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Wang Y, Sha H, Li X, Zhou T, Luo X, Zou G, Chai Y, Liang H. Microsatellite Characteristics of Silver Carp ( Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations. Genes (Basel) 2022; 13:genes13071267. [PMID: 35886050 PMCID: PMC9320178 DOI: 10.3390/genes13071267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled H. molitrix genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the H. molitrix genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on H. molitrix.
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Affiliation(s)
- Yajun Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, China;
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Hang Sha
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Xiaohui Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Tong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Xiangzhong Luo
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Yi Chai
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, China;
- Correspondence: (Y.C.); (H.L.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
- Correspondence: (Y.C.); (H.L.)
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The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
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Cheng H, Zhou R. Decoding genome recombination and sex reversal. Trends Endocrinol Metab 2022; 33:175-185. [PMID: 35000844 DOI: 10.1016/j.tem.2021.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022]
Abstract
Over the past 440 years since the discovery of the medicinal value of swamp eels, much progress has been made in the study of their biology. The fish is emerging as an important model animal in sexual development, in addition to economic and pharmaceutical implications. Tracing genomic history that shapes speciation of the fish has led to discovery of the whole genome-wide chromosome fission/fusion events. Natural intersex differentiation is a compelling feature for sexual development research. Notably, identification of progenitors of germline stem cells that have bipotential to differentiate into either male or female germline stem cells provides new insight into sex reversal. Here, we review these advances that have propelled the field forwards and present unsolved issues that will guide future investigations to finally elucidate vertebrate sexual development using the new model.
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Affiliation(s)
- Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
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Liu T, Yi TL, Yang DQ, Tao YX. Regulation of melanocortin-5 receptor pharmacology by two isoforms of MRAP2 in ricefield eel (Monopterus albus). Gen Comp Endocrinol 2021; 314:113928. [PMID: 34653433 DOI: 10.1016/j.ygcen.2021.113928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 11/18/2022]
Abstract
The melanocortin-5 receptor (MC5R) has been implicated in the regulation of exocrine gland secretion, immune regulation, and muscle fatty acid oxidation in mammals. Melanocortin-2 receptor accessory protein 2 (MRAP2) can modulate trafficking, ligand binding, and signaling of melanocortin receptors. To explore potential interaction between ricefield eel (Monopterus albus) MC5R and MRAP2s (maMC5R, maMRAP2X1, and maMRAP2X2), herein we studied the pharmacological characteristics of maMC5R and its modulation by maMRAP2s expressed in the human embryonic kidney cells. Three agonists, α-melanocyte-stimulating hormone (α-MSH), ACTH (1-24), and [Nle4, D-Phe7]-α-MSH, could bind to maMC5R and induce intracellular cAMP production dose-dependently. Compared with human MC5R (hMC5R), maMC5R displayed decreased maximal binding but higher binding affinity to α-MSH or ACTH (1-24). When stimulated with α-MSH or ACTH (1-24), maMC5R showed significantly lower EC50 and maximal response than hMC5R. Two maMRAP2s had no effect on cell surface expression of maMC5R, whereas they significantly increased maximal binding. Only maMRAP2X2 significantly decreased the binding affinity of ACTH (1-24). Both maMRAP2X1 and maMRAP2X2 significantly reduced maMC5R efficacy but did not affect ligand sensitivity. The availability of maMC5R pharmacological characteristics and modulation by maMRAP2s will assist the investigation of its roles in regulating diverse physiological processes in ricefield eel.
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Affiliation(s)
- Ting Liu
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States
| | - Ti-Lin Yi
- School of Animal Science, Yangtze University, Jingzhou 434020, Hubei, China
| | - Dai-Qin Yang
- School of Animal Science, Yangtze University, Jingzhou 434020, Hubei, China
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States.
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Jackson T, Ishengoma E, Rhode C. Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:560-575. [PMID: 34241713 DOI: 10.1007/s10126-021-10046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.
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Affiliation(s)
- T Jackson
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - E Ishengoma
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
- Department of Biological Sciences, Mkwawa University College of Education, University of Dar Es Salaam, P.O. Box 2329, Dar es Salaam, Tanzania
| | - C Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
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Tian HF, Hu QM, Li Z. Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus). Sci Prog 2021; 104:368504211035597. [PMID: 34375541 PMCID: PMC10358632 DOI: 10.1177/00368504211035597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. METHODS The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. RESULTS A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. CONCLUSIONS The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes (FIS = 0.155) in one breeding population provide baseline information for future breeding program.
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Affiliation(s)
- Hai-feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Qiao-mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
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7
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Yeesin P, Buasriyot P, Ditcharoen S, Chaiyasan P, Suwannapoom C, Juntaree S, Jantarat S, Talumphai S, Cioffi MDB, Liehr T, Tanomtong A, Supiwong W. Comparative study of four Mystus species (Bagridae, Siluriformes) from Thailand: insights into their karyotypic diversity. COMPARATIVE CYTOGENETICS 2021; 15:119-136. [PMID: 33959235 PMCID: PMC8093182 DOI: 10.3897/compcytogen.v15i2.60649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Karyotypes of four catfishes of the genus Mystus Scopoli, 1777 (family Bagridae), M. atrifasciatus Fowler, 1937, M. mysticetus Roberts, 1992, M. singaringan (Bleeker, 1846) and M. wolffii (Bleeker, 1851), were analysed by conventional and Ag-NOR banding as well as fluorescence in situ hybridization (FISH) techniques. Microsatellite d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeat probes were applied in FISH. The obtained data revealed that the four studied species have different chromosome complements. The diploid chromosome numbers (2n) and the fundamental numbers (NF) range between 52 and 102, 54 and 104, 56 and 98, or 58 and 108 in M. mysticetus, M. atrifasciatus, M. singaringan or M. wolffii, respectively. Karyotype formulae of M. mysticetus, M. atrifasciatus, M. singaringan and M. wolffii are 24m+26sm+4a, 26m+24sm+2a, 24m+18sm+14a and 30m+22sm+6a, respectively. A single pair of NORs was identified adjacent to the telomeres of the short arm of chromosome pairs 3 (metacentric) in M. atrifasciatus, 20 (submetacentric) in M. mysticetus, 15 (submetacentric) in M. singaringan, and 5 (metacentric) in M. wolffii. The d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeats were abundantly distributed in species-specific patterns. Overall, we present a comparison of cytogenetic and molecular cytogenetic patterns of four species from genus Mystus providing insights into their karyotype diversity in the genus.
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Affiliation(s)
- Pun Yeesin
- Department of Technology and Industries, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Muang, Pattani 94000, Thailand
| | - Phichaya Buasriyot
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Sukhonthip Ditcharoen
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Patcharaporn Chaiyasan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, Thailand
| | - Sippakorn Juntaree
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Mueng, Pattani 94000, Thailand
| | - Sucheela Talumphai
- Major Biology, Department of Science and Technology, Faculty of Liberal Arts and Science, Roi Et Rajabhat University, Roi Et 45120, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747, Jena, Germany
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Weerayuth Supiwong
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
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Genomic approach for conservation and the sustainable management of endangered species of the Amazon. PLoS One 2021; 16:e0240002. [PMID: 33626057 PMCID: PMC7904187 DOI: 10.1371/journal.pone.0240002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas’ whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.
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9
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Ditcharoen S, Sassi FDMC, Bertollo LAC, Molina WF, Liehr T, Saenjundaeng P, Tanomtong A, Supiwong W, Suwannapoom C, Cioffi MDB. Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species. Genet Mol Biol 2020; 43:e20200091. [PMID: 33156890 PMCID: PMC7654372 DOI: 10.1590/1678-4685-gmb-2020-0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Francisco de Menezes Cavalcante Sassi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Luiz Antonio Carlos Bertollo
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do NorteUniversidade Federal do Rio Grande do NorteDepartamento de Biologia Celular e GenéticaNatalRNBrazilUniversidade Federal do Rio Grande do Norte (UFRN), Centro de
Biociências, Departamento de Biologia Celular e Genética, Natal, RN,
Brazil.
| | - Thomas Liehr
- University Hospital JenaUniversity Hospital JenaInstitute of Human GeneticsJenaGermanyUniversity Hospital Jena, Institute of Human Genetics, Jena,
Germany.
| | - Pasakorn Saenjundaeng
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Alongklod Tanomtong
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Weerayuth Supiwong
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Chatmongkon Suwannapoom
- University of PhayaoUniversity of PhayaoDepartment of FisherySchool of Agriculture and Natural ResourcesMuang PhayaoThailandUniversity of Phayao, School of Agriculture and Natural
Resources, Department of Fishery, Muang Phayao, Thailand.
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
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10
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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11
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Suntronpong A, Singchat W, Kruasuwan W, Prakhongcheep O, Sillapaprayoon S, Muangmai N, Somyong S, Indananda C, Kraichak E, Peyachoknagul S, Srikulnath K. Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements. Genomics 2020; 112:3097-3107. [PMID: 32470643 DOI: 10.1016/j.ygeno.2020.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/21/2020] [Accepted: 05/24/2020] [Indexed: 01/04/2023]
Abstract
Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species.
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Affiliation(s)
- Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worarat Kruasuwan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ornjira Prakhongcheep
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand.
| | - Suthasinee Somyong
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand.
| | - Chantra Indananda
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ekaphan Kraichak
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand; Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan.
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12
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Chen X, Fang S, Wei L, Zhong Q. Systematic evaluation of the gut microbiome of swamp eel ( Monopterus albus) by 16S rRNA gene sequencing. PeerJ 2019; 7:e8176. [PMID: 31875148 PMCID: PMC6927349 DOI: 10.7717/peerj.8176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
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Affiliation(s)
- Xuan Chen
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiwang Zhong
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
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13
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García E, Cross I, Portela-Bens S, Rodríguez ME, García-Angulo A, Molina B, Cuadrado A, Liehr T, Rebordinos L. Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome. Sci Rep 2019; 9:17146. [PMID: 31748593 PMCID: PMC6868151 DOI: 10.1038/s41598-019-53673-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/05/2019] [Indexed: 01/07/2023] Open
Abstract
Repetitive sequences play an essential role in the structural and functional evolution of the genome, particularly in the sexual chromosomes. The Senegalese sole (Solea senegalensis) is a valuable flatfish in aquaculture albeit few studies have addressed the mapping and characterization of repetitive DNA families. Here we analyzed the Simple Sequence Repeats (SSRs) and Transposable elements (TEs) content from fifty-seven BAC clones (spanning 7.9 Mb) of this species, located in chromosomes by multiple fluorescence in situ hybridization (m-BAC-FISH) technique. The SSR analysis revealed an average density of 675.1 loci per Mb and a high abundance (59.69%) of dinucleotide coverage was observed, being ‘AC’ the most abundant. An SSR-FISH analysis using eleven probes was also carried out and seven of the 11 probes yielded positive signals. ‘AC’ probes were present as large clusters in almost all chromosomes, supporting the bioinformatic analysis. Regarding TEs, DNA transposons (Class II) were the most abundant. In Class I, LINE elements were the most abundant and the hAT family was the most represented in Class II. Rex/Babar subfamily, observed in two BAC clones mapping to chromosome pair 1, showed the longest match. This chromosome pair has been recently reported as a putative sexual proto-chromosome in this species, highlighting the possible role of the Rex element in the evolution of this chromosome. In the Rex1 phylogenetic tree, the Senegalese sole Rex1 retrotransposon could be associated with one of the four major ancient lineages in fish genomes, in which it is included O. latipes.
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Affiliation(s)
- Emilio García
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María E Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Aglaya García-Angulo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Belén Molina
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Angeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcala, 28871, Alcalá de Henares (Madrid), Spain
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain.
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14
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Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol Evol 2019; 11:3291-3308. [PMID: 31687752 PMCID: PMC7145574 DOI: 10.1093/gbe/evz240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 12/22/2022] Open
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
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Affiliation(s)
- Srinidhi Varadharajan
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Pasi Rastas
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Finland
| | - Michael Matschiner
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Department of Paleontology and Museum, University of Zurich, Switzerland
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Baocheng Guo
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, China
| | - Alexander J Nederbragt
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Norway
| | - Kjetill S Jakobsen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
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15
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Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol Evol 2019. [PMID: 31687752 DOI: 10.1101/741751] [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] [Indexed: 05/13/2023] Open
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
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Affiliation(s)
- Srinidhi Varadharajan
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Pasi Rastas
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Finland
| | - Michael Matschiner
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Department of Paleontology and Museum, University of Zurich, Switzerland
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Baocheng Guo
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, China
| | - Alexander J Nederbragt
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Norway
| | - Kjetill S Jakobsen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
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16
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Genetic diversity and population structure of the threatened chocolate mahseer (Neolissochilus hexagonolepis McClelland 1839) based on SSR markers: implications for conservation management in Northeast India. Mol Biol Rep 2019; 46:5237-5249. [DOI: 10.1007/s11033-019-04981-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/12/2019] [Indexed: 10/26/2022]
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17
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Chen F, Fengling Lai, Luo M, Han YS, Cheng H, Zhou R. The genome-wide landscape of small insertion and deletion mutations in Monopterus albus. J Genet Genomics 2019; 46:75-86. [PMID: 30867123 DOI: 10.1016/j.jgg.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/21/2018] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Insertion and deletion (indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ∼1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to non-indel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.
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Affiliation(s)
- Feng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Majing Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, "National Taiwan University", Taipei, 10617, Taiwan, China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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18
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Supiwong W, Pinthong K, Seetapan K, Saenjundaeng P, Bertollo LAC, de Oliveira EA, Yano CF, Liehr T, Phimphan S, Tanomtong A, B Cioffi M. Karyotype diversity and evolutionary trends in the Asian swamp eel Monopterus albus (Synbranchiformes, Synbranchidae): a case of chromosomal speciation? BMC Evol Biol 2019; 19:73. [PMID: 30849933 PMCID: PMC6408769 DOI: 10.1186/s12862-019-1393-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Synbranchidae or swamp eels are fishes belonging to the order Synbranchiformes that occur in both freshwater and occasionally in brackish. They are worldwide distributed in tropical and subtropical rivers of four different continents. A large degree of chromosomal variation has been found in this family, mainly through the use of conventional cytogenetic investigations. Inside this group, a still almost unexplored species under the cytogenetic point of view is the Asian swamp eel Monopterus albus, a widely distributed species throughout Asia. Here, we tested the hypothesis of chromosomal speciation, where a case of sympatric speciation may occur as the primary consequence of chromosomal rearrangements. We performed a comparative chromosomal analysis of M. albus from 22 different localities in Thailand, using distinct staining methods (C-banding, Ag-NO3, and Chromomycin A3), and FISH with repetitive DNA probes (5S rDNA, 18S rDNA, Rex1 element and microsatellite repeats). RESULTS This approach evidenced two contrasting karyotypes (named karyomorphs A and B) that varied concerning their 2n and repetitive DNAs distribution, where chromosomal fusions and pericentric inversions were involved in such differentiation. While the karyomorph A has 2n = 24 chromosomes, the karyomorph B has only 2n = 18, both with NF = 24. In addition, karyomorph A contains only acrocentric chromosomes, while karyomorph B contains three unique metacentric pairs. These features highlight that M. albus has already gone through a significant genomic divergence, and may include at least two cryptic species. CONCLUSIONS This marked chromosomal differentiation, likely linked to the lifestyle of these fishes, point to the occurrence of a chromosomal speciation scenario, in which fusions and inversions had a prominent role. This highlights the biodiversity of M. albus and justifies its taxonomic revision, since this nominal species may constitute a species complex.
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Affiliation(s)
- Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Surin, 32000 Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao, 56000 Thailand
| | - Pasakorn Saenjundaeng
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Sumalee Phimphan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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