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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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Kim JM, Kim HS, Yi CH. The complete mitochondrial genome of Helicana japonica (Crustacea, Decapoda, Varunidae) from South Korea. Mitochondrial DNA B Resour 2023; 8:872-876. [PMID: 37600504 PMCID: PMC10434999 DOI: 10.1080/23802359.2023.2246686] [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: 09/19/2022] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
Helicana japonica mainly inhabits burrowed holes in the mudflats and intertidal zones. Specimens from the Republic of Korea were collected and whole genomic DNA from the cheliped muscle tissue was extracted. We determined the complete mitochondrial genome using Illumina HiSeq X Ten. The mitogenome is 16,535 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. A phylogenetic tree was reconstructed using the maximum-likelihood of phylogeny methods. H. japonica formed a sister clade with Helicana wuana, which is another Helicana species.
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Affiliation(s)
- Ji-Min Kim
- Department of Ecology and Conservation, Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
- School of Marine Biology, College of Marine Science, Kunsan National University, Gunsan, Republic of Korea
| | - Hyung-Seop Kim
- School of Marine Biology, College of Marine Science, Kunsan National University, Gunsan, Republic of Korea
| | - Chang-Ho Yi
- Department of Ecology and Conservation, Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
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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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Full Mitochondrial Genomes Reveal Species Differences between the Venerid Clams Ruditapes philippinarum and R. variegatus. Genes (Basel) 2022; 13:genes13112157. [DOI: 10.3390/genes13112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022] Open
Abstract
In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification.
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Duan X, Dong X, Li J, Lü J, Guo B, Xu K, Ye Y. The Complete Mitochondrial Genome of Pilumnopeus Makianus (Brachyura: Pilumnidae), Novel Gene Rearrangements, and Phylogenetic Relationships of Brachyura. Genes (Basel) 2022; 13:1943. [PMID: 36360180 PMCID: PMC9690104 DOI: 10.3390/genes13111943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/16/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2023] Open
Abstract
Pilumnopeus makianus is a crab that belongs to Pilumnidae, Brachyura. Although many recent studies have focused on the phylogeny of Brachyura, the internal relationships in this clade are far from settled. In this study, the complete mitogenome of P. makianus was sequenced and annotated for the first time. The length of the mitogenome is 15,863 bp, and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and 2 ribosomal RNA genes (rRNA). The mitogenome exhibits a high AT content (72.26%), with a negative AT-skew (-0.01) and a GC-skew (-0.256). In the mitogenome of P. makianus, all the tRNA genes are folded into the typical cloverleaf secondary structure, except trnS1 (TCT). A comparison with the ancestors of Brachyura reveals that gene rearrangement occurred in P. makianus. In addition, phylogenetic analyses based on thirteen PCGs indicated that P. makianus, Pilumnus vespertilio, and Echinoecus nipponicus clustered into a well-supported clade that supports the monophyly of the family Pilumnidae. These findings enabled a better understanding of phylogenetic relationships within Brachyura.
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Affiliation(s)
- Xinbing Duan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiangli Dong
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiayin Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Huang L, Sun HQ, Li CJ, Zhao WX, Yao YX. The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications. Int J Parasitol Parasites Wildl 2022; 18:249-259. [PMID: 35800109 PMCID: PMC9253838 DOI: 10.1016/j.ijppaw.2022.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 01/04/2023]
Abstract
Platygaster robiniae is economically important as a highly specific parasitoid of the invasive pest Obolodiplosis robiniae which was introduced into the Euro-Asia region in the last decade. Despite being a critical and specific parasitoid of the invasive pest O. robiniae and its use as an effective biocontrol agent, the absence of sequence information from P. robiniae have limited its genetic applications for pest management in forests. Mitochondrial (mt) genomes generally contain abundant nucleotide information and thus are helpful for understanding species history. Here, we sequenced the complete mt genome of P. robiniae using next generation sequencing, and annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 702 bp noncoding region. Comparative analysis indicated that this mt genome has a normal A + T content and codons use, however possessed both the expected and unique rearrangements. Ten tRNAs at four gene blocks COII-ATP8, COIII-ND3, ND3-ND5 and the A + T-rich region-ND2 were rearranged, including gene shuffles, transpositions and inversions. Notably, two genes tRNASer(UCN) and tRNALeu(CUN) had undergone long-range inversions, which is the first record of this rearrangement type in the superfamily Platygastroidea. The D-loops of both tRNAIle and tRNALeu(CUN) were absent from the tRNA secondary structure, which has not been reported from hymenopteran previously. Phylogenetic analysis based with the maximum likelihood and Bayesian methods showed that P. robiniae grouped with other species of Platygastridae, and that the superfamily Platygastridea is sister to the other Proctotrupomorpha superfamilies. Our tree strongly supports the monophyly of the five superfamilies of Proctotrupomorpha. This study discovered some unique characters of P. robiniae, and contributes to our understanding of genome rearrangements in the order Hymenoptera. Assemble the complete mitochondria genome of the obligate parasitoid (Platygaster robiniae) of Obolodiplosis robiniae. Discover some unique tRNA secondary structures. Discover some unique rearrangements of Platygaster robiniae and Platygastroidea. The abundance rearrangements in the order Hymenoptera.
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Zhang Z, Li S, Zhang J, Song W, Yang J, Mu J. The complete mitochondrial genome of an endangered minnow Aphyocypris lini (Cypriniformes: Xenocyprididae): genome characterization and phylogenetic consideration. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Luque J, Xing L, Briggs DEG, Clark EG, Duque A, Hui J, Mai H, McKellar RC. Crab in amber reveals an early colonization of nonmarine environments during the Cretaceous. SCIENCE ADVANCES 2021; 7:eabj5689. [PMID: 34669480 PMCID: PMC8528423 DOI: 10.1126/sciadv.abj5689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Amber fossils provide snapshots of the anatomy, biology, and ecology of extinct organisms that are otherwise inaccessible. The best-known fossils in amber are terrestrial arthropods—principally insects—whereas aquatic organisms are rarely represented. Here, we present the first record of true crabs (Brachyura) in amber—from the Cretaceous of Myanmar [~100 to 99 million years (Ma)]. The new fossil preserves large compound eyes, delicate mouthparts, and even gills. This modern-looking crab is nested within crown Eubrachyura, or “higher” true crabs, which includes the majority of brachyuran species living today. The fossil appears to have been trapped in a brackish or freshwater setting near a coastal to fluvio-estuarine environment, bridging the gap between the predicted molecular divergence of nonmarine crabs (~130 Ma) and their younger fossil record (latest Cretaceous and Paleogene, ~75 to 50 Ma) while providing a reliable calibration point for molecular divergence time estimates for higher crown eubrachyurans.
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Affiliation(s)
- Javier Luque
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06520-8109, USA
- Smithsonian Tropical Research Institute, Balboa–Ancón, 0843-03092 Panamá, Panamá
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Lida Xing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- School of the Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
| | - Derek E. G. Briggs
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06520-8109, USA
| | - Elizabeth G. Clark
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06520-8109, USA
- Biology Department, Duke University, Durham, NC 27708, USA
| | - Alex Duque
- Computer Animation and Visual Effects, College of Communication and Design, Lynn University, 2601 North Military Trail, Boca Raton, FL 33431, USA
| | - Junbo Hui
- Longyin Amber Museum, Xishan District, Kunming 650228, Yunnan, China
| | - Huijuan Mai
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, Yunnan, China
- MEC International Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, Yunnan, China
| | - Ryan C. McKellar
- Royal Saskatchewan Museum, Regina, SK S4P 4W7, Canada
- Biology Department, University of Regina, Regina, SK S4S 0A2, Canada
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Li YT, Xin ZZ, Tang YY, Yang TT, Tang BP, Sun Y, Zhang DZ, Zhou CL, Liu QN, Yu XM. Comparative Mitochondrial Genome Analyses of Sesarmid and Other Brachyuran Crabs Reveal Gene Rearrangements and Phylogeny. Front Genet 2020; 11:536640. [PMID: 33240311 PMCID: PMC7667018 DOI: 10.3389/fgene.2020.536640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/28/2020] [Indexed: 01/26/2023] Open
Abstract
Mitochondrial genomes (mitogenomes) are important for understanding molecular evolution and phylogenetic relationships. The complete mitogenome of Perisesarma bidens was determined, which is 15,641 bp in length. The A + T content of P. bidens mitogenome was 74.81%. The AT skew was slightly negative (-0.021). The 22 tRNAs ranged from 65 to 73 bp and were highly A + T biased. All tRNA genes had typical cloverleaf structures, except for the trnS1 gene, which lacked a dihydrouridine (DHU) arm. The gene order within the P. bidens mitogenome was identical to the pancrustacean ground pattern, except for the translocation of the trnH. Additionally, the gene order of trnI-trnQ-trnM in pancrustacean ground pattern became trnQ-trnI-trnM in P. bidens. Phylogenetic analyses supported the inclusion of P. bidens in Sesarmidae and the promotion of Sesarminae to Sesarmidae. The results will help us to better understand the status and evolutionary history of Grapsoidea crabs.
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Affiliation(s)
- Yue-Tian Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Life Sciences, Nankai University, Tianjin, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Ying-Yu Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Yue Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Xiao-Min Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
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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]
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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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13
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Bian D, Dai M, Ye W, Lu Z, Li M, Fang Y, Qu J, Su W, Li F, Sun H, Li B. Complete mitochondrial genome of Spilosoma lubricipedum (Noctuoidea: Erebidae) and implications for phylogeny of noctuid insects. Genomics 2020; 112:4577-4584. [PMID: 32758539 DOI: 10.1016/j.ygeno.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/13/2020] [Accepted: 08/01/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genomes (mitogenomes) have been widely used for studies on phylogenetic relationships and molecular evolutionary biology. Here, the complete mitogenome sequence of Spilosoma lubricipedum (Noctuoidea: Erebidae: Arctiinae) was determined (total length 15,375 bp) and phylogenetic analyses S. lubricipedum were inferred from available noctuid sequence data. The mitogenome of S. lubricipedum was found to be highly A + T-biased (81.39%) and exhibited negative AT- and GC-skews. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for cox1 with CGA. All tRNAs exhibited typical clover-leaf secondary structures, except for trnS1. The gene order of the S. lubricipedum mitogenome was trnM-trnI-trnQ-nad2. The A + T-rich region of S. lubricipedum contained several conservative features common to noctuid insects. Phylogenetic analysis within Noctuoidea was carried out based on mitochondrial data. Results showed that S. lubricipedum belonged to Erebidae and the Noctuoidea insects could be divided into five well-supported families (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).
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Affiliation(s)
- Dandan Bian
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Minli Dai
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Wentao Ye
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Zhengting Lu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Mengxue Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Yilong Fang
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Jianwei Qu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Wujie Su
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Fanchi Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China
| | - Haina Sun
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China.
| | - Bing Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, Jiangsu, People's Republic of China; Sericulture Institute of Soochow University, Suzhou 215123, Jiangsu, People's Republic of China.
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14
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Sun H, Zhao W, Lin R, Zhou Z, Huai W, Yao Y. The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga. Genomics 2020; 112:3713-3721. [PMID: 32360911 DOI: 10.1016/j.ygeno.2020.04.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Abstract
In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.
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Affiliation(s)
- Huiquan Sun
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruozhu Lin
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhongfu Zhou
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Huai
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanxia Yao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
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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.
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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.
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16
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Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura. Genomics 2019; 112:1804-1812. [PMID: 31655177 DOI: 10.1016/j.ygeno.2019.10.012] [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: 08/06/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships among organisms, as well as useful information about the process of molecular evolution and gene rearrangement mechanisms. However, knowledge on the complete mitogenome of Coenobitidae (Decapoda: Anomura) is quite scarce. Here, we describe in detail the complete mitogenome of Coenobita brevimanus, which is 16,393 bp in length, and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region. The genome composition shows a moderate A + T bias (65.0%), and exhibited a negative AT-skew (-0.148) and a positive GC-skew (0.183). Five gene clusters (or genes) involving eleven tRNAs and two PCGs were found to have rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination models were determined as most likely to explain the observed large-scale gene rearrangements. Phylogenetic analysis placed all Coenobitidae species into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was inconsistence with previous findings on Anomura. Taken together, our results help to better understand gene rearrangement process and the evolutionary status of C. brevimanus and lay a foundation for further phylogenetic studies of Anomura.
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17
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Li Q, Xiang D, Wan Y, Wu Q, Wu X, Ma C, Song Y, Zhao G, Huang W. The complete mitochondrial genomes of five important medicinal Ganoderma species: Features, evolution, and phylogeny. Int J Biol Macromol 2019; 139:397-408. [DOI: 10.1016/j.ijbiomac.2019.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/10/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
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18
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Yang ZH, Yang TT, Liu Y, Zhang HB, Tang BP, Liu QN, Ma YF. The complete mitochondrial genome of Sinna extrema (Lepidoptera: Nolidae) and its implications for the phylogenetic relationships of Noctuoidea species. Int J Biol Macromol 2019; 137:317-326. [DOI: 10.1016/j.ijbiomac.2019.06.238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 10/26/2022]
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19
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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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20
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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.
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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
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21
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Liu Y, Yang TT, Xin ZZ, Liu QN, Zhang DZ, Tang BP. The complete mitochondrial genome sequence of Metaplax longipes (Grapsoidea: Varunidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- 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, China
| | - Ting-Ting Yang
- 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, 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, 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, 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, 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 Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
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Guinot D, Ng NK, Moreno PAR. Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838). ZOOSYSTEMA 2018. [DOI: 10.5252/zoosystema2018v40a26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Danièle Guinot
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, case postale 53, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
| | - Ngan Kee Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Republic of Singapore)
| | - Paula A. Rodríguez Moreno
- Direction générale déléguée aux Collections, Muséum national d'Histoire naturelle, case postale 30, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
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Mitochondrial genome of the yellow catfish Pelteobagrus fulvidraco and insights into Bagridae phylogenetics. Genomics 2018; 111:1258-1265. [PMID: 30118781 DOI: 10.1016/j.ygeno.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/02/2018] [Accepted: 08/13/2018] [Indexed: 11/21/2022]
Abstract
The mitochondrial genome (mitogenome) can provide important information for understanding phylogenetic analysis and molecular evolution. Herein, we amplified the complete mitogenome sequence of Pelteobagrus fulvidraco. The mitogenome was 16,526 bp in length and included 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and a non-coding control region (D-loop). Both the organization and location of genes in the mitogenome were consistent with those from Siluriformes fishes previously published in GenBank. The phylogenetic relationships based on Bayesian inference (BI) and Maximum likelihood (ML) methods showed that P. fulvidraco has close relationships with Pelteobagrus eupogon and Tachysurus intermedius, suggesting that P. fulvidraco belongs to Tachysurus. This study provides evidence that Tachysurus, Pseudobagrus and Leiocassis do not form monophyly, but that these three genera form a monophyletic group. Our results provide reference for further phylogenetic research of the Bagridae species.
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