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Kim J.-E.,Seeders Inc. | Oh S.-K.,Seoul National University | Lee J.-H.,Seeders Inc. | Lee B.-M.,Seeders Inc. | Jo S.-H.,Seeders Inc.
Molecules and Cells

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies. © The Korean Society for Molecular and Cellular Biology. All rights reserved. Source

Seo E.,Seoul National University | Yeom S.-I.,Seoul National University | Jo S.,Seeders Inc. | Jeong H.,Seoul National University | And 2 more authors.
Molecules and Cells

Secreted proteins are known to have multiple roles in plant development, metabolism, and stress response. In a previous study to understand the roles of secreted proteins, Capsicum annuum secreted proteins (CaS) were isolated by yeast secretion trap. Among the secreted proteins, we further characterized Capsicum annuum senescence-delaying 1 (CaSD1), a gene encoding a novel secreted protein that is present only in the genus Capsicum. The deduced CaSD1 contains multiple repeats of the amino acid sequence KPPIHNHKPTDYDRS. Interestingly, the number of repeats varied among cultivars and species in the Capsicum genus. CaSD1 is constitutively expressed in roots, and Agrobacterium-mediated transient overexpression of CaSD1 in Nicotiana benthamiana leaves resulted in delayed senescence with a dramatically increased number of trichomes and enlarged epidermal cells. Furthermore, senescence- and cell division-related genes were differentially regulated by CaSD1-overexpressing plants. These observations imply that the pepper-specific cell wall protein CaSD1 plays roles in plant growth and development by regulating cell division and differentiation. © 2012 KSMCB. Source

Lee K.J.,Korea Atomic Energy Research Institute | Lee K.J.,National Agrobiodiversity Center | Kim D.S.,Korea Atomic Energy Research Institute | Kim J.-B.,Korea Atomic Energy Research Institute | And 4 more authors.
Molecular Genetics and Genomics

Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In this study, we performed whole genome resequencing by Illumina HiSeq to identify changes in flowering genes using an early-flowering phenotype of soybean mutant line Josaengserori (JS) derived from Korean landrace, Seoritae (SR), and we obtained mapped reads of 131,769,690 and 167,669,640 bp in JS and SR, respectively. From the whole genome sequencing results between JS and SR, we identified 332,821 polymorphic SNPs and 65,178 indels, respectively. Among these, 30 flowering genes were in SNPs and 25 were in indels. Among 30 flowering genes detected in SNPs, Glyma02g33040, Glyma06g22650, Glyma10g36600, Glyma13g01290, Glyma14g10530, Glyma16g01980, Glyma17g11040, Glyma18g53690, and Glyma20g29300 were non-synonymous substitutions between JS and SR. Changes in Glyma10g36600 (GI), Glya02g33040 (AGL18), Glyma17g11040 (TOC1), and Glyma14g10530 (ELF3) in JS affected the expression of GmFT2a and resulted in early flowering. These results provide insight into the regulatory pathways of flowering in soybean mutants and help to improve our knowledge of soybean mutation breeding. © 2016 Springer-Verlag Berlin Heidelberg Source

Park M.,Seoul National University | Jo S.,Seeders Inc. | Jo S.,Korea Research Institute of Bioscience and Biotechnology | Kwon J.-K.,Seoul National University | And 9 more authors.
BMC Genomics

Background: Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.Results: For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.Conclusions: Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family. © 2011 Park et al; licensee BioMed Central Ltd. Source

Ahn S.Y.,Yeungnam University | Kim S.A.,Yeungnam University | Jo S.H.,Seeders Inc. | Yun H.K.,Yeungnam University
Plant Genetic Resources: Characterisation and Utilisation

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers. © NIAB 2014. Source

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