A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.
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ABSTRACT:
SUBMITTER: Cheng J
PROVIDER: S-EPMC4703971 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: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.
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Project description:Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1-4 bp length, designated LSSR(1-4)) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5-11 bp length, designated LSSR(5-11)) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR(1-4) are likely maintained by selection. This is consistent with the established role of some LSSR(1-4) in enhancing antigenic variance. By contrast, abundance of LSSR(5-11) in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed.
| S-EPMC1895974 | biostudies-literature
Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.
2011-09-08 | GSE29215 | GEO
Project description:An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC-MS and headspace GC-MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum-C. chinense-C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0432-6) contains supplementary material, which is available to authorized users.
| S-EPMC3548101 | biostudies-literature
Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. 1 sample TF68 accession examined
2011-09-08 | E-GEOD-29215 | biostudies-arrayexpress
Project description:Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6?nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of?>650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb.
| S-EPMC5533116 | biostudies-literature
Project description:BackgroundMicrosatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars.ObjectiveThis is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species.MethodsWe identified and compared perfect SSRs with 1-6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, Elaeis oleifera, and Elaeis guineensis.ResultsA total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs.ConclusionWe envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes.
| S-EPMC7181556 | biostudies-literature
Project description:Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
| S-EPMC10484947 | biostudies-literature
Project description:BackgroundHepatitis E virus (HEV) is small (27-34 nm diameter) non-enveloped with positive sense ssRNA genome. Microsatellites or simple sequence repeats (SSR) are short tandem repeat sequences present across coding and non-coding regions of both prokaryotes and eukaryotes. They are involved with genome function and evolution at multiple levels.ResultsThe complete genome sequences of 22 HEV genomes of the family Hepeviridae and genus Orthohepevirus (21 species) and Piscihepevirus (1 species) were extracted from NCBI database ( http://www.ncbi.nlm.nih.gov/ ). The extraction of microsatellites was done using Imperfect Microsatellite Extractor (IMEx) in 'Advance-Mode'. The average genome size of the studied HEV genomes was 7003nt and it ranged from 6649nt (HEV11) to 7310nt (HEV22). The average GC content of the genomes was ~ 55%. A total of 519 SSRs and 21 cSSRS were extracted from the HEV genomes with an average incidence of 24 per genome ranging from 14 (HEV13) to 34 (HEV19). The cSSR incidence ranged from 0 (eight species) to 4 (HEV19). The genomes with no cSSR incidence had an SSR incidence range from 14 to 28. There were just four hexa-nucleotide repeat motifs and 5 penta-nucleotide repeat motifs observed. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were "C", "GT/TG", and "GAC/CTG" respectively. The studied genomes had a minimum of ~ 90% incident SSRs present in the coding regions. Viruses with same or similar hosts are placed together on the phylogenetic tree implicating viral host being one of the driving forces for evolution. Conclusions Host range in viruses is being decided by multiple factors aided by the unique genome SSR signature and genomes of varied compositions need to be analyzed to forge a widely acceptable rule for predicting the same.
| S-EPMC9114184 | biostudies-literature
Project description:Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.
| S-EPMC8728187 | biostudies-literature