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Li Y, Yi H, Zhu Y. Novel insights into adaptive evolution based on the unusual AT-skew in Acheilognathus gracilis mitogenome and phylogenetic relationships of bitterling. Gene 2024; 902:148154. [PMID: 38218382 DOI: 10.1016/j.gene.2024.148154] [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: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Acheilognathus gracilis, a bitterling species, distribute in lower reaches of Yangtze River. They are identified as the top-priority bitterling species for conservation as having high evolutionary distinctiveness and are at risk of extinction. In present study, we first sequenced the complete mitogenome of A. gracilis and analyzed its phylogenetic position using 13 PCGs. The A. gracilis mitogenome is 16,774 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of A. gracilis in descending order is T 27.9 %, A 27.7 %, C 26.1 % and G 18.3 %, shows a unusual AT-skew with slightly negative. Further investigation revealed A. gracilis uses excess T over A in NADH dehydrogenase 5 (nd5), whereas the most of other bitterlings are biased toward to use A not T, implying there is likely to be unique strategy of adaptive evolution in A. gracilis. We also compared 13 PCGs of 30 bitterling mitogenomes and the results exhibit highly conservative. Phylogenetic trees constructed by 13 PCGs strongly support the monophyly of Acheilognathus and the paraphyly of Rhodeus and Tanakia. Current results will provide valuable information for follow-up research on conservation of species facing with serious population decline and can provide novel insights into the phylogenetic analysis and evolutionary biology research.
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Affiliation(s)
- Yuxuan Li
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Yi
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China.
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2
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Sun S, Xiao N, Sha Z. Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea). ZOOL SCR 2022. [DOI: 10.1111/zsc.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shao'e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
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3
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Feng JT, Guo YH, Yan CR, Ye YY, Li JJ, Guo BY, Lü ZM. Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda. Sci Rep 2020; 10:19277. [PMID: 33159159 PMCID: PMC7648102 DOI: 10.1038/s41598-020-76410-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 01/15/2023] Open
Abstract
To improve the systematics and taxonomy of Patellogastropoda within the evolution of gastropods, we determined the complete mitochondrial genome sequences of Lottia goshimai and Nipponacmea fuscoviridis in the family Lottiidae, which presented sizes of 18,192 bp and 18,720 bp, respectively. In addition to 37 common genes among metazoa, we observed duplication of the trnM gene in L. goshimai and the trnM and trnW genes in N. fuscoviridis. The highest A + T contents of the two species were found within protein-coding genes (59.95% and 54.55%), followed by rRNAs (56.50% and 52.44%) and tRNAs (56.42% and 52.41%). trnS1 and trnS2 could not form the canonical cloverleaf secondary structure due to the lack of a dihydrouracil arm in both species. The gene arrangements in all Patellogastropoda compared with those of ancestral gastropods showed different levels of gene rearrangement, including the shuffling, translocation and inversion of single genes or gene fragments. This kind of irregular rearrangement is particularly obvious in the Lottiidae family. The results of phylogenetic and gene rearrangement analyses showed that L. goshimai and Lottia digitalis clustered into one group, which in turn clustered with N. fuscoviridis in Patellogastropoda. This study demonstrates the significance of complete mitogenomes for phylogenetic analysis and enhances our understanding of the evolution of Patellogastropoda.
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Affiliation(s)
- Jian-Tong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ya-Hong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Cheng-Rui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Ji-Ji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhen-Ming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Hogan RI, Hopkins K, Wheeler AJ, Allcock AL, Yesson C. Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:764-777. [PMID: 31317811 DOI: 10.1080/24701394.2019.1634699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.
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Affiliation(s)
- Raissa I Hogan
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
| | - Andrew J Wheeler
- School of Biological, Earth and Environmental Sciences/iCRAG/ERI, University College Cork , Cork , Ireland
| | - A Louise Allcock
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
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Lee SY, Lee HJ, Kim YK. Comparative analysis of complete mitochondrial genomes with Cerithioidea and molecular phylogeny of the freshwater snail, Semisulcospira gottschei (Caenogastropoda, Cerithioidea). Int J Biol Macromol 2019; 135:1193-1201. [PMID: 31176862 DOI: 10.1016/j.ijbiomac.2019.06.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/19/2019] [Accepted: 06/05/2019] [Indexed: 11/26/2022]
Abstract
In this study, we determined the complete mitochondrial genome (mt genome) of Semisulcospira gottschei for the first time and then compared it with the mt genome of species belonging to Cerithioidea. The mt genome consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and non-coding region with a total length of 16,101 bp. The type of constitutive genes and the direction of the coding strand which appeared in the mt genome were the same as the ones observed in Cerithioidea except for the tRNA-Q and tRNA-R positions. The S. gottschei mt genome had a non-coding region with an AT-rich loop between tRNA-F and tRNA-C regions. In regard to molecular phylogeny, two types of analysis were performed to confirm the introgressive hybridization of S. gottschei and to identify the phylogenetic location among the species in Caenogastropoda. As a result, S. gottschei used in this study belonged to the same clade as other non-introgressed S. gottschei. As for the molecular phylogenic analysis of species belonging to Caenogastropoda, S. gottschei was found to be the closest to S. coreana taxonomically and to be included in Cerithioidea.
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Affiliation(s)
- Sang Yoon Lee
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Hwa Jin Lee
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Yi Kyung Kim
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung 25457, South Korea; Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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7
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Zhou Y, Cheng H, Zhang D, Wang C. The mitochondrial genome of a slit limpet Pseudorimula sp. (Vetigastropoda: Lepetodrilidae) from hydrothermal vent on the Southwest Indian Ridge. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Yadong Zhou
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, China
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, China
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Dongsheng Zhang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, China
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, China
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, China
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ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
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Guo Z, Jiang Z, Han L, Ding Y, Hou X. Characterisation of the complete mitochondrial genome of the black-footed abalone Haliotis iris. NEW ZEALAND JOURNAL OF ZOOLOGY 2018. [DOI: 10.1080/03014223.2018.1495655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zhansheng Guo
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Zhaoyang Jiang
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Leng Han
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Yi Ding
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Xuguang Hou
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
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