1
|
Migration of repetitive DNAs during evolution of the permanent translocation heterozygosity in the oyster plant (Tradescantia section Rhoeo). Chromosoma 2022; 131:163-173. [PMID: 35896680 PMCID: PMC9470650 DOI: 10.1007/s00412-022-00776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture.
Collapse
|
2
|
Negi A, Singh K, Jaiswal S, Kokkat JG, Angadi UB, Iquebal MA, Umadevi P, Rai A, Kumar D. Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:846937. [PMID: 35712605 PMCID: PMC9197322 DOI: 10.3389/fpls.2022.846937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Black pepper (Piper nigrum), the "King of Spices," is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ~70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphic markers. The major limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.
Collapse
Affiliation(s)
- Ankita Negi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Kalpana Singh
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Johnson George Kokkat
- Indian Council of Agricultural Research-Indian Institute of Spices Research, Kozhikode, India
| | - Ulavappa B. Angadi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - P. Umadevi
- Indian Council of Agricultural Research-Indian Institute of Spices Research, Kozhikode, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, India
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendragarh, India
| |
Collapse
|
3
|
Mandal K, Dutta S, Upadhyay A, Panda A, Tripathy S. Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes. Front Microbiol 2022; 13:806398. [PMID: 35369471 PMCID: PMC8967354 DOI: 10.3389/fmicb.2022.806398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.
Collapse
Affiliation(s)
- Kajal Mandal
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subhajeet Dutta
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Upadhyay
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Panda
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, United States
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
4
|
Duhan N, Kaundal R. LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement. Int J Mol Sci 2021; 22:ijms222111350. [PMID: 34768782 PMCID: PMC8583334 DOI: 10.3390/ijms222111350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.
Collapse
Affiliation(s)
- Naveen Duhan
- Department of Plants, Soils and Climate, CAAS, Utah State University, Logan, UT 84321, USA;
- Center for Integrated BioSystems (CIB), CAAS, Utah State University, Logan, UT 84321, USA
| | - Rakesh Kaundal
- Department of Plants, Soils and Climate, CAAS, Utah State University, Logan, UT 84321, USA;
- Center for Integrated BioSystems (CIB), CAAS, Utah State University, Logan, UT 84321, USA
- Department of Computer Science, CoS, Utah State University, Logan, UT 84321, USA
- Correspondence: ; Tel.: +1-435-797-4117; Fax: +1-435-797-2766
| |
Collapse
|
5
|
Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Mol Ecol 2021; 30:2710-2723. [PMID: 33955064 DOI: 10.1111/mec.15936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023]
Abstract
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
Collapse
Affiliation(s)
- Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Alexander Suh
- School of Biological Sciences - Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
6
|
Song X, Yang T, Zhang X, Yuan Y, Yan X, Wei Y, Zhang J, Zhou C. Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level. Front Genet 2021; 12:622724. [PMID: 33719337 PMCID: PMC7953163 DOI: 10.3389/fgene.2021.622724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.
Collapse
Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Xinyi Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Ying Yuan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yi Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Jun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| |
Collapse
|
7
|
Bueno GDP, Gatto KP, Gazolla CB, Leivas PT, Struett MM, Moura M, Bruschi DP. Cytogenetic characterization and mapping of the repetitive DNAs in Cycloramphus bolitoglossus (Werner, 1897): More clues for the chromosome evolution in the genus Cycloramphus (Anura, Cycloramphidae). PLoS One 2021; 16:e0245128. [PMID: 33439901 PMCID: PMC7806164 DOI: 10.1371/journal.pone.0245128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/22/2020] [Indexed: 01/13/2023] Open
Abstract
Cycloramphus bolitoglossus (Werner, 1897) is a rare species with a low population density in the Serra do Mar region of Paraná and Santa Catarina, in southern Brazil. Currently, it has been assigned to the Near Threatened (NT) category in the Brazilian List of Endangered Animal Species. Here, we described the karyotype of this species for the first time and investigated the patterns of some repetitive DNA classes in the chromosomes using molecular cytogenetic approaches. We isolated, sequenced and mapped the 5S rDNA and the satellite DNA PcP190 of C. bolitoglossus, as well as mapped the telomeric sequences and seven microsatellites motifies [(GA)15, (CA)15, (GACA)4, (GATA)8, (CAG)10, (CGC)10, and (GAA)]10. Cycloramphus bolitoglossus has 2n = 26 chromosomes and a fundamental number (FN) equal to 52, with a highly conserved karyotype compared to other genus members. Comparative cytogenetic under the phylogenetic context of genus allowed evolutionary interpretations of the morphological changes in the homologs of pairs 1, 3, and 6 along with the evolutionary history of Cycloramphus. Two subtypes of 5S rDNA type II were isolated in C. bolitoglossus genome, and several comparative analysis suggests mixed effects of concerted and birth-and-death evolution acting in this repetitive DNA. The 5S rDNA II subtype "a" and "b" was mapped on chromosome 1. However, their different position along chromosome 1 provide an excellent chromosome marker for future studies. PcP190 satellite DNA, already reported for species of the families Hylidae, Hylodidae, Leptodactylidae, and Odontophrynidae, is scattered throughout the C. bolitoglossus genome, and even non-heterochromatic regions showed hybridization signals using the PcP190 probe. Molecular analysis suggests that PcP190 satellite DNA exhibit a high-level of homogenization of this sequence in the genome of C. bolitoglossus. The PcP190 satDNA from C. bolitoglossus represents a novel sequence group, compared to other anurans, based on its hypervariable region. Overall, the present data on repetitive DNA sequences showed pseudogenization evidence and corroborated the hypothesis of the emergence of satDNA from rDNA 5S clusters. These two arguments that reinforced the importance of the birth-and-death evolutionary model to explain 5S rDNA patterns found in anuran genomes.
Collapse
Affiliation(s)
- Gislayne de Paula Bueno
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Kaleb Pretto Gatto
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, (UNESP), Rio Claro, São Paulo, Brazil
| | - Camilla Borges Gazolla
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Peterson T. Leivas
- Curso de Ciências Biológicas, Universidade Positivo (UP), Curitiba, Paraná, Brazil
| | - Michelle M. Struett
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Maurício Moura
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| |
Collapse
|
8
|
Song X, Yang T, Yan X, Zheng F, Xu X, Zhou C. Comparison of microsatellite distribution patterns in twenty-nine beetle genomes. Gene 2020; 757:144919. [PMID: 32603771 DOI: 10.1016/j.gene.2020.144919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 01/20/2023]
Abstract
Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.
Collapse
Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Fake Zheng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
| |
Collapse
|
9
|
Ernetti JR, Gazolla CB, Recco-Pimentel SM, Luca EM, Bruschi DP. Non-random distribution of microsatellite motifs and (TTAGGG)n repeats in the monkey frog Pithecopus rusticus (Anura, Phyllomedusidae) karyotype. Genet Mol Biol 2020; 42:e20190151. [PMID: 31968045 PMCID: PMC7198017 DOI: 10.1590/1678-4685-gmb-2019-0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
The monkey frog, Pithecopus rusticus (Anura, Phyllomedusidae) is endemic to the grasslands of the Araucarias Plateau, southern Brazil. This species is known only from a small population found at the type locality. Here, we analyzed for the first time the chromosomal organization of the repetitive sequences, including seven microsatellite repeats and telomeric sequences (TTAGGG)n in the karyotype of the species by Fluorescence in situ Hybridization. The dinucleotide motifs had a pattern of distribution clearly distinct from those of the tri- and tetranucleotides. The dinucleotide motifs are abundant and widely distributed in the chromosomes, located primarily in the subterminal regions. The tri- and tetranucleotides, by contrast, tend to be clustered, with signals being observed together in the secondary constriction of the homologs of pair 9, which are associated with the nucleolus organizer region. As expected, the (TTAGGG)n probe was hybridized in all the telomeres, with hybridization signals being detected in the interstitial regions of some chromosome pairs. We demonstrated the variation in the abundance and distribution of the different microsatellite motifs and revealed their non-random distribution in the karyotype of P. rusticus. These data contribute to understand the role of repetitive sequences in the karyotype diversification and evolution of this taxon.
Collapse
Affiliation(s)
- Julia R Ernetti
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
| | - Camilla B Gazolla
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Shirlei M Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Elaine M Luca
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
- Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Campus de Palmeira das Missões, Palmeira das Missões, RS, Brazil
| | - Daniel P Bruschi
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Purwoko D, Cartealy IC, Tajuddin T, Dinarti D, Sudarsono S. SSR identification and marker development for sago palm based on NGS genome data. BREEDING SCIENCE 2019; 69:1-10. [PMID: 31086478 PMCID: PMC6507712 DOI: 10.1270/jsbbs.18061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Sago palm (Metroxylon sagu Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. De novo assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.
Collapse
Affiliation(s)
- Devit Purwoko
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Imam Civi Cartealy
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Teuku Tajuddin
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Diny Dinarti
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
| | - Sudarsono Sudarsono
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
| |
Collapse
|
13
|
Jasrotia RS, Yadav PK, Iquebal MA, Bhatt SB, Arora V, Angadi UB, Tomar RS, Jaiswal S, Rai A, Kumar D. VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5506750. [PMID: 31147679 PMCID: PMC6542692 DOI: 10.1093/database/baz055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 11/25/2022]
Abstract
Genus Vigna represented by more than 100 species is a source of nutritious edible seeds and sprouts that are rich sources of protein and dietary supplements. It is further valuable because of therapeutic attributes due to its antioxidant and anti-diabetic properties. A highly diverse and an extremely ecological niche of different species can be valuable genomic resources for productivity enhancement. It is one of the most underutilized crops for food security and animal feeds. In spite of huge species diversity, only three species of Vigna have been sequenced; thus, there is a need for molecular markers for the remaining species. Computational approach of microsatellite marker discovery along with evaluation of polymorphism utilizing available genomic data of different genotypes can be a quick and an economical approach for genomic resource development. Cross-species transferability by e-PCR over available genomes can further prioritize the potential SSR markers, which could be used for genetic diversity and population differentiation of the remaining species saving cost and time. We present VigSatDB—the world’s first comprehensive microsatellite database of genus Vigna, containing >875 K putative microsatellite markers with 772 354 simple and 103 865 compound markers mined from six genome assemblies of three Vigna species, namely, Vigna radiata (Mung bean), Vigna angularis (Adzuki bean) and Vigna unguiculata (Cowpea). It also contains 1976 validated published markers. Markers can be selected on the basis of chromosomes/location specificity, and primers can be generated using Primer3core tool integrated at backend. Efficacy of VigSatDB for microsatellite loci genotyping has been evaluated by 15 markers over a panel of 10 diverse genotype of V. radiata. Our web genomic resources can be used in diversity analysis, population and varietal differentiation, discovery of quantitative trait loci/genes, marker-assisted varietal improvement in endeavor of Vigna crop productivity and management.
Collapse
Affiliation(s)
- Rahul Singh Jasrotia
- Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India.,Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Pramod Kumar Yadav
- Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - S B Bhatt
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Rukam Singh Tomar
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| |
Collapse
|
14
|
Comparative analysis on precise distribution-patterns of microsatellites in HIV-1 with differential statistical method. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, Imanishi T. Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics 2016; 291:1851-69. [PMID: 27290643 DOI: 10.1007/s00438-016-1219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 05/21/2016] [Indexed: 12/30/2022]
Abstract
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.
Collapse
Affiliation(s)
- Makoto K Shimada
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan. .,National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan. .,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan.
| | - Ryoko Sanbonmatsu
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yumi Yamaguchi-Kabata
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Chisato Yamasaki
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Ranajit Chakraborty
- Health Science Center, University of North Texas, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Takashi Gojobori
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Ibn Al-Haytham Building (West), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tadashi Imanishi
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| |
Collapse
|
16
|
Mahfooz S, Singh SP, Rakh R, Bhattacharya A, Mishra N, Singh PC, Chauhan PS, Nautiyal CS, Mishra A. A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development. Front Microbiol 2016; 7:575. [PMID: 27199911 PMCID: PMC4846858 DOI: 10.3389/fmicb.2016.00575] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.
Collapse
Affiliation(s)
- Sahil Mahfooz
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Satyendra P Singh
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Ramraje Rakh
- Maharashtra Institute of Medical Sciences and Research Medical College Latur, India
| | - Arpita Bhattacharya
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Nishtha Mishra
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Poonam C Singh
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Puneet S Chauhan
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Chandra S Nautiyal
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| | - Aradhana Mishra
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India
| |
Collapse
|
17
|
Ruiz-Ruano FJ, Cuadrado Á, Montiel EE, Camacho JPM, López-León MD. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes. Chromosoma 2014; 124:221-34. [PMID: 25387401 DOI: 10.1007/s00412-014-0492-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022]
Abstract
Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.
Collapse
Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | | | | | | | | |
Collapse
|
18
|
Hettiarachchi N, Kryukov K, Sumiyama K, Saitou N. Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol 2014; 6:2527-42. [PMID: 25364802 PMCID: PMC4202324 DOI: 10.1093/gbe/evu188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/01/2023] Open
Abstract
Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise that lineage-specific CNSs define lineage-specific characters and functions in groups of organisms. We identified 27 eudicot, 204 monocot, 6,536 grass, 19 angiosperm, and 2 vascular plant lineage-specific CNSs(lengths range from 16 to 1,517 bp) that presumably originated in their respective common ancestors. A stronger constraint on the CNSs located in the untranslated regions was observed. The CNSs were often flanked by genes involved in transcription regulation. A drop of A+T content near the border of CNSs was observed and CNS regions showed a higher nucleosome occupancy probability. These CNSs are candidate regulatory elements, which are expected to define lineage-specific features of various plant groups.
Collapse
Affiliation(s)
- Nilmini Hettiarachchi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kenta Sumiyama
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| |
Collapse
|
19
|
Cosson P, Decroocq V, Revers F. Development and characterization of 96 microsatellite markers suitable for QTL mapping and accession control in an Arabidopsis core collection. PLANT METHODS 2014; 10:2. [PMID: 24447639 PMCID: PMC3899612 DOI: 10.1186/1746-4811-10-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/20/2014] [Indexed: 05/14/2023]
Abstract
BACKGROUND To identify plant genes involved in various key traits, QTL mapping is a powerful approach. This approach is based on the use of mapped molecular markers to identify genomic regions controlling quantitative traits followed by a fine mapping and eventually positional cloning of candidate genes. Mapping technologies using SNP markers are still rather expensive and not feasible in every laboratory. In contrast, microsatellite (also called SSR for Simple Sequence Repeat) markers are technologically less demanding and less costly for any laboratory interested in genetic mapping. RESULTS In this study, we present the development and the characterization of a panel of 96 highly polymorphic SSR markers along the Arabidopsis thaliana genome allowing QTL mapping among accessions of the Versailles 24 core collection that covers a high percentage of the A. thaliana genetic diversity. These markers can be used for any QTL mapping analysis involving any of these accessions. We optimized the use of these markers in order to reveal polymorphism using standard PCR conditions and agarose gel electrophoresis. In addition, we showed that the use of only three of these markers allows differentiating all 24 accessions which makes this set of markers a powerful tool to control accession identity or any cross between any of these accessions. CONCLUSION The set of SSR markers developed in this study provides a simple and efficient tool for any laboratory focusing on QTL mapping in A. thaliana and a simple means to control seed stock or crosses between accessions.
Collapse
Affiliation(s)
- Patrick Cosson
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
| | - Véronique Decroocq
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
| | - Frédéric Revers
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
| |
Collapse
|
20
|
Shi J, Huang S, Fu D, Yu J, Wang X, Hua W, Liu S, Liu G, Wang H. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species. PLoS One 2013; 8:e59988. [PMID: 23555856 PMCID: PMC3610691 DOI: 10.1371/journal.pone.0059988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.
Collapse
Affiliation(s)
- Jiaqin Shi
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shunmou Huang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Jinyin Yu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Hua
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guihua Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
| |
Collapse
|
21
|
Kritsas K, Wuest SE, Hupalo D, Kern AD, Wicker T, Grossniklaus U. Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res 2012; 22:2455-66. [PMID: 22987666 PMCID: PMC3514675 DOI: 10.1101/gr.129346.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.
Collapse
Affiliation(s)
- Konstantinos Kritsas
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University Zürich, CH-8008 Zürich, Switzerland
| | | | | | | | | | | |
Collapse
|
22
|
Grover A, Aishwarya V, Sharma PC. Searching microsatellites in DNA sequences: approaches used and tools developed. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2012; 18:11-9. [PMID: 23573036 PMCID: PMC3550526 DOI: 10.1007/s12298-011-0098-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.
Collapse
Affiliation(s)
- Atul Grover
- />University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C Dwarka, New Delhi, 110075 India
- />Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio Energy Research, Goraparao, Haldwani, 263139 India
| | - Veenu Aishwarya
- />University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C Dwarka, New Delhi, 110075 India
- />Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - P. C. Sharma
- />University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C Dwarka, New Delhi, 110075 India
| |
Collapse
|
23
|
Martin JF, Pech N, Meglécz E, Ferreira S, Costedoat C, Dubut V, Malausa T, Gilles A. Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing. BMC Genomics 2010; 11:560. [PMID: 20939885 PMCID: PMC3091709 DOI: 10.1186/1471-2164-11-560] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Accepted: 10/12/2010] [Indexed: 01/30/2023] Open
Abstract
Background Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes. Results The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase. Conclusions This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.
Collapse
Affiliation(s)
- Jean-Francois Martin
- Centre de biologie et de gestion des Populations, Montpellier SupAgro, INRA, IRD, CIRAD, Campus International de Baillarguet, CS30016, Montferrier sur Lez cedex, France.
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Heterogeneous distribution of SNPs in the human genome: microsatellites as predictors of nucleotide diversity and divergence. Genomics 2009; 95:151-9. [PMID: 20026267 DOI: 10.1016/j.ygeno.2009.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/10/2009] [Accepted: 12/11/2009] [Indexed: 01/22/2023]
Abstract
Understanding the forces that govern the distribution of single nucleotide polymorphisms is vital for many of their applications. Here we conducted a systematic search to quantify how both SNP density and human-chimpanzee divergence vary around different repetitive sequences. We uncovered a highly complicated picture in which these quantities often differ significantly from the genome-wide average in regions extending more than 20 kb, the direction of the deviation varying with repeat number and motif. AT microsatellites in particular are potent predictors of SNP density, long (AT)(n) repeat tracts tending to be found in regions of significantly reduced SNP density and low GC content. Although the causal relationships remain difficult to determine, our results indicate a strong relationship between microsatellites and the DNA that flanks them. Our results help to explain the mixed picture that emerges from other studies and have important implications for the way in which genetic diversity is distributed in our genomes.
Collapse
|