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Márquez EJ, Gómez-Chavarría DA, Alzate JF. Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes). PLoS One 2024; 19:e0300830. [PMID: 39190628 PMCID: PMC11349099 DOI: 10.1371/journal.pone.0300830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.
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Affiliation(s)
- Edna Judith Márquez
- Laboratorio de Biología Molecular y Celular, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | - Daniel Alfredo Gómez-Chavarría
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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Shen B, Shen A, Liu L, Tan Y, Li S, Tan Z. Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value. BMC PLANT BIOLOGY 2024; 24:255. [PMID: 38594641 PMCID: PMC11003039 DOI: 10.1186/s12870-024-04962-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published. RESULTS Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647 bp in length and consisted of 19 circular subgenomes ranging in size from 21,995 bp to 48,212 bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes. CONCLUSION In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.
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Affiliation(s)
- Baoming Shen
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Airong Shen
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Lina Liu
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Yun Tan
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Sainan Li
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China
| | - Zhuming Tan
- Institute of Forest and Grass Cultivation, Hunan Academy of Forestry, 658 Shaoshan South Road, Tianxin District, Changsha City, 410004, China.
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Yao Z, Long S, Wang C, Huang C, Zhang H, Jian L, Huang J, Guo Y, Dong Z, Wang Z. Population genetic characteristics of Hainan medaka with whole-genome resequencing. Front Genet 2022; 13:946006. [PMID: 36313474 PMCID: PMC9597887 DOI: 10.3389/fgene.2022.946006] [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] [Received: 05/17/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022] Open
Abstract
The DMY gene is deleted in all males of the Sanya population (SY-medaka) of the Hainan medaka, Oryzias curvinotus, as recently reported by us. However, due to limited knowledge regarding their population genetic background, it is difficult to explore the possible evolutionary pathway. Herein, we resequenced the whole genome of four populations, including SY-medaka. A total of 56 mitogenomes and 32,826,105 SNPs were identified. We found that the genetic differentiation is highest between SY-medaka and the other populations. The results of the population history of the O. curvinotus suggest that the SY-medaka has been in a bottleneck period recently. Further analysis shows that SY-medaka are the most strongly affected by environmental selection. Moreover, we screened some potential genomic regions, and the genes contained in these regions may explain the potential mechanism of the selection process of the SY-medaka. In conclusion, our study can provide new clues for the adaptation process of medaka in the new environment of Sanya.
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Affiliation(s)
- Zebin Yao
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Shuisheng Long
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chun Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chengqin Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Hairui Zhang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Liao Jian
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jingru Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yusong Guo
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- *Correspondence: Zhongduo Wang,
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Ogoh K, Futahashi R, Ohmiya Y. Intraspecific nucleotide polymorphisms in seven complete sequences of mitochondrial DNA of the luminous ostracod, Vargula hilgendorfii (Crustacea, Ostracoda). GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Sharma A, Siva C, Ali S, Sahoo PK, Nath R, Laskar M, Sarma D. The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications. Int J Biol Macromol 2020; 164:939-948. [DOI: 10.1016/j.ijbiomac.2020.07.142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/24/2023]
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Schroeter JC, Maloy AP, Rees CB, Bartron ML. Fish mitochondrial genome sequencing: expanding genetic resources to support species detection and biodiversity monitoring using environmental DNA. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01111-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing. G3-GENES GENOMES GENETICS 2019; 9:217-228. [PMID: 30482798 PMCID: PMC6325896 DOI: 10.1534/g3.118.200779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The genome-wide data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually an origin of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on chromosomal genetic diversity.
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Marques JP, Sotelo G, Larsson T, Johannesson K, Panova M, Faria R. Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis. Mar Genomics 2016; 32:41-47. [PMID: 27867038 DOI: 10.1016/j.margen.2016.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/16/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
The flat periwinkles, Littorina fabalis and L. obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L. saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L. saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L. fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on dN/dS ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.
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Affiliation(s)
- João P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Graciela Sotelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Tomas Larsson
- University of Gothenburg, Department of Marine Sciences, Box 460, SE -405 30 Gothenburg, Sweden.
| | - Kerstin Johannesson
- University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden.
| | - Marina Panova
- University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden.
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; IBE, Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Pompeu Fabra University, Doctor Aiguader 88, 08003 Barcelona, Spain.
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9
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Tsuboko S, Kimura T, Shinya M, Suehiro Y, Okuyama T, Shimada A, Takeda H, Naruse K, Kubo T, Takeuchi H. Genetic control of startle behavior in medaka fish. PLoS One 2014; 9:e112527. [PMID: 25393539 PMCID: PMC4231031 DOI: 10.1371/journal.pone.0112527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/06/2014] [Indexed: 11/24/2022] Open
Abstract
Genetic polymorphisms are thought to generate intraspecific behavioral diversities, both within and among populations. The mechanisms underlying genetic control of behavioral properties, however, remain unclear in wild-type vertebrates, including humans. To explore this issue, we used diverse inbred strains of medaka fish (Oryzias latipes) established from the same and different local populations. Medaka exhibit a startle response to a visual stimulus (extinction of illumination) by rapidly bending their bodies (C-start) 20-ms after the stimulus presentation. We measured the rates of the response to repeated stimuli (1-s interval, 40 times) among four inbred strains, HNI-I, HNI-II, HO5, and Hd-rR-II1, and quantified two properties of the startle response: sensitivity (response rate to the first stimulus) and attenuation of the response probability with repeated stimulus presentation. Among the four strains, the greatest differences in these properties were detected between HNI-II and Hd-rR-II1. HNI-II exhibited high sensitivity (approximately 80%) and no attenuation, while Hd-rR-II1 exhibited low sensitivity (approximately 50%) and almost complete attenuation after only five stimulus presentations. Our findings suggested behavioral diversity of the startle response within a local population as well as among different populations. Linkage analysis with F2 progeny between HNI-II and Hd-rR-II1 detected quantitative trait loci (QTL) highly related to attenuation, but not to sensitivity, with a maximum logarithm of odds score of 11.82 on linkage group 16. The three genotypes (homozygous for HNI-II and Hd-rR-II1 alleles, and heterozygous) at the marker nearest the QTL correlated with attenuation. Our findings are the first to suggest that a single genomic region might be sufficient to generate individual differences in startle behavior between wild-type strains. Further identification of genetic polymorphisms that define the behavioral trait will contribute to our understanding of the neural mechanisms underlying behavioral diversity, allowing us to investigate the adaptive significance of intraspecific behavioral polymorphisms of the startle response.
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Affiliation(s)
- Satomi Tsuboko
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tetsuaki Kimura
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
- National Institute for Basic Biology Center of the Interuniversity Bio-Backup Project, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Minori Shinya
- Model Fish Genomics Resource, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biology, Keio University, Yokohama, Kanagawa, Japan
| | - Yuji Suehiro
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Shinjuku, Tokyo, Japan
| | - Teruhiro Okuyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
- National Institute for Basic Biology Center of the Interuniversity Bio-Backup Project, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hideaki Takeuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail:
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Watanabe-Asaka T, Sekiya Y, Wada H, Yasuda T, Okubo I, Oda S, Mitani H. Regular heartbeat rhythm at the heartbeat initiation stage is essential for normal cardiogenesis at low temperature. BMC DEVELOPMENTAL BIOLOGY 2014; 14:12. [PMID: 24564206 PMCID: PMC3936829 DOI: 10.1186/1471-213x-14-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/14/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND The development of blood flow in the heart is crucial for heart function and embryonic survival. Recent studies have revealed the importance of the extracellular matrix and the mechanical stress applied to the valve cushion that controls blood flow to the formation of the cardiac valve during embryogenesis. However, the events that trigger such valve formation and mechanical stress, and their temperature dependence have not been explained completely. Medaka (Oryzias latipes) inhabits a wide range of East Asia and adapts to a wide range of climates. We used medaka embryos from different genomic backgrounds and analyzed heartbeat characteristics including back-and-forth blood flow and bradyarrhythmia in embryos incubated at low temperature. We also used high-speed imaging analysis to examine the heartbeat of these animals after transient exposure to low temperature. RESULTS Embryos of the Hd-rR medaka strain exhibited back-and-forth blood flow in the heart (blood regurgitation) after incubation at 15 °C. This regurgitation was induced by exposure to low temperature around the heartbeat initiation period and was related to abnormalities in the maintenance or pattern of contraction of the atrium or the atrioventricular canal. The Odate strain from the northern Japanese group exhibited normal blood flow after incubation at 15 °C. High-speed time-lapse analysis of the heartbeat revealed that bradyarrhythmia occurred only in Hd-rR embryos incubated at 15 °C. The coefficient of contraction, defined as the quotient of the length of the atrium at systole divided by its length at diastole, was not affected in either strain. The average heart rate after removing the effect of arrhythmia did not differ significantly between the two strains, suggesting that the mechanical stress of individual myocardial contractions and the total mechanical stress could be equivalent, regardless of the presence of arrhythmia or the heart rate. Test-cross experiments suggested that this circulation phenotype was caused by a single major genomic locus. CONCLUSIONS These results suggest that cardiogenesis at low temperature requires a constant heartbeat. Abnormal contraction rhythms at the stage of heartbeat initiation may cause regurgitation at later stages. From the evolutionary viewpoint, strains that exhibit normal cardiogenesis during development at low temperature inhabit northern environments.
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Affiliation(s)
| | | | | | | | | | | | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwa-no-ha, Kashiwa, Chiba 277-8562, Japan.
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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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Terencio ML, Schneider CH, Gross MC, Feldberg E, Porto JIR. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish. ACTA ACUST UNITED AC 2012; 24:74-82. [PMID: 22954310 DOI: 10.3109/19401736.2012.717934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.
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Affiliation(s)
- Maria Leandra Terencio
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Pesquisas em Biologia Aquática, Av. André Araújo, 2936, Petrópolis, 69011-970 Manaus, AM, Brazil.
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Sasano Y, Yoshimura A, Fukamachi S. Reassessment of the function of somatolactin alpha in lipid metabolism using medaka mutant and transgenic strains. BMC Genet 2012; 13:64. [PMID: 22827540 PMCID: PMC3467165 DOI: 10.1186/1471-2156-13-64] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 07/09/2012] [Indexed: 01/12/2023] Open
Abstract
Background Somatolactin alpha (SLa) is a fish-specific peptide hormone secreted from the pituitary. In medaka, SLa functions to darken the skin color and lack of SLa makes it pale. Transcription of SLa is enhanced or suppressed when fish are kept in dark or bright conditions, respectively, indicating SLa’s important role in background acclimation of the skin color. Bizarrely, however, the lack of SLa seems to cause the additional defect of increased triglycerides in organs, which could not be rescued (decreased) by its overexpression. Results To assess this enigmatic result, we investigated genetic (the SLa, Slc45a2, r, and Y genes) and nongenetic (age, fasting, water temperature, and background color) effects on hepatic triglycerides. These experiments found that percent hepatic triglycerides quickly change in response to external/internal environments. Effects of SLa seemed to be much less obvious, although it may increase the proportion of hepatic triglycerides at least during certain breeding conditions or under certain genetic backgrounds. Conclusions The present results do not exclude the possibility that SLa takes part in lipid metabolism or other physiological processes. However, we suggest that skin-color regulation is the only definite role of SLa so far demonstrated in this species.
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Affiliation(s)
- Yuko Sasano
- Laboratory of Evolutionary Genetics, Department of Chemical and Biological Sciences, Japan Women's University, Mejirodai 2-8-1, Bunkyo-ku, Tokyo, 112-8681, Japan
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Hwang DS, Kim BM, Au DWT, Lee JS. Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae). ACTA ACUST UNITED AC 2012; 23:308-9. [PMID: 22708854 DOI: 10.3109/19401736.2012.683181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.
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Affiliation(s)
- Dae-Sik Hwang
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea
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15
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Panarari-Antunes RS, Prioli AJ, Prioli SMAP, Gomes VN, Júlio HF, Agostinho CS, Silva Filho JP, Boni TA, Prioli LM. Genetic divergence among invasive and native populations of Plagioscion squamosissimus (Perciformes, Sciaenidae) in Neotropical regions. JOURNAL OF FISH BIOLOGY 2012; 80:2434-2447. [PMID: 22650426 DOI: 10.1111/j.1095-8649.2012.03290.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The genetic divergence among invasive and native populations of Plagioscion squamosissimus from four Neotropical hydrographic basins was assessed using the hypervariable domain of the mitochondrial DNA (mtDNA) control region. Plagioscion squamosissimus is native to the neighbouring hydrographic basins of the Parnaíba and Amazon Rivers, and the latter includes the Araguaia-Tocantins drainage, but it is invasive in other basins due to introductions. The mtDNA nucleotide polymorphism supported the hypothesis that the Amazon and Parnaíba populations constitute the same species and are separated into two independent evolutionary lineages. Absence of nucleotide polymorphism was observed within and among P. squamosissimus populations invasive to the uppper and middle Paraná River basins. Nucleotide divergence was null or low comparing the Paraná invasive populations with the populations native to the Parnaíba River basin, whereas it was significantly high compared to Tocantins populations. These results ascertain that P. squamosissimus populations invasive to the upper Paraná River basin and to the middle Paraná River basin downstream of the Itaipu dam are derived from the Parnaíba River basin. The genetic data presented are potentially useful to assist further studies on P. squamosissimus taxonomic and geographic distribution, development of ecological guidelines for managing populations invasive to the upper Paraná River basin and for preservation of native fish diversity.
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Affiliation(s)
- R S Panarari-Antunes
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, PR, Brasil
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16
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KATSUMURA TAKAFUMI, ODA SHOJI, TSUKAMOTO KENTARO, SEKIYA YOSHIO, YAMASHITA TOSHIKAZU, ASO MASANORI, HATA MASAYOSHI, NONAKA MASARU, MANO SHUHEI, ISHIDA HAJIME, MITANI HIROSHI, KAWAMURA SHOJI, OOTA HIROKI. A population genetic study on the relationship between medaka fish and the spread of wet-rice cultivation across the Japanese archipelago. ANTHROPOL SCI 2012. [DOI: 10.1537/ase.110525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- TAKAFUMI KATSUMURA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - SHOJI ODA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - KENTARO TSUKAMOTO
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoaki
| | - YOSHIO SEKIYA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - TOSHIKAZU YAMASHITA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - MASANORI ASO
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - MASAYOSHI HATA
- International Coastal Research Center, Ocean Research Institute, University of Tokyo, Otsuchi
| | - MASARU NONAKA
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo
| | - SHUHEI MANO
- Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tachikawa
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, University of the Ryukyus Faculty of Medicine, Nishihara
| | - HIROSHI MITANI
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - SHOJI KAWAMURA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa
| | - HIROKI OOTA
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara
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17
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Munwes I, Geffen E, Friedmann A, Tikochinski Y, Gafny S. Variation in repeat length and heteroplasmy of the mitochondrial DNA control region along a core-edge gradient in the eastern spadefoot toad (Pelobates syriacus). Mol Ecol 2011; 20:2878-87. [PMID: 21645158 DOI: 10.1111/j.1365-294x.2011.05134.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peripheral populations are those situated at the distribution margins of a species and are often subjected to more extreme abiotic and biotic conditions than those at the core. Here, we hypothesized that shorter repeat length and fewer heteroplasmic mitochondrial DNA (mtDNA) copies, which are associated with more efficient mitochondrial function, may be related to improved survival under extreme environmental conditions. We sampled eastern spadefoot toads (mostly as tadpoles) from 43 rain pools distributed along a 300-km gradient from core to edge of the species' distribution. We show that mean pool tandem repeat length and heteroplasmy increase from edge to core, even after controlling for body size. We evaluate several alternative hypotheses and propose the Fisher hypothesis as the most likely explanation. However, additional sequential sampling and experimental studies are required to determine whether selection under extreme conditions, or alternative mechanisms, could account for the gradient in heteroplasmy and repeat length in the mtDNA control region.
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Affiliation(s)
- Inbar Munwes
- School of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel
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