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Dadkhah K, Mianji GR, Barzegar A, Farhadi A. Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA. BMC Ecol Evol 2023; 23:55. [PMID: 37749487 PMCID: PMC10521412 DOI: 10.1186/s12862-023-02166-2] [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: 10/18/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. RESULTS In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. CONCLUSIONS In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.
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Affiliation(s)
- Khadijeh Dadkhah
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Ghodrat Rahimi Mianji
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Li Y, Lou F, Song P, Liu S, Siyal FK, Lin L. New perspective on the genetic structure and habitat adaptation of Pampus minor off the coast of China based on RAD-seq. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100865. [PMID: 34167063 DOI: 10.1016/j.cbd.2021.100865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022]
Abstract
Understanding the genetic diversity and habitat adaptation patterns of different geographic populations of marine organisms is essential for the rational maintenance, development, and utilization of their resources. Pampus minor Liu and Li 1998 is an economically valuable marine fish species. To determine the population genetic structure and elucidate the genetic mechanism underlying the habitat adaptation of this species, restriction site-associated DNA sequencing (RAD-seq) was used to scan the whole genomes of three P. minor putative populations along the coast of China for single-nucleotide polymorphism (SNPs) and outlier SNPs. Our population genetic structure analysis based on 2388 SNPs and 731 outlier SNPs throughout the genome revealed no significant genetic differentiation among the three populations. Results suggested that the life-cycle characteristics of P. minor, its relatively large population sizes, and ocean current transport might have shaped its current genetic pattern. The annotation information of both assembled sequences (which included outlier SNPs) and candidate loci associated with adaptations indicated that genes involved in many processes, including ion exchange, osmotic pressure regulation, metabolism, and the immune response, have been very important in the adaptations of P. minor to its heterogeneous habitats. Against the background of increased human activities, increased fishing intensity, and destruction of marine habitats, the results of this study provide basic genetic information for the accurate division of protection units of P. minor.
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Affiliation(s)
- Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Fangrui Lou
- School of Ocean, Yantai University, Yantai, Shandong 264005, China
| | - Puqing Song
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Shigang Liu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Fozia Khan Siyal
- Faculty of Natural Sciences, Shah Abdul Latif University, Khairpur, Sindh 66020, Pakistan
| | - Longshan Lin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China.
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Yin G, Pan Y, Sarker A, Baki MA, Kim JK, Wu H, Li C. Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment. Mol Phylogenet Evol 2019; 140:106595. [PMID: 31421244 DOI: 10.1016/j.ympev.2019.106595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/15/2022]
Abstract
Pomfret fishes of the genus Pampus are commercially important in the Indo-Pacific region, yet the phylogenetic relationships and taxonomy of Pampus remain contentious. Here, we sampled 151 specimens, representing all known species of the genus, as well as two outgroup species (two families). We collected sequences from 17,292 single-copy nuclear coding loci using target-gene enrichment and Illumina sequencing for a subset samples of P. echinogaster, P. argenteus, P. cinereus, P. liuorum, P. chinensis, P. minor, and P. punctatissimus, which were carefully examined according to their species descriptions. Concatenated gene tree and species tree analyses resulted in identical and highly supported phylogenies, in which P. argenteus was sister to P. minor in one clade and P. cinereus sister to P. chinensis and P. punctatissimus in the other clade. Phylogenetic reconstruction using sequences of cytochrome c oxidase subunit I (COI) collected by us and those retrieved from NCBI suggests extensive misidentification of Pampus species in the NCBI database. We also measured morphological characters of each species as well as observed their osteological structure using micro-CT. Both molecular and morphological results suggest that P. echinogaster is a synonym of P. argenteus, and P. liuorum is a synonym of P. cinereus. Pampus cinereus from China, Bangladesh and an uncertain origin were grouped into three clades according to their sampling localities, but we could not find decisive morphological characters to describe the "cryptic species" of P. cinereus. Finally, based on the results of the molecular analyses and morphological reexamination, we created an identification key for the genus of Pampus.
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Affiliation(s)
- Guoxing Yin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China
| | - Yiling Pan
- Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, 510 West Beijing Rd, Jing'an District, Shanghai 200041, China
| | - Anirban Sarker
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; Department of Zoology, Jagannath University, Dhaka 1100, Bangladesh
| | - Mohammad A Baki
- Department of Zoology, Jagannath University, Dhaka 1100, Bangladesh
| | - Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan 608-737, South Korea
| | - Hanlin Wu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China.
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Wang S, Zhao L, Li Y, Zhang Z, Wang Z, Gao T. Complete mitochondrial DNA genome of grey pomfret Pampus cinereus (Bloch, 1795) (Perciformes: Stromateidae). Mitochondrial DNA B Resour 2018; 3:683-684. [PMID: 33490530 PMCID: PMC7800252 DOI: 10.1080/23802359.2018.1481788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome of Pampus cinereus (Bloch, 1795). This mitochondrial genome, consisting of 16,540 base pairs (bp), contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two mainly noncoding regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region with 846 bp in length, is located between tRNAPro and tRNAPhe. The overall base composition of the heavy strand shows 27.4% of T, 27.5% of C, 30.0% of A, and 15.2% of G, with a slight A + T rich bias (57.4%). The complete mitochondrial genome data will provide useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
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Affiliation(s)
- Shouqiang Wang
- College of Environmental Scinence and Engineering, Ocean University of China, Qingdao, P.R. China
- The First Institute of Oceanography, SOA, Qingdao, P.R. China
| | - Linlin Zhao
- The First Institute of Oceanography, SOA, Qingdao, P.R. China
| | - Yuan Li
- Third Institute of Oceanography, SOA, Xiamen, P.R. China
| | - Zhaohui Zhang
- The First Institute of Oceanography, SOA, Qingdao, P.R. China
| | - Zongling Wang
- The First Institute of Oceanography, SOA, Qingdao, P.R. China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, P.R. China
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Zhuang X, Qu M, Zhang X, Ding S. A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One 2013; 8:e73561. [PMID: 23951357 PMCID: PMC3739747 DOI: 10.1371/journal.pone.0073561] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.
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Affiliation(s)
- Xuan Zhuang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Meng Qu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Xiang Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
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Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics 2012; 13:631. [PMID: 23153176 PMCID: PMC3533576 DOI: 10.1186/1471-2164-13-631] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. RESULTS We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. CONCLUSIONS Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.
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