1
|
Ruan X, Cheng H, Xuan Z, Li Z, Yu J, Zhao H. The complete mitochondrial genome of Allogalathea elegans (Adams & White, 1848) (Decapoda: Galatheidae). Mitochondrial DNA B Resour 2023; 8:857-861. [PMID: 37583939 PMCID: PMC10424596 DOI: 10.1080/23802359.2023.2242625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
The genus Allogalathea belongs to the subfamily Galatheoidea of the family Galatheidae. Here, we report a mitogenome of Allogalathea elegans (Adams & White, 1848). In this study, we obtained the complete mitochondrial genome of Allogalathea elegans by sequencing, which was 16,263 bp in length. The mitogenome contained 37 genes, including the typical set of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 Ribosomal RNA (rRNA) genes. The nucleotides A, C, G, and T distribution was 36.40%, 19.44%, 9.09%, and 35.07%, respectively. The length of the total protein-coding genes was 11,172 bp, which accounts for 68.69% of the whole mitochondrial genome. The phylogenetic result generated by IQ-Tree based on 13 PGCs showed that the infraorder Anomura is monophyletic, and the infraorder Anomura is a sister group of the infraorder Glypheidea. The discovery of the complete mitochondrial genome of A. elegans would help to conduct in-depth research on the infraorder Anomura.
Collapse
Affiliation(s)
- Xinhe Ruan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huitao Cheng
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zijie Xuan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zongyang Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jie Yu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Akhtar T, Ali G, Shafi N, Akhtar W, Khan AH, Latif Z, Wali A, Ain-ul-Batool S, Khan AR, Mumtaz S, Altaf SI, Khawaja S, Sadia, Khalid M, Rehman FU, Javid Q. Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5980135. [PMID: 33490246 PMCID: PMC7787735 DOI: 10.1155/2020/5980135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/29/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.
Collapse
Affiliation(s)
- Tasleem Akhtar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Wasim Akhtar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Hameed Khan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Latif
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Wali
- Faculty of Life Sciences & Informatics, BUITEMS, 87100 Quetta, Pakistan
| | - Syeda Ain-ul-Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Rehman Khan
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Mumtaz
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syed Iftikhar Altaf
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sundus Khawaja
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Madiha Khalid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Biotechnology, Women University Bagh, Pakistan
| | - Fazal Ur Rehman
- Department of Microbiology, University of Balochistan, Quetta 87300, Pakistan
| | - Qudir Javid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| |
Collapse
|
4
|
Zhang Y, Gong L, Lu X, Jiang L, Liu B, Liu L, Lü Z, Li P, Zhang X. Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura. Int J Biol Macromol 2020; 162:704-714. [DOI: 10.1016/j.ijbiomac.2020.06.196] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 11/25/2022]
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Lu X, Gong L, Zhang Y, Chen J, Liu L, Jiang L, Lü Z, Liu B, Tong G, Wei X. The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura. Genomics 2020; 112:2516-2523. [PMID: 32045669 DOI: 10.1016/j.ygeno.2020.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/08/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (-0.010) and GC-skew (-0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.
Collapse
Affiliation(s)
- Xinting Lu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China.
| | - Ying Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Jian Chen
- Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Lihua Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Guixiang Tong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Xinxian Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China.
| |
Collapse
|
7
|
Gong L, Jiang H, Zhu K, Lu X, Liu L, Liu B, Jiang L, Ye Y, Lü Z. Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura. Gene 2019; 695:75-83. [PMID: 30738095 DOI: 10.1016/j.gene.2019.01.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (-0.006) and GC-skew (-0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.
Collapse
Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Kehua Zhu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Xinting Lu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Lihua Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Yingying Ye
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| |
Collapse
|
8
|
Lee DJ, Lee HB, Kim IC. The whole mitochondrial genome of the freshwater crab, Geothelphusa sp. (Stimpson, 1858) (Decapoda, Potamidae) and its phylogenetic relationship. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1598793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Dong Ju Lee
- Department of Biological Sciences, Institute of Basic Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hae Bum Lee
- Department of Biological Sciences, Institute of Basic Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Il-Chul Kim
- Department of Biological Sciences, Institute of Basic Sciences, Chonnam National University, Gwangju, Republic of Korea
| |
Collapse
|
9
|
Mu W, Liu J, Zhang H. The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida. Ecol Evol 2018; 8:10673-10686. [PMID: 30519397 PMCID: PMC6262923 DOI: 10.1002/ece3.4427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023] Open
Abstract
Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world's oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep-sea member of the order Brisingida. Similar to other starfish, it contained 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty-two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep-sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila's adaptation to deep-sea environment.
Collapse
Affiliation(s)
- Wendan Mu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jun Liu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Haibin Zhang
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| |
Collapse
|
10
|
Kim NK, Andriyono S, Kim AR, Lee CI, Kim HW. Characterization of complete mitochondrial genome of two-spot swimming crab Charybdis bimaculata (Miers, 1886). Mitochondrial DNA B Resour 2018; 3:900-901. [PMID: 33474358 PMCID: PMC7799594 DOI: 10.1080/23802359.2018.1501292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/08/2018] [Indexed: 11/03/2022] Open
Abstract
The two-spot swimming crab Charybdis bimaculata (Miers, 1886) is an important decapod species in the benthic ecosystem of Korean waters. In this study, we determined its complete mitochondrial genome by the combination of NGS analysis using MiSeq platform and PCR-based cloning method. The circular mitochondrial genome of C. bimaculata was 15,714 bp in length in which the standard set of 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes were encoded. Phylogenic analysis showed that C.bimaculata is most closely related to Charybdis feriata. The complete mitogenome sequence information of C. bimaculata would provide useful data for the conservation of their population in the Pacific ocean.
Collapse
Affiliation(s)
- Nack-Keun Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Sapto Andriyono
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
- Department of Marine, Fisheries and Marine Faculty, Universitas Airlangga C Campus Jl, Mulyorejo Surabaya East Java, Indonesia
| | - Ah Ran Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Chung Il Lee
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Hyun-Woo Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
| |
Collapse
|
11
|
Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep 2018; 8:6893. [PMID: 29720606 PMCID: PMC5931980 DOI: 10.1038/s41598-018-25225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
Collapse
Affiliation(s)
- Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Department of Functional Ecology, PO Box 120161, 27515, Bremerhaven, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
| | - Michael V Westbury
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leon Hilgers
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Fabian Deister
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
| | - Hermann Neumann
- Senckenberg am Meer, Department for Marine Research, Südstrand 40, 26382, Wilhelmshaven, Germany
| | - Michael J Raupach
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
- Senckenberg am Meer, German Center of Marine Biodiversity (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Zhang Huilun, Ruoran W, Da P, Hongying S. Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). Zookeys 2017; 705:41-60. [PMID: 29118611 PMCID: PMC5674035 DOI: 10.3897/zookeys.705.11852] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/04/2017] [Indexed: 01/26/2023] Open
Abstract
Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs. Mitogenomic comparisons using rapid next-generation sequencing and a much wider taxonomic sample are required for a high-resolution examination of the phylogenetic relationships within the Eubrachyura.
Collapse
Affiliation(s)
- Xing Yuhui
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhou Lijun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Hou Yue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Wang Xiaoqi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhang Huilun
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ruoran
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pan Da
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Sun Hongying
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| |
Collapse
|
15
|
Yang X, Ma H, Waiho K, Fazhan H, Wang S, Wu Q, Shi X, You C, Lu J. The complete mitochondrial genome of the swimming crab Charybdis natator (Herbst) (Decapoda: Brachyura: Portunidae) and its phylogeny. Mitochondrial DNA B Resour 2017; 2:530-531. [PMID: 33473887 PMCID: PMC7799874 DOI: 10.1080/23802359.2017.1365639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/07/2017] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genome of Charybdis natator (family Portunidae) was obtained using Illumina and Sanger dideoxy sequencing. This genome was a typically circular molecule with a length of 15,664 bp and encoded 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of this mitogenome was 34.00% for A, 11.06% for G, 36.36% for T, and 18.58% for C, respectively, with a higher A + T content (70.36%). The gene composition and arrangement were accordant to the closely published species. The phylogenetic analysis suggested that C. natator had the closest relationship with C. japonica.
Collapse
Affiliation(s)
- Xiaolong Yang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Shuqi Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Qingyang Wu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Cuihong You
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Jianxue Lu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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]
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Meng X, Jia F, Zhang X, Liu P, Li J. Complete sequence and characterization of mitochondrial genome in the swimming crab Portunus sanguinolentus (Herbst, 1783) (Decapoda, Brachyura, Portunidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3052-3. [PMID: 26153754 DOI: 10.3109/19401736.2015.1063130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The three-spot swimming crab Portunus sanguinolentus (Herbst, 1783) is a commercially important fishery species, widely distributed in the Indo-Pacific region. In this study, we present the complete mitochondrial genome of P. sanguinolentus. The genome is 16 027 bp in length with circular organization, encoding the standard set of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The overall A + T content is 65.60%, which is lower than that of its congeneric species Portunus pelagicus and Portunus trituberculatus. The mitogenome carries 1254 bp of intergenic region constituting 7.82% of the genome, and six pairs of overlapping genes with the overlap size from 1 to 7 bp. The complete mitogenome sequence information of P. sanguinolentus would provide useful data for further studies on population genetics and molecular systematics.
Collapse
Affiliation(s)
- Xianliang Meng
- a Key Laboratory of Sustainable Development of Marine Fisheries , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , People's Republic of China
| | - Fulong Jia
- a Key Laboratory of Sustainable Development of Marine Fisheries , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , People's Republic of China
| | - Xiaohui Zhang
- a Key Laboratory of Sustainable Development of Marine Fisheries , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , People's Republic of China
| | - Ping Liu
- a Key Laboratory of Sustainable Development of Marine Fisheries , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , People's Republic of China
| | - Jian Li
- a Key Laboratory of Sustainable Development of Marine Fisheries , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , People's Republic of China
| |
Collapse
|
20
|
Meng XL, Jia FL, Liu P, Li J. The complete mitogenome of blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2789-90. [DOI: 10.3109/19401736.2015.1053068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Xian-liang Meng
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Fu-long Jia
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| |
Collapse
|
21
|
Shi G, Cui Z, Hui M, Liu Y, Chan TY, Song C. The complete mitochondrial genomes of Umalia orientalis and Lyreidus brevifrons: The phylogenetic position of the family Raninidae within Brachyuran crabs. Mar Genomics 2015; 21:53-61. [PMID: 25744934 DOI: 10.1016/j.margen.2015.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 11/25/2022]
Abstract
The complete mitochondrial genome (mitogenome) sequences of two primitive crabs, Umalia orientalis and Lyreidus brevifrons (Decapoda: Brachyura: Raninidae) were determined. The mitogenomes of the two species are 15,466 and 16,112bp in length with AT content of 68.0% and 70.6%, respectively. Each genome contains 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. The gene arrangement of U. orientalis is the same with those reported for most brachyuran species. Nevertheless, the gene arrangement of L. brevifrons differs from that of U. orientalis in having an additional non-coding region. The newly found non-coding region is located between nad3 and trnA with 641bp in length. Its nucleotide composition and secondary structure are similar to the typical control region. In L. brevifrons, the secondary structures of trnS-AGN and trnI are significantly different from those in U. orientalis and other brachyuran species. The start codon for cox1 is ATG in all reported Eubrachyura mitogenomes, while a common start codon ACG is found in the Podotremata. Phylogenetic analyses for crustacean decapods based on the nucleotide and amino acid of 13 PCGs indicate that Homolidae is more primitive in Brachyura, and Raninidae is a sister group to Eubrachyura. This implies that Raninidae is closer to Eubrachyura than to Homolidae, and Podotremata may be a paraphyletic assemblage. The results also indicate that the subfamily Lyreidinae is closer to Notopodinae than to Ranininae within Raninidae. The novel mitogenome data provides useful information for refining the phylogenetic relationships within Brachyura.
Collapse
Affiliation(s)
- Guohui Shi
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoxia Cui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China.
| | - Min Hui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuan Liu
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Tin-Yam Chan
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chengwen Song
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
22
|
Hui M, Liu Y, Cui Z. First complete mitochondrial genome of primitive crabHomologenus malayensis(Decapoda: Brachyura: Podotremata: Homolidae). ACTA ACUST UNITED AC 2014; 27:859-60. [DOI: 10.3109/19401736.2014.919476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
23
|
Park K, Kwak IS. Characterize and Gene Expression of Heat Shock Protein 90 in Marine Crab Charybdis japonica following Bisphenol A and 4-Nonylphenol Exposures. ENVIRONMENTAL HEALTH AND TOXICOLOGY 2014; 29:e2014002. [PMID: 24955332 PMCID: PMC4064113 DOI: 10.5620/eht.2014.29.e2014002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/07/2014] [Indexed: 05/03/2023]
Abstract
OBJECTIVES Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone important in the maturation of a broad spectrum of protein. In this study, an HSP90 gene was isolated from Asian paddle crab, Charybdis japonica, as a bio-indicator to monitor the marine ecosystem. METHODS This work reports the responses of C. japonica HSP90 mRNA expression to cellular stress by endocrine disrupting chemicals (EDCs), such as bisphenol A (BPA) and 4-nonylphenol (NP) using real-time. reverse transcription polymerase chain reaction. RESULTS The deduced amino acid sequence of HSP90 from C. japonica shared a high degree of homology with their homologues in other species. In a phylogenetic analysis, C. japonica HSP90 is evolutionally related with an ortholog of the other crustacean species. The expression of HSP90 gene was almost distributed in all the examined tissues of the C. japonica crab but expression levels varied among the different body parts of the crabs. We examined HSP90 mRNA expression pattern in C. japonica crabs exposed to EDCs for various exposure times. The expression of HSP90 transcripts was significantly increased in C. japonica crabs exposed to BPA and NP at different concentrations for 12, 24, 48 and 96 hours. The mRNA expression of HSP90 gene was significantly induced in a concentration- and time-dependent manner after BPA or NP exposures for 96 hours. CONCLUSIONS Taken together, expression analysis of Asian paddle crab HSP90 gene provided useful molecular information about crab responses in stress conditions and potential ways to monitor the EDCs stressors in marine environments.
Collapse
Affiliation(s)
- Kiyun Park
- Department of Fisheries and Ocean Science, Chonnam National University, Yeosu, Korea
| | - Ihn-Sil Kwak
- Department of Fisheries and Ocean Science, Chonnam National University, Yeosu, Korea
| |
Collapse
|
24
|
Ma H, Ma C, Li X, Xu Z, Feng N, Ma L. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene 2013; 519:120-7. [PMID: 23384716 DOI: 10.1016/j.gene.2013.01.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
Collapse
Affiliation(s)
- 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, 200090, China
| | | | | | | | | | | |
Collapse
|
25
|
Jondeung A, Karinthanyakit W, Kaewkhumsan J. The complete mitochondrial genome of the black mud crab, Scylla serrata (Crustacea: Brachyura: Portunidae) and its phylogenetic position among (pan)crustaceans. Mol Biol Rep 2012; 39:10921-37. [PMID: 23053985 DOI: 10.1007/s11033-012-1992-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
The black mud crab, Scylla serrata (Forskål 1775), is the most economically important edible crab in South-East Asia. In the present study, the complete mitochondrial genome of black mud crab, S. serrata, was determined with the sequential polymerase chain reaction and primer walking sequencing. The complete mitochondrial genome was 15,721 bp in length with an A+T content of 69.2 % and contained 37 mitochondrial genes (13 protein coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR). The analysis of the CR sequence shows that it contains a multitude of repetitive fragments which can fold into hairpin-like or secondary structures and conserved elements as in other arthropods. The gene order of S. serrata mainly retains as the pancrustacean ground pattern, except for a single translocation of trnH. The gene arrangement of S. serrata appears to be a typical feature of portunid crabs. Phylogenetic analyses with concatenated amino acid sequences of 12 PCGs establishes that S. serrata in a well-supported monophyletic Portunidae and is consistent with previous morphological classification. Moreover, the phylogenomic results strongly support monophyletic Pancrustacea (Hexapoda plus "Crustaceans"). Within Pancrustacea, this study identifies Malacostraca + Entomostraca and Branchiopoda as the sister group to Hexapoda, which confirms that "Crustacea" is not monophyletic. Cirripedia + Remipedia appear to be a basal lineage of Pancrustacea. The present study also provides considerable data for the application of both population and phylogenetic studies of other crab species.
Collapse
Affiliation(s)
- Amnuay Jondeung
- Department of Genetics, Kasetsart University, Bangkok, 10900, Thailand.
| | | | | |
Collapse
|
26
|
Johansson ML, Sremba AL, Feinberg LR, Banks MA, Peterson WT. The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree. Mol Biol Rep 2012; 39:9009-21. [PMID: 22733485 DOI: 10.1007/s11033-012-1772-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 06/09/2012] [Indexed: 11/29/2022]
Abstract
Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 + base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 + bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.
Collapse
Affiliation(s)
- Mattias L Johansson
- Cooperative Institute for Marine Resources Studies, Oregon State University, Newport, OR, USA.
| | | | | | | | | |
Collapse
|
27
|
Kilpert F, Held C, Podsiadlowski L. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Mol Phylogenet Evol 2012; 64:106-17. [PMID: 22491068 DOI: 10.1016/j.ympev.2012.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
Abstract
In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.
Collapse
Affiliation(s)
- Fabian Kilpert
- Institute of Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| | | | | |
Collapse
|
28
|
Zhang D, Ding G, Ge B, Zhang H, Tang B. Development and characterization of microsatellite loci of Oratosquilla oratoria (Crustacea: Squillidae). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-011-9495-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Kim S, Park MH, Jung JH, Ahn DH, Sultana T, Kim S, Park JK, Choi HG, Min GS. The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00534.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Shi H, Liu R, Sha Z, Ma J. Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster. Mar Genomics 2011; 6:7-15. [PMID: 22578654 DOI: 10.1016/j.margen.2011.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/15/2011] [Accepted: 11/08/2011] [Indexed: 11/26/2022]
Abstract
As a phylogenetically valuable decapoda, a complete mitochondrial genome from Stenopodidea has not been reported to date. Here, we determined the complete mitochondrial DNA sequence of Stenopus hispidus (Olivier, 1811). The 15,528 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs) and two ribosomal RNA (rRNA) genes plus the putative control region (CR). This finding is similar to other metazoan animals but with the exception of 23 transfer RNA (tRNA) genes, which contain an additional tRNA-Gln compared with other crustaceans. With respect to the pancrustacean ground pattern mitochondria gene order, 5 tRNAs appear to be rearranged (tRNAs-Leu (CUN), Arg, Glu, Gln, and Met), one of which has also undergone inversion (tRNA-Leu (CUN)). Phylogenetic analyses reveal Stenopodidea and Reptantia form a clade sister to Caridea, which agrees with Abele and Felgenhauer's (1986) hypothesis. This topology contrasts with previous results based on morphological and some molecular data.
Collapse
Affiliation(s)
- HuaFeng Shi
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | | | | | | |
Collapse
|
31
|
Cheng R, Zheng X, Lin X, Yang J, Li Q. Determination of the complete mitochondrial DNA sequence of Octopus minor. Mol Biol Rep 2011; 39:3461-70. [PMID: 21710247 DOI: 10.1007/s11033-011-1118-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 06/20/2011] [Indexed: 01/31/2023]
Abstract
In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus minor. It is 15,974 nucleotide pairs and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion's own protein synthesizing system. Seven of thirteen proteins are encoded by the H-strand, while the other six proteins, as well as the two ribosomal RNAs are encoded by the L-strand. The nucleotide composition of the proteins showed a nucleotide bias against G encoded by the H-strand, while they showed a nucleotide bias against A and C encoded by the L-strand. Two of the 13 protein coding genes of O. minor began with the unorthodox translation initiation codon ATA and all others use the standard ATG. In addition, six of thirteen mt proteins of O. minor have unambiguous termination codons. There are four cases where tRNA genes appear to overlap. The long noncoding region (LNCR) of O. minor was 930 nucleotides and no repeated sequences were found in this LNCR. The gene arrangements of O. minor showed remarkable similarity to that of O. ocellatus and O. vulgaris. Phylogenetic analysis demonstrated that O. minor appears as sister taxan to the monophyletic group combined by O. ocellatus and O. vulgaris, suggesting a relative distant genetic relationship between O. minor and the other two octopus species.
Collapse
Affiliation(s)
- Rubin Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
| | | | | | | | | |
Collapse
|
32
|
Yuan Y, Li Q, Kong L, Yu H. The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region. Mol Biol Rep 2011; 39:1287-92. [PMID: 21598108 DOI: 10.1007/s11033-011-0861-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/12/2011] [Indexed: 01/22/2023]
Abstract
Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)(12) element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.
Collapse
Affiliation(s)
- Yang Yuan
- Fisheries College, Ocean University of China, Qingdao, China
| | | | | | | |
Collapse
|
33
|
QIAN GUANGHUI, ZHAO QIANG, WANG AN, ZHU LIN, ZHOU KAIYA, SUN HONGYING. Two new decapod (Crustacea, Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda. Zool J Linn Soc 2011. [DOI: 10.1111/j.1096-3642.2010.00686.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
34
|
Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2010; 38:1103-14. [DOI: 10.1007/s11033-010-0207-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
|
35
|
Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations. Mol Biol Rep 2010; 38:403-10. [PMID: 20352347 DOI: 10.1007/s11033-010-0122-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 03/17/2010] [Indexed: 02/08/2023]
Abstract
The genetics and molecular biology of the commercially important Chinese spiny lobster, Panulirus stimpsoni are little known. Here, we present the complete mitochondrial genome sequence of P. stimpsoni, determined by the long polymerase chain reaction and primer walking sequencing method. The entire genome is 15,677 bp in length, encoding the standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The overall A+T content of the genome is 65.6%, lower than most malacostracan species. The gene order is consistent with the pancrustacean ground pattern. Several conserved elements were identified from P. stimpsoni control region, viz. one [TA(A)]n-block, two GA-blocks and three hairpin structures. However, the position of [TA(A)]n-block and number of hairpin structure are different from those in the congeneric P. japonicus and other decapods. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes do not support the monophyly of suborder Pleocyemata, which is in contrast to most morphological and molecular results. However, the position of Palinura and Astacidea is unstable, as represented by the basal or sister branches to other Reptantia species. P. stimpsoni, as the second species of Palinura with complete mitochondrial genome available, will provide important information on both genomics and conservation biology of the group.
Collapse
|