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The Complete Chloroplast Genome Sequence of Korean Landrace “Subicho” (Capsicum annuum var. annuum)
Sebastin Raveendar,Young-Ah Jeon,Jung-Ro Lee,Gi-An Lee,Kyung Jun Lee,Yang-Hee Cho,Kyung-Ho Ma,Sok-Young Lee,Jong-Wook Chung 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Chloroplast DNA sequences are a versatile tool for species identification and phylogenetic reconstruction of land plants. Different chloroplast loci have been utilized for phylogenetic classification of plant species. However, there is no evidence for a short sequence that can distinguish all plant species from each other. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Thus, the complete chloroplast genome sequence of Korean landrace “Subicho” pepper (Capsicum annuum var. annuum) has been determined here. The total length of the chloroplast genome is 156,878 bp, with 37.7% overall GC content. A pair of IRs (inverted repeats) of 25,801 bp was separated by a small single copy (SSC) region of 17,929 bp and a large single copy (LSC) region of 87,347 bp. The chloroplast genome harbors 132 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of seven of these genes are duplicated in the inverted repeat regions, nine genes and six tRNA genes contain one intron, while two genes and a ycf have two introns. Analysis revealed 144 simple sequence repeat (SSR) loci and 96 variants, mostly located in the non-coding regions. The types and abundances of repeat units in Capsicum species were relatively conserved and these loci will be useful for developing molecular markers.
Sebastin Raveendar,이기안,이경준,신명재,김성훈,이정로,조규택,현도윤 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.3
Since traditional taxonomic studies possess intrinsic limitations with plant species identification, combinations of DNA barcodes have been considered a powerful tool to discover undetected genetic variation within species across large geographic areas, providing more precise estimates of biodiversity. However, the lack of efficient and universal markers is often considered a peculiar challenge in molecular taxonomic studies across plant taxa. Similarly, many loci have been proposed for DNA barcodes; still standardizing regions as a DNA barcode is vital for making them efficiently discriminate plant species. In this study, we tested the phylogenetic utility of nuclear (nrDNA) region (ITS2) with chloroplast (cpDNA) regions (matK, psbA-trnH, and rbcL) for efficient discrimination of Triticum species. A total of 109 accessions representing 16 recognized genotypes in the Triticum genus have been sampled to assess the efficiency of barcoding loci to resolve species discrimination. As expected from earlier studies, our results also revealed that a single locus has difficulty in discriminating Triticum species. Species discrimination in Triticum taxa was martially improved by using a combination of gene loci; however, the closely related species, T. aestivum and T. turgidum, had no DNA barcode to separate them. Thus, we recommend further research on finding species-specific SNP using intragenic regions as standard DNA barcode loci in Poaceae.
The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing
Sebastin Raveendar,Jung-Ro Lee,Donghwan Shim,Kyung Jun Lee,Kyung-Ho Ma,Sok-Young Lee,Jong-Wook Chung 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC, SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.
( Sebastin Raveenadar ),( Gi-an Lee ),( Jung-ro Lee ),( Kyung Jun Lee ),( Sok-young Lee ),( Gyu-taek Cho ),( Kyung-ho Ma ),( Jong-wook Chung ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.3
The phylogenetic relationships among species and subspecies in the genus Vigna were investigated using sequence data from the chloroplast and nuclear regions as DNA barcodes. We analysed 156 accessions of 56 species of the taxonomically best-known groups in the genus and evaluated the effectiveness of three chloroplast regions and a nuclear dataset currently employed as DNA barcodes using the barcoding gap, applied similarity, and tree-based methods. The chloroplast regions were able to identify fewer than 44% of the species, whereas the nuclear datasets identified more than 62% of the species using the “best match” and “best close match” options in the TaxonDNA software. All species had high interspecific pairwise distances that did not fully overlap with the intraspecific distances, and the tree-based analysis resolved more than 80% of the species. The nuclear ribosomal internal transcribed spacer 2 (ITS2) region was the most useful as a single barcode and the four-barcode combinations that included ITS2 provided the best discriminatory power. Therefore, we suggest that the ITS2 barcoding region should be used as a starting point to identify Vigna species.
Sebastin Raveendar,소윤섭,이경준,이동진,성좌경,정종욱 한국작물학회 2017 Journal of crop science and biotechnology Vol.20 No.4
The wild species are considered as primary and secondary genepools for the world’s most important food crops. Here, we sequenced the complete chloroplast (cp) genome sequence of an American wild licorice, Glycyrrhiza lepidota for the first time to investigate their phylogenetic relationship among inverted-repeat-lacking clade (IRLC) legumes. The total length of the chloroplast genome is 127,939 bp, with 34.2% overall GC content. The chloroplast genome harbors 110 known genes, including 76 protein-coding genes, four ribosomal RNA genes, and 30 tRNA genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. A total of 464 cp microsatellites (cpSSRs) were analyzed in the G. lepidota. The majority of the SSRs in this cp genome are penta-nucleotides (61.6%). Locally collinear blocks (LCBs) identified between the Glycyrrhiza glabra and G. lepidota cp genomes were showed that they were well conserved with respect to gene organization and order. Moreover, the phylogenetic analysis indicates that G. lepidota is closely related to its confamilial counterparts than to the other taxa of the IRLC legumes.
Complete Chloroplast Genome Sequencing and Genetic Relationship Analysis of Capsicum chinense Jacq
Sebastin Raveendar,이경준,신명재,조규택,이정로,마경호,이기안,정종욱 한국육종학회 2017 Plant Breeding and Biotechnology Vol.5 No.4
Capsicum chinense is one of the five domesticated pepper species belonging to the Solanaceae family. Capsicum sp. have been used as model systems in comparative and evolutionary genomics because their superior availability of chloroplast genome in the solanaceae family. Similarly, molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. So far however, only partial taxonomic and phylogenetic analyses have been carried out for the genus. Thus, the complete chloroplast genome sequence of a cultivated pepper (C. chinense) has been reported here. The total length of the chloroplast genome is 156,936 bp, with 37.7% overall GC content. A pair of inverted repeats (IRs) of 25,847 bp was separated by a small single copy (SSC) region of 17,912 bp and a large single copy (LSC) region of 87,330 bp. The chloroplast genome harbors 113 known genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA (tRNA) genes. In all, 21 of these genes are duplicated in the inverted repeat regions, 15 genes and six tRNA genes contain a single intron, while two genes have two introns. Analysis revealed 117 simple sequence repeat (SSR) loci, which are mostly located in the intergenic regions. The complete chloroplast genome reported here enriches our knowledge of the genetic complement of C. chinense, and contributes to our understanding of the genetic relationships within the genus Capsicum.
( Sebastin Raveendar ),( Jong-wook Chung ),( Gi-an Lee ),( Jung-ro Lee ),( Kyung-jun Lee ),( Myoung-jae Shin ),( Yang-hee Cho ),( Kyung-ho Ma ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.3
Tomato (Solanum lycopersicum L.) is one of the most economically important plants in the family Solanaceae. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The objective of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall FST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.
Identification of Genus Vigna using ITS2 and matK as a Two-Locus DNA Barcode
( Sebastin Raveendar ),( Jung Ro Lee ),( Jae Wan Park ),( Gi An Lee ),( Young Ah Jeon ),( Won Hee Lee ),( Gyu Taek Cho ),( Kyung Ho Ma ),( Sok Young Lee ),( Jong Wook Chung ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2
DNA barcoding is the use of short DNA sequences of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended a 2-locus combination as the standard plant barcode. The evolutions of the chloroplast regions combined with nuclear gens are sufficiently rapid to allow discrimination between closely related species. We evaluated the efficacy of the proposed plant barcoding loci, matK, along with ITS2 for barcoding the Vigna species. To assess the discriminatory ability of barcoding loci for identifying the Vigna species, we sampled 52 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses were able to discriminate some closely related Vigna species. Thus, we used concatenated data to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vigna because characterization of the nucleotide sequences of the matK region was easier and more cost-effective than that of the ITS region.