Won Joo Hwang

Bio: Won Joo Hwang is an academic researcher from Seoul National University. The author has contributed to research in topics: Vigna & Quantitative trait locus. The author has an hindex of 7, co-authored 7 publications receiving 459 citations.

Genome sequence of mungbean and insights into evolution within Vigna species

Abstract: Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

Draft genome sequence of adzuki bean, Vigna angularis.

Abstract: Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits

Abstract: Jatropha curcas (physic nut), a non‐edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up‐regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Genome-wide analysis of mutations in a dwarf soybean mutant induced by fast neutron bombardment

Abstract: Fast neutron (FN) bombardment is a powerful mutagen that can be effectively employed for functional genomics studies in the post-genome era. In soybean, dwarfism is a desirable agricultural characteristic that improves lodging resistance. In the present study, we selected a dwarf mutant soybean among approximately 10,000 M4 progeny lines derived from FN-irradiated seeds of cultivar Williams 82. This dwarf mutant exhibited reduced plant height, only approximately 20 % of wild type. Using mutant plants homozygous for this dwarf phenotype, we performed whole genome sequencing by Illumina HiSeq to identify the deletion site responsible for the dwarfism. Comparative sequence analysis by mapping the mutant reads to the soybean reference genome sequence (wild type) predicted 13 large deletion regions. Among these, three loci (designated del1–3, del2–3, and del3–15) were validated by two complementary PCRs using two allele-specific reverse primers, respectively. We found that the del1–3 and del2–3 loci are positioned in non-coding regions of chromosome 3. In del3–15, the mutated allele has an 803-bp deletion including the first partial exon of Glyma15g05831 (peroxidase superfamily protein) on chromosome 15, resulting in the loss of a start codon. Reverse transcription-PCR analysis revealed that the expression of the gene Glyma15g05831 was completely abolished in the dwarf mutant. A lack of peroxidase (which catalyzes the generation of reactive oxygen species) coupled with indole-3-acetic acid oxidation may be responsible for the dwarfing of this mutant.

Genome-wide comparative analysis of flowering genes between Arabidopsis and mungbean

Abstract: Mungbean is one of the major crops grown in South, East and Southeast Asia because of a high quality of amino acid profile; however, its asynchronous flowering time makes difficult to harvest at a time. Synchronization of flowering time is important to reduce labor costs for harvesting. With the availability of next generation sequencing data of mungbean, we approached a strategy of comparative genomics to identify mungbean homologous counterpart of A. thaliana genes that are known to be involved in flowering pathways, followed by a comparative soybean quantitative trait loci (QTL) analysis of the putative mungbean flowering-related genes. Co-localization of mungbean QTL associated with days to first flower day (FLD) was also identified using the EST-SSR markers from a previous study. Additionally, based on the mungbean transcriptome data with a distinct flowering stage of R2, FPKM (Fragments Per Kilobase per Million mapped reads) expression analysis of all the genes found in paralogous synteny blocks was conducted to examine expression patterns of the genes that have undergone a whole genome duplication event. Our results indicate that the paralogous flowering genes along with other genes within a same synteny block have evolved together at the macro-synteny scale. This study provides insights into mungbean flowering genes, in which they can be used as tools in order to improve flowering synchronization and to increase yield.

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

Abstract: The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

Abstract: PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.

Evolution of plant genome architecture

Abstract: We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.

A reference genome for pea provides insight into legume genome evolution

Abstract: We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

The genome of cowpea (Vigna unguiculata [L.] Walp.)

Abstract: Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.