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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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Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [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: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
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Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Muhala V, Guimarães-Costa A, Bessa-Silva AR, Rabelo LP, Carneiro J, Macate IE, Watanabe L, Balcázar OD, Gomes GE, Vallinoto M, Sampaio I. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species. Sci Rep 2024; 14:3358. [PMID: 38336845 PMCID: PMC10858209 DOI: 10.1038/s41598-024-52979-4] [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: 07/27/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.
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Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil.
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chokwe, 1204, Mozambique.
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Jeferson Carneiro
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Oscar David Balcázar
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Grazielle Evangelista Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
- Laboratório Associado, Campus agrário de Vairão, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Iracilda Sampaio
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
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Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [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: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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lü J, Dong X, Li J, Ye Y, Xu K. Novel gene re-arrangement in the mitochondrial genome of Pisidiaserratifrons (Anomura, Galatheoidea, Porcellanidae) and phylogenetic associations in Anomura. Biodivers Data J 2023; 11:e96231. [PMID: 38327357 PMCID: PMC10848379 DOI: 10.3897/bdj.11.e96231] [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: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 02/25/2023] Open
Abstract
To improve the taxonomy and systematics of Porcellanidae within the evolution of Anomura, we describe the complete mitochondrial genomes (mitogenomes) sequence of Pisidiaserratifrons, which is 15,344 bp in size, contains the entire set of 37 genes and has an AT-rich region. Compared with the pancrustacean ground pattern, at least five gene clusters (or genes) are significantly different with the typical genes, involving eleven tRNA genes and four PCGs and the tandem duplication/random loss and recombination models were used to explain the observed large-scale gene re-arrangements. The phylogenetic results showed that all Porcellanidae species clustered together as a group with well nodal support. Most Anomura superfamilies were found to be monophyletic, except Paguroidea. Divergence time estimation implies that the age of Anomura is over 225 MYA, dating back to at least the late Triassic. Most of the extant superfamilies and families arose during the late Cretaceous to early Tertiary. In general, the results obtained in this study will contribute to a better understanding of gene re-arrangements in Porcellanidae mitogenomes and provide new insights into the phylogeny of Anomura.
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Affiliation(s)
- Jiayin lü
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Xiangli Dong
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Jiji Li
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Yingying Ye
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Kaida Xu
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
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Zhang C, Zhang K, Peng Y, Zhou J, Liu Y, Liu B. Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae. Front Genet 2022; 13:922634. [PMID: 35754812 PMCID: PMC9213810 DOI: 10.3389/fgene.2022.922634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.
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Affiliation(s)
- Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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Sureshan SC, Tanavade RV, Ghosh S, Ghosh S, Sella RN, Mohideen HS. Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India. Sci Rep 2021; 11:23738. [PMID: 34887433 PMCID: PMC8660866 DOI: 10.1038/s41598-021-02881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and - 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.
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Affiliation(s)
- Shruthi Chalil Sureshan
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Ruchi Vivekanand Tanavade
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Sewali Ghosh
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, 600042 Tamil Nadu India
| | - Saswati Ghosh
- grid.506009.aDepartment of Virology, King Institute of Preventive Medicine and Research, Chennai, 600032 Tamil Nadu India
| | - Raja Natesan Sella
- grid.412742.60000 0004 0635 5080Membrane Protein Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India.
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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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Zhang K, Zhu K, Liu Y, Zhang H, Gong L, Jiang L, Liu L, Lü Z, Liu B. Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes. Sci Rep 2021; 11:2411. [PMID: 33510193 PMCID: PMC7844273 DOI: 10.1038/s41598-021-81622-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.
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Affiliation(s)
- Kun Zhang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Kehua Zhu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Yifan Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Hua Zhang
- grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Li Gong
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Lihua Jiang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Liqin Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Zhenming Lü
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Bingjian Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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11
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qMGR: A new approach for quantifying mitochondrial genome rearrangement. Mitochondrion 2020; 52:20-23. [DOI: 10.1016/j.mito.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/26/2019] [Accepted: 02/07/2020] [Indexed: 11/20/2022]
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12
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Shi W, Yu H. The complete mitochondrial genome sequence of Rhynchoconger ectenurus (Anguilliformes: Congridae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1741464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Wei Shi
- College of Life Science, Foshan University, Foshan, China
| | - Hui Yu
- College of Life Science, Foshan University, Foshan, China
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13
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Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int J Biol Macromol 2020; 149:1232-1240. [DOI: 10.1016/j.ijbiomac.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 11/24/2022]
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14
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Shi W, Gong L, Yu H. Double control regions of some flatfish mitogenomes evolve in a concerted manner. Int J Biol Macromol 2019; 142:11-17. [PMID: 31785298 DOI: 10.1016/j.ijbiomac.2019.11.204] [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: 06/13/2019] [Revised: 11/03/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
Abstract
Mitochondrial genomes (mitogenomes) typically contain 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region (CR). Flatfish mitochondrial genomes (mitogenomes) from three different genera in Bothidae (bothids) contain double CRs that evolved in a concerted manner. How these double CRs maintained identical sequences throughout the evolutionary process is an interesting issue. In the present study, over four hundred arrays of the double CRs of mitogenomes from three bothids (Arnoglossus tenuis, Lophonectes gallus and Psettina iijimae) were performed. Interesting variations between double CRs were observed in P. iijimae mitogenomes, and the networks of CR sequences from P. iijimae indicated a high possibility of genetic information exchange between CRs. No recombination product was detected in our results, indicating that the mechanism of the concerted evolution between the double CRs of P. iijimae was not recombination. We speculate that mismatch repair, a mitochondrial DNA repair mechanism, is a potential explanation for the concerted evolution between these double CRs.
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Affiliation(s)
- Wei Shi
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science, Foshan University, Foshan, Guangdong 528231, China
| | - Li Gong
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science, Foshan University, Foshan, Guangdong 528231, China.
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15
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Luo H, Kong X, Chen S, Shi W. Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae). BMC Genomics 2019; 20:792. [PMID: 31666003 PMCID: PMC6821024 DOI: 10.1186/s12864-019-6128-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 09/23/2019] [Indexed: 12/03/2022] Open
Abstract
Background The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. Conclusions This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.
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Affiliation(s)
- Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.
| | - Shixi Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China
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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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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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Chen S, Dong J, Luo H, Shi W, Kong X. The complete mitochondrial genome sequence of Cynoglossus roulei (Pleuronectiformes: Cynoglossidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1598821] [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)
- Shixi Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiangxing Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Turanov SV, Lee YH, Kartavtsev YP. Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:264-272. [PMID: 29991298 DOI: 10.1080/24701394.2018.1484117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.
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Affiliation(s)
- Sergei V Turanov
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University , Vladivostok , Russia
| | - Youn-Ho Lee
- c Laboratory of Marine Genomics, Korean Institute of Ocean Science and Technology , Ansan , Republic of Korea
| | - Yuri Ph Kartavtsev
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,d Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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20
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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Zou H, Jakovlić I, Chen R, Zhang D, Zhang J, Li WX, Wang GT. The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class. BMC Genomics 2017; 18:840. [PMID: 29096600 PMCID: PMC5669012 DOI: 10.1186/s12864-017-4237-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes. RESULTS The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder. CONCLUSIONS Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Xin ZZ, Yu-Liu, Zhang DZ, Wang ZF, Zhang HB, Tang BP, Zhou CL, Chai XY, Liu QN. Mitochondrial genome of Helice tientsinensis (Brachyura: Grapsoidea: Varunidae): Gene rearrangements and higher-level phylogeny of the Brachyura. Gene 2017. [DOI: 10.1016/j.gene.2017.06.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Xin ZZ, Yu Liu, Zhu XY, Wang Y, Zhang HB, Zhang DZ, Zhou CL, Tang BP, Liu QN. Mitochondrial Genomes of Two Bombycoidea Insects and Implications for Their Phylogeny. Sci Rep 2017; 7:6544. [PMID: 28747720 PMCID: PMC5529375 DOI: 10.1038/s41598-017-06930-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81.5%) but is lower than that of R. menciana (82.2%). The AT skew is slightly positive and the GC skew is negative in these two mt genomes. Except for cox1, which started with CGA, all other 12PCGs started with ATN codons. The A + T-rich regions of A. rubiginosa and R. menciana were 399 bp and 604 bp long and consist of several features common to Bombycoidea insects. The order and orientation of A. rubiginosa and R. menciana mitogenomes with the order trnM-trnI-trnQ-nad2 is different from the ancestral insects in which trnM is located between trnQ and nad2 (trnI-trnQ-trnM-nad2). Phylogenetic analyses indicate that A. rubiginosa belongs in the Sphingidae family, and R. menciana belongs in the Bombycidae family.
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Affiliation(s)
- 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, 224051, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR 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, 224051, PR China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
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Wang JG, Zhang D, Jakovlić I, Wang WM. Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda). PLoS One 2017; 12:e0181699. [PMID: 28742843 PMCID: PMC5526530 DOI: 10.1371/journal.pone.0181699] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/04/2017] [Indexed: 11/21/2022] Open
Abstract
Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers. To help resolve their phylogenetic relationships, the complete mitogenomes of eight Chinese viviparid snails, Viviparus chui, Cipangopaludina chinensis, C. ussuriensis, C. dianchiensis (endangered), Margarya melanioides (endangered), M. monodi (critically endangered), Bellamya quadrata and B. aeruginosa, were sequenced and compared to almost all of the available caenogastropod mitogenomes. Viviparidae possess the largest mitogenomes (16 392 to 18 544 bp), exhibit the highest A+T bias (72.5% on average), and some exhibit unique gene orders (a rearrangement of the standard MYCWQGE box), among the Caenogastropoda. Apart from the Vermetidae family and Cerithioidea superfamily, which possessed unique gene orders, the remaining studied caenogastropod mitogenomes exhibited highly conserved gene order, with minimal variations. Maximum likelihood and Bayesian inference analyses, used to reconstruct the phylogenetic relationships among 49 almost complete (all 37 genes) caenogastropod mitogenomes, produced almost identical tree topologies. Viviparidae were divided into three clades: a) Margarya and Cipangopaludina (except C. ussuriensis), b) Bellamya and C. ussuriensis, c) Viviparus chui. Our results present evidence that some Cipangopaludina species (dianchiensis and cathayensis) should be renamed into the senior genus Margarya. The phylogenetic resolution obtained in this study is insufficient to fully resolve the relationships within the 'b' clade, but if C. chinensis proves to be a valid representative of the genus, C. ussuriensis may have to be reassigned a different genus (possibly Bellamya, or even a new genus). Non-monophyly also remains pervasive among the higher (above the family-level) Caenogastropod taxonomic classes. Gene order distance matrix produced a different phylogenetic signal from the nucleotide sequences, which indicates a limited usability of this approach for inferring caenogastropod phylogenies. As phenotypic homoplasy appears to be widespread among some viviparid genera, in order to effectively protect the rapidly diminishing endemic Viviparid populations in China, further detailed molecular phylogenetic studies are urgently needed to resolve the taxonomic status of several species.
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Affiliation(s)
- Ju-Guang Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
| | - Dong Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, PR China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, China
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26
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Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura. Sci Rep 2017. [PMID: 28646134 PMCID: PMC5482888 DOI: 10.1038/s41598-017-04489-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.
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27
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Tang BP, Xin ZZ, Liu Y, Zhang DZ, Wang ZF, Zhang HB, Chai XY, Zhou CL, Liu QN. The complete mitochondrial genome of Sesarmops sinensis reveals gene rearrangements and phylogenetic relationships in Brachyura. PLoS One 2017; 12:e0179800. [PMID: 28622362 PMCID: PMC5473591 DOI: 10.1371/journal.pone.0179800] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genome (mitogenome) is very important to understand molecular evolution and phylogenetics. Herein, in this study, the complete mitogenome of Sesarmops sinensis was reported. The mitogenome was 15,905 bp in size, and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew and the GC skew are both negative in the mitogenomes of S. sinensis. The nucleotide composition of the S. sinensis mitogenome was also biased toward A + T nucleotides (75.7%). All tRNA genes displayed a typical mitochondrial tRNA cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. S. sinensis exhibits a novel rearrangement compared with the Pancrustacean ground pattern and other Brachyura species. Based on the 13 PCGs, the phylogenetic analysis showed that S. sinensis and Sesarma neglectum were clustered on one branch with high nodal support values, indicating that S. sinensis and S. neglectum have a sister group relationship. The group (S. sinensis + S. neglectum) was sister to (Parasesarmops tripectinis + Metopaulias depressus), suggesting that S. sinensis belongs to Grapsoidea, Sesarmidae. Phylogenetic trees based on amino acid sequences and nucleotide sequences of mitochondrial 13 PCGs using BI and ML respectively indicate that section Eubrachyura consists of four groups clearly. The resulting phylogeny supports the establishment of a separate subsection Potamoida. These four groups correspond to four subsections of Raninoida, Heterotremata, Potamoida, and Thoracotremata.
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Affiliation(s)
- Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, PR China
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28
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Xia Y, Zheng Y, Murphy RW, Zeng X. Intraspecific rearrangement of mitochondrial genome suggests the prevalence of the tandem duplication-random loss (TDLR) mechanism in Quasipaa boulengeri. BMC Genomics 2016; 17:965. [PMID: 27881087 PMCID: PMC5122201 DOI: 10.1186/s12864-016-3309-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tandem duplication followed by random loss (TDRL) is the most frequently invoked model to explain the diversity of gene rearrangements in metazoan mitogenomes. The initial stages of gene rearrangement are difficult to observe in nature, which limits our understanding of incipient duplication events and the subsequent process of random loss. Intraspecific gene reorganizations may represent intermediate states, and if so they potentially shed light on the evolutionary dynamics of TDRL. RESULTS Nucleotide sequences in a hotspot of gene-rearrangement in 28 populations of a single species of frog, Quasipaa boulengeri, provide such predicted intermediate states. Gene order and phylogenetic analyses support a single tandem duplication event and a step-by-step process of random loss. Intraspecific gene rearrangements are not commonly found through comparison of all mitochondrial DNA records of amphibians and squamate reptiles in GenBank. CONCLUSIONS The intraspecific variation in Q. boulengeri provides insights into the rate of partial duplications and deletions within a mitogenome, and reveals that fixation and gene-distribution in mitogenomic reorganization is likely non-adaptive.
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Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Wei M, Liu Y, Guo H, Zhao F, Chen S. Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes. Gene 2016; 591:369-75. [PMID: 27312953 DOI: 10.1016/j.gene.2016.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can provide basic information for phylogenetic analysis and evolutionary studies. We present here the mitochondrial genome of Cynoglossus gracilis, which is 16,565bp in length. Numerous distinct regions were identified, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, a light-strand replication origin, and a control region. Interestingly, we detected rearrangement of genes in C. gracilis, including a control region translocation, tRNA(Gln) gene inversion, and tRNA(Ile) gene shuffling. Additionally, a phylogenetic analysis based on the nucleotide sequences of the 13 PCGs using maximum likelihood and Bayesian inference methods reveals that C. gracilis is closely related to Cynoglossus semilaevis. This study provides important mitogenomic data for analyzing phylogenetic relationships in the Cynoglossinae.
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Affiliation(s)
- Min Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Yang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Hua Guo
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Fazhen Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Songlin Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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30
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Song F, Li H, Shao R, Shi A, Bai X, Zheng X, Heiss E, Cai W. Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae). Sci Rep 2016; 6:25725. [PMID: 27180804 PMCID: PMC4867608 DOI: 10.1038/srep25725] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/21/2016] [Indexed: 11/08/2022] Open
Abstract
The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae.
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Affiliation(s)
- Fan Song
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Renfu Shao
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia
| | - Aimin Shi
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Xiaoshuan Bai
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xiaorong Zheng
- Department of Entomology, China Agricultural University, Beijing 100193, China
- Department of Plant Pathology and Crop Protection, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Ernst Heiss
- Tiroler Landesmuseum, Josef-Schraffl-Strassbe 2a, A-6020 Innsbruck, Austria
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing 100193, China
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Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations. Int J Mol Sci 2015; 16:25031-49. [PMID: 26492246 PMCID: PMC4632788 DOI: 10.3390/ijms161025031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.
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