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Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024; 277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
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Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Station of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Station of CMFRI, Digha, West Bengal, India
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Zheng S, Zhang C, Zhou J, Zhang S, Liu Y, Jin X, Wang Y, Liu B. Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda. Biochem Genet 2024; 62:3030-3051. [PMID: 38063953 DOI: 10.1007/s10528-023-10594-4] [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: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 07/31/2024]
Abstract
In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.
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Affiliation(s)
- Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China.
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of 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
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China.
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Wei Z, Yang Y, Meng L, Zhang N, Liu S, Meng L, Li Y, Shao C. The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution. Int J Mol Sci 2024; 25:8218. [PMID: 39125787 PMCID: PMC11311739 DOI: 10.3390/ijms25158218] [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: 04/08/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes.
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Affiliation(s)
- Zhanfei Wei
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Yang Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Lihui Meng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
| | - Nannan Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Yang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
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Kong D, Gan Z, Li X. Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes. Gene 2024; 896:148054. [PMID: 38042216 DOI: 10.1016/j.gene.2023.148054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023]
Abstract
The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.
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Affiliation(s)
- Deming Kong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhibin Gan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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5
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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.
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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
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Wang Z, Zheng Y, Zhao X, Xu X, Xu Z, Cui C. Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences. BIOLOGY 2023; 12:974. [PMID: 37508404 PMCID: PMC10376310 DOI: 10.3390/biology12070974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.
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Affiliation(s)
- Zhengfei 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 224001, China
| | - Yuqing Zheng
- 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 224001, China
| | - Xinyue Zhao
- 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 224001, China
| | - Xinyi Xu
- 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 224001, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200000, China
| | - Zhiwen Xu
- 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 224001, China
| | - Chong Cui
- 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 224001, China
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Zhang C, Wang Y, Chen H, Huang J. Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability. Genes (Basel) 2023; 14:1240. [PMID: 37372420 DOI: 10.3390/genes14061240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143-16,803 bp and 15,933-16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica.
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Affiliation(s)
- Caihong Zhang
- Department of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, China
| | - Yalian Wang
- Department of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, China
| | - Hongwei Chen
- Department of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, China
| | - Jia Huang
- Department of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
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Kobayashi G, Itoh H, Nakajima N. Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes. Zoolog Sci 2023; 40:224-234. [PMID: 37256570 DOI: 10.2108/zs220063] [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: 08/02/2022] [Accepted: 01/02/2023] [Indexed: 06/01/2023]
Abstract
Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.
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Affiliation(s)
- Genki Kobayashi
- Ishinomaki Senshu University, Minamisakai, Ishinomaki, Miyagi 986-8580, Japan,
| | - Hajime Itoh
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuyoshi Nakajima
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
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Ji YT, Zhou XJ, Yang Q, Lu YB, Wang J, Zou JX. Adaptive evolution characteristics of mitochondrial genomes in genus Aparapotamon (Brachyura, Potamidae) of freshwater crabs. BMC Genomics 2023; 24:193. [PMID: 37041498 PMCID: PMC10091551 DOI: 10.1186/s12864-023-09290-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/01/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes. RESULTS A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs. CONCLUSIONS Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.
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Affiliation(s)
- Yu-Tong Ji
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Xiao-Juan Zhou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Qian Yang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China.
- Department of Parasitology, School of Basic Medical Science, Nanchang University, 461 Bayi Avenue, Nanchang City, 330006, Jiangxi Province, China.
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Cheng M, Liu Y, Zheng X, Zhang R, Feng K, Yue B, Du C, Zhou C. Characterization of Seventeen Complete Mitochondrial Genomes: Structural Features and Phylogenetic Implications of the Lepidopteran Insects. INSECTS 2022; 13:998. [PMID: 36354822 PMCID: PMC9694843 DOI: 10.3390/insects13110998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Lepidoptera (moths and butterflies) are widely distributed in the world, but high-level phylogeny in Lepidoptera remains uncertain. More mitochondrial genome (mitogenome) data can help to conduct comprehensive analysis and construct a robust phylogenetic tree. Here, we sequenced and annotated 17 complete moth mitogenomes and made comparative analysis with other moths. The gene order of trnM-trnI-trnQ in 17 moths was different from trnI-trnQ-trnM of ancestral insects. The number, type, and order of genes were consistent with reported moths. The length of newly sequenced complete mitogenomes ranged from 14,231 bp of Rhagastis albomarginatus to 15,756 bp of Numenes albofascia. These moth mitogenomes were typically with high A+T contents varied from 76.0% to 81.7% and exhibited negative GC skews. Among 13 protein coding genes (PCGs), some unusual initiations and terminations were found in part of newly sequenced moth mitogenomes. Three conserved gene-overlapping regions and one conserved intergenic region were detected among 17 mitogenomes. The phylogenetic relationship of major superfamilies in Macroheterocera was as follows: (Bombycoidea + Lasiocampoidea) + ((Drepanoidea + Geometroidea) + Noctuoidea)), which was different from previous studies. Moreover, the topology of Noctuoidea as (Notodontidae + (Erebidae + Noctuidae)) was supported by high Bayesian posterior probabilities (BPP = 1.0) and bootstrapping values (BSV = 100). This study greatly enriched the mitogenome database of moth and strengthened the high-level phylogenetic relationships of Lepidoptera.
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Affiliation(s)
- Meiling Cheng
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
- State Forestry and Grassland Administration Key Laboratory of Conservation Biology for Rare Animals of the Giant Panda State Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Yi Liu
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641000, China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Rusong Zhang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Kaize Feng
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Chao Du
- Baotou Teachers College, Baotou 014060, China
| | - Chuang Zhou
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
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11
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Seiblitz IGL, Vaga CF, Capel KCC, Cairns SD, Stolarski J, Quattrini AM, Kitahara MV. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol Phylogenet Evol 2022; 175:107565. [PMID: 35787457 DOI: 10.1016/j.ympev.2022.107565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.
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Affiliation(s)
- I G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil.
| | - C F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, PL-00-818 Warsaw, Poland
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - M V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil.
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12
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Pang X, Han C, Guo B, Liu K, Lin X, Lu X. The First Complete Mitochondrial Genome of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) and Phylogenetic Relationships within Infraorder Brachyura. Genes (Basel) 2022; 13:genes13071127. [PMID: 35885910 PMCID: PMC9323885 DOI: 10.3390/genes13071127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Characterizing the complete mitochondrial genome (mitogenome) of an organism is useful for genomic studies in taxonomy and evolution. The mitogenomic characteristics of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) have never been studied. The present study decodes the first mitogenome of E. crenata by high-throughput sequencing (HTS). The length of the mitogenome is 15,597 bp, and it contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL), and 22 transfer RNA genes. There are 14 and 23 genes observed on the heavy and light strands, respectively. E. crenata possesses a trnH-cac translocation, with the trnH-cac shifted between trnE-gaa and trnF-ttc instead of the usual location between nad5 and nad4 in decapods. Phylogenetic analyses based on the current dataset of 33 Brachyuran mitogenomes indicate that E. crenata. is closely related to Ashtoret lunaris of Matutidae. The similar codon usage and rearrangements in the two species provide evidence for their close phylogenetic relationship. Positive selection analysis showed that one residue located in cox1 was identified as a positively selected site with high BEB value (>95%), indicating that this gene was under positive selection pressure. This study is the first complete mitogenome record for the family Goneplacidae, and the results obtained may improve the understanding of the phylogeny of Goneplacidae in Brachyura.
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Affiliation(s)
- Xiaoke Pang
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
| | - Chenglong Han
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
| | - Biao Guo
- Tianjin Fisheries Research Institute, Tianjin 300457, China; (B.G.); (K.L.)
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin 300457, China; (B.G.); (K.L.)
| | - Xiaolong Lin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (X.L.); (X.L.)
| | - Xueqiang Lu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
- Correspondence: (X.L.); (X.L.)
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13
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Li Z, Ma B, Li X, Lv Y, Jiang X, Ren C, Hu C, Luo P. The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position. Genes (Basel) 2022; 13:genes13050825. [PMID: 35627210 PMCID: PMC9141342 DOI: 10.3390/genes13050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/21/2023] Open
Abstract
The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.
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Affiliation(s)
- Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Marin College, Beibu Gulf University, Qinzhou 535011, China;
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence:
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14
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Zuo Q, Zhang Z, Shen Y. Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda. Ecol Evol 2022; 12:e8764. [PMID: 35356579 PMCID: PMC8948135 DOI: 10.1002/ece3.8764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/29/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
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Affiliation(s)
- Qing Zuo
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Zhisheng Zhang
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal BiologySchool of Life SciencesChongqing Normal UniversityChongqingChina
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15
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Lü J, Xia L, Liu X, Ma Y, Li J, Ye Y, Guo B. The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura. Sci Rep 2022; 12:2104. [PMID: 35136145 PMCID: PMC8826855 DOI: 10.1038/s41598-022-06080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.
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Affiliation(s)
- Jiayin Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liping Xia
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yanwen Ma
- 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.
| | - Yingying Ye
- 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
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16
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A novel gene order and remolded tRNAs revealed in the mitogenome of Asian gecarcinucid freshwater crabs (Brachyura, Gecarcinucidae). Gene 2021; 813:146102. [PMID: 34933078 DOI: 10.1016/j.gene.2021.146102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Here we report the first mitochondrial genomes (mitogenomes) of four species of gecarcinucid freshwater crabs (FWCs) in two genera, two from China (Somanniathelphusa hainanensis and S. yangshanensis), one from Laos (Esanthelphusa dugasti), and one from Myanmar (Esanthelphusa keyini). A novel gecarcinucid mitochondrial gene order (GMGO2) that was only found in E. dugasti that contains a total of 42 genes, including one pseudogene, two remolded tRNAs and two duplicated tRNAs. The GMGO2 of E. dugasti was compared with the brachyuran ground-pattern mitochondrial gene order (BMGO), revealing the rearrangements of the positions of 10 tRNAs, two PCGs, and one mNCR. The three other gecarcinucids in this study were all found to possess a previously reported gecarcinucid mitochondrial gene order (GMGO1). The phylogenetic tree reconstructed using the secondary structures of 22 tRNAs of the mitogenomes of 41 species of FWCs provides insights into the evolution of the mitogenome of E. dugasti (GMGO2) which includes remolded and duplicated tRNAs.
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Lau NS, Sam KK, Ahmad AB, Siti KA, Ahmad Zafir AW, Shu-Chien AC. Gene Arrangement and Adaptive Evolution in the Mitochondrial Genomes of Terrestrial Sesarmid Crabs Geosesarma faustum and Geosesarma penangensis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.778570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea. Sci Rep 2021; 11:21833. [PMID: 34750431 PMCID: PMC8576005 DOI: 10.1038/s41598-021-01338-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/11/2021] [Indexed: 11/27/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.
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Feng JT, Xia LP, Yan CR, Miao J, Ye YY, Li JJ, Guo BY, Lü ZM. Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships. Sci Rep 2021; 11:11748. [PMID: 34083683 PMCID: PMC8175686 DOI: 10.1038/s41598-021-91313-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Neritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.
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Affiliation(s)
- Jian-Tong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Li-Ping Xia
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Cheng-Rui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jing Miao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Ji-Ji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Zhen-Ming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
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Xu X, Wang Q, Wu Q, Xu J, Wang J, Wang Z. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura. Biochem Genet 2021; 59:617-636. [PMID: 33415669 DOI: 10.1007/s10528-020-10025-8] [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: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.
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Affiliation(s)
- Xinyi Xu
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qi Wang
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qiong Wu
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jiayan Xu
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jie Wang
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Zhengfei Wang
- 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 Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China.
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Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Int J Biol Macromol 2021; 170:717-727. [PMID: 33412200 DOI: 10.1016/j.ijbiomac.2020.12.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 12/29/2020] [Indexed: 11/23/2022]
Abstract
Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.
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Kobayashi G, Itoh H, Fukuda H, Kojima S. The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position. Genomics 2020; 113:831-839. [PMID: 33091547 DOI: 10.1016/j.ygeno.2020.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/29/2020] [Accepted: 10/16/2020] [Indexed: 01/19/2023]
Abstract
The mitochondrial genome has become commonly used for the molecular phylogenetic analysis of animals. Most phylogenetic studies on brachyurans using mitogenome sequences have indicated the paraphyly of superfamilies Grapsoidea and Ocypodoidea but taxon sampling remains limited. The phylogenetic position of Scopimera has been tested in several previous studies using nuclear and/or mitochondrial DNA sequences, but the phylogenetic relationship within the family remains to be resolved. We newly sequenced the complete mitochondrial genome of the sand bubbler crab Scopimera globosa (Ocypodoidea: Dotillidae). Scopimera globosa was clustered with Ilyoplax despite the morphological similarity between Scopimera and Dotilla. The mitochondrial gene order of S. globosa was unique, whereas that of other genera in the family was the same. These results suggest that phylogenetic analysis based on mitogenome sequences and gene order comparison would provide a more robust phylogeny of Dotillidae.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan.
| | - Hajime Itoh
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Hideki Fukuda
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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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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