogenetic relationship. This genome was 18 642 bp in size, and contained 37 classic genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The gene organization and nucleotide composition were the same with those found in most other Gobiidae fishes. In contrast, gene NADH 6 was obviously larger than the same gene identified from other Gobiidae species. Two big repeat regions were detected on both sides of D-loop region. The A + T content (71.2%) of D-loop region was higher than any other region in this genome. Among 37 genes, 28 were encoded by the heavy strand, while nine were encoded by the light strand. The total nucleotide composition of this genome was 28.6% for A, 15.8% for G, 27.2% for C, and 28.3% for T, with a high A + T content of 56.9%. Phylogeny analysis of 22 fish species within Gobioidei showed that A. hexanema and Chaeturichthys stigmatias first formed a single cluster, then they together with other 17 species grouped a big branch. This work should be helpful for the studies on population genetic diversity and molecular evolution of Gobiidae fish species.
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Affiliation(s)
- Fenfang Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Yong Ni
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Xun Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Yongyong Meng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Mengdi Zhao
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation , Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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Zhang D, Gong F, Liu T, Guo H, Zhang N, Zhu K, Jiang S. Shotgun assembly of the mitochondrial genome from Fenneropenaeus penicillatus with phylogenetic consideration. Mar Genomics 2015; 24 Pt 3:379-86. [PMID: 26429699 DOI: 10.1016/j.margen.2015.09.005] [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] [Received: 03/06/2015] [Revised: 08/26/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding of the genome-level characteristics and phylogenetic relationships among related species. In this study, Fenneropenaeus penicillatus mitochondrial genome sequence was determined by next-generation sequencing. The complete genome DNA was 16,040 bp in length and consisted of a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). The gene arrangement is identical to the pancrustacean pattern. The overall base composition of its mitochondrial genome is estimated to be 34.1% for A, 34.1% for T, 12.5% for G and 19.3% for C with a high A+T content (68.2%). The analysis of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group. The phylogenetic analysis based on mitochondrial sequences and 13 concatenated protein-coding genes showed strong statistic support for the following relationship among the five genera ((Penaeus s.s+Fenneropenaeus)+(Litopenaeus+Farfantepenaeus))+Marsupenaeus. The sequence data of F. penicillatus can provide useful information for the studies on molecular systematics, population structure, stock evaluation and conservation genetics.
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Affiliation(s)
- Dianchang Zhang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Fahui Gong
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life, Shanghai Ocean University, Shanghai; 201306, China
| | - Tiantian Liu
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life, Shanghai Ocean University, Shanghai; 201306, China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shigui Jiang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
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Zhao M, Ma H, Ma C, Zhang H, Zhang X, Meng Y, Wei H, Chen F, Ma L. The complete mitochondrial genome and gene organization of Cubiceps squamiceps (Perciformes: nomeidae) with phylogenetic consideration. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4296-4297. [PMID: 26404517 DOI: 10.3109/19401736.2015.1082103] [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
In this study, we reported the complete mitochondrial DNA sequence of Cubiceps squamiceps, and its phylogenetic relationship. The full length of this mitogenome was 16 510 bp, including 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and a putative control region. The location of genes in mitochondrial genome was similar to other fish species within family Nomeidae. Twenty-eight genes were located on the heavy strand, while nine genes were located on the light strand. The nucleotide composition of this mitogenome was 27.5% for A, 28.5% for C, 17.5% for G, and 26.5% for T. From the NJ phylogenetic tree, we can find that C. squamiceps was genetically closest to C. pauciradiatus among 20 species within suborder Stromateoidei. This study could lay the basis for the future studies in population genetic diversity, taxonomic status, molecular systematics, and conservation genetics in C. squamiceps.
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Affiliation(s)
- Mengdi Zhao
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Heng Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Xun Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Yongyong Meng
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Fenfang Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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Wei H, Ma H, Ma C, Zhang F, Wang W, Chen W, Ma L. The complete mitochondrial genome sequence and gene organization of Tridentiger trigonocephalus (Gobiidae: Gobionellinae) with phylogenetic consideration. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3725-6. [PMID: 26370266 DOI: 10.3109/19401736.2015.1079876] [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 complete mitochondrial genome plays an important role in studies of genome-level characteristics and phylogenetic relationships. Here we determined the complete mitogenome sequence of Tridentiger trigonocephalus (Perciformes, Gobiidae), and discovered its phylogenetic relationship. This circular genome was 16 662 bp in length, and consisted of 37 typical genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The gene order of T. trigonocephalus mitochondrial genome was identical to those observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the others were encoded by light strand. The phylogenetic tree constructed by 13 concatenated protein-coding genes showed that T. trigonocephalus was closest to T. bifasciatus, and then to T. barbatus among the 20 species within suborder Gobioidei. This work should facilitate the studies on population genetic diversity, and molecular evolution in Gobioidei fishes.
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Affiliation(s)
- Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Fengying Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Wang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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Ma H, Ma C, Li C, Lu J, Zou X, Gong Y, Wang W, Chen W, Ma L, Xia L. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics. Sci Rep 2015. [PMID: 26225473 PMCID: PMC4520191 DOI: 10.1038/srep11524] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we first described the complete mitochondrial genome for the red crab (Charybdis feriata), elucidated its phylogenetic relationship among 20 species within Decapoda, and estimated the population genetic diversity. The mitochondrial genome was 15,660 bp in size and encoded 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes. The gene arrangement of the mitochondrial genome was the same as that of its sister species, C. japonica. Phylogenomic analysis suggested that genus Charybdis should be classified into subfamily Portuninae but not into subfamily Thalamitinae. Moreover, a total of 33 haplotypes of complete cytochrome c oxidase subunit I gene were defined in 70 individuals of C. feriata derived from three localities. Haplotype diversity and nucleotide diversity values among three localities indicated a high level of genetic diversity in C. feriata. AMOVA analysis suggested a low level of genetic differentiation among the three localities (FST = 0.0023, P > 0.05). Neutrality tests and mismatch analysis revealed that C. feriata might have undergone a population expansion event that possibly occurred in the last 61,498 to 43,814 years. This study should be helpful to better understand the evolutionary status, and population genetic diversity of C. feriata and related species.
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Affiliation(s)
- Hongyu Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Chunyan Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Chenhong Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jianxue Lu
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Xiong Zou
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Yangyang Gong
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Wei Wang
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Wei Chen
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Lingbo Ma
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
| | - Lianjun Xia
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China
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MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Mol Phylogenet Evol 2015; 85:180-8. [DOI: 10.1016/j.ympev.2015.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/20/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
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Li W, Zhang XC, Zhao J, Shi Y, Zhu XP. Complete mitochondrial genome of Cuora trifasciata (Chinese three-striped box turtle), and a comparative analysis with other box turtles. Gene 2014; 555:169-77. [PMID: 25445281 DOI: 10.1016/j.gene.2014.10.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/22/2014] [Accepted: 10/31/2014] [Indexed: 11/26/2022]
Abstract
Cuora trifasciata has become one of the most critically endangered species in the world. The complete mitochondrial genome of C. trifasciata (Chinese three-striped box turtle) was determined in this study. Its mitochondrial genome is a 16,575-bp-long circular molecule that consists of 37 genes that are typically found in other vertebrates. And the basic characteristics of the C. trifasciata mitochondrial genome were also determined. Moreover, a comparison of C. trifasciata with Cuora cyclornata, Cuora pani and Cuora aurocapitata indicated that the four mitogenomics differed in length, codons, overlaps, 13 protein-coding genes (PCGs), ND3, rRNA genes, control region, and other aspects. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 12 protein-coding genes of the genus Cuora indicated the phylogenetic position of C. trifasciata within Cuora. The phylogenetic analysis also showed that C. trifasciata from Vietnam and China formed separate monophyletic clades with different Cuora species. The results of nucleotide base compositions, protein-coding genes and phylogenetic analysis showed that C. trifasciata from these two countries may represent different Cuora species.
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Affiliation(s)
- Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Xin-Cheng Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Jian Zhao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yan Shi
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Xin-Ping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China.
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Ma H, Ma C, Li S, Jiang W, Li X, Liu Y, Ma L. Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery. PLoS One 2014; 9:e102668. [PMID: 25054331 PMCID: PMC4108364 DOI: 10.1371/journal.pone.0102668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/20/2014] [Indexed: 11/28/2022] Open
Abstract
In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species.
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Affiliation(s)
- Hongyu Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Shujuan Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Wei Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Xincang Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Yuexing Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Lingbo Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- * E-mail:
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Ma H, Jiang W, Liu P, Feng N, Ma Q, Ma C, Li S, Liu Y, Qiao Z, Ma L. Identification of transcriptome-derived microsatellite markers and their association with the growth performance of the mud crab (Scylla paramamosain). PLoS One 2014; 9:e89134. [PMID: 24551232 PMCID: PMC3923883 DOI: 10.1371/journal.pone.0089134] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 01/20/2014] [Indexed: 11/18/2022] Open
Abstract
Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of the claw, fixed finger width of the claw, fixed finger height of the claw, meropodite length of pereiopod 2, and meropodite length of pereiopod 3 (MLP3) (P<0.05). Locus Scpa75 was significantly associated with five growth traits, namely, internal carapace width, AW, carapace width at spine 8, distance between lateral spine 2 (DLS2), and MLP3 (P<0.05). Locus Spm30 was significantly associated with BH, DLS2, and body weight (P<0.05). Further analysis suggested a set of genotypes (BC at Scpa36, BC and BD at Scpa75, and AC at Spm30) that have great potential in the selection of S. paramamosain for growth traits. These findings will facilitate the development of population conservation genetics and molecular marker-assisted selective breeding of S. paramamosain and other closely related species.
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Affiliation(s)
- Hongyu Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wei Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Ping Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Nana Feng
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Qunqun Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Shujuan Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Yuexing Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Zhenguo Qiao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
| | - Lingbo Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai, China
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Mu XD, Liu C, Wang XJ, Liu Y, Hu YC, Luo JR. Complete mitochondrial genome of Zebra tilapia, Tilapia buttikoferi. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:44-5. [PMID: 24438265 DOI: 10.3109/19401736.2013.869687] [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
We determined the complete mitochondrial genome of Tilapia buttikoferi, which was 16,577 bp in length with an A + T content of 53.0%, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a complete control region. The gene arrangement was similar to that of typical fishes. The total base composition of the mitogenome was 25.6% T, 30.8% C, 27.4% A and 16.2% G. Of the 13 protein-coding genes, 12 genes start with an ATG codon, except for COX1 with GTG. Seven (ND1, ND2, COX1, ATPase8, ATPase6, ND4L and ND6) used TAA or AGA as the termination codon, whereas six (COX2, COX3, ND3, ND4, ND5 and cyt b) had incomplete stop codon T. Its control region was atypical in being short at 861 bp, and contained TACAT motif and one microsatellite-like region (TA)7. This mitogenome sequence data may be useful for phylogenetic and systematic analyses within the family Cichlaidae.
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Affiliation(s)
- Xi-Dong Mu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Chao Liu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Xue-Jie Wang
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Yi Liu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Yin-Chang Hu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Jian-Ren Luo
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
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Keith Barker F, Oyler-McCance S, Tomback DF. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences. ACTA ACUST UNITED AC 2013; 26:384-8. [DOI: 10.3109/19401736.2013.840588] [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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