Seong-Han Sohn

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.

Interaction of the host protein NbDnaJ with Potato virus X minus-strand stem-loop 1 RNA and capsid protein affects viral replication and movement.

Plant viruses must interact with host cellular components to replicate and move from cell to cell. In the case of Potato virus X (PVX), it carries stem-loop 1 (SL1) RNA essential for viral replication and movement. Using two-dimensional electrophoresis northwestern blot analysis, we previously identified several host proteins that bind to SL1 RNA. Of those, we further characterized a DnaJ-like protein from Nicotiana benthamiana named NbDnaJ. An electrophoretic mobility shift assay confirmed that NbDnaJ binds only to SL1 minus-strand RNA, and bimolecular fluorescence complementation (BiFC) indicated that NbDnaJ interacts with PVX capsid protein (CP). Using a series of deletion mutants, the C-terminal region of NbDnaJ was found to be essential for the interaction with PVX CP. The expression of NbDnaJ significantly changed upon infection with different plant viruses such as PVX, Tobacco mosaic virus, and Cucumber mosaic virus, but varied depending on the viral species. In transient experiments, both PVX replication and movement were inhibited in plants that over-expressed NbDnaJ but accelerated in plants in which NbDnaJ was silenced. In summary, we suggest that the newly identified NbDnaJ plays a role in PVX replication and movement by interacting with SL1(-) RNA and PVX CP.

Use of an anthocyanin production phenotype as a visible selection marker system in transgenic tobacco plant

To develop a potentially alternative method for the selection of transgenic plants instead of antibiotic and herbicide resistance, anthocyanin pigmentation phenotype was examined to provide a visible selection marker system. Two regulatory genes of the anthocyanin biosynthetic pathway, the R2R3 MYB mPAP1 gene from Arabidopsis and the basic helix loop helix B-Peru gene from maize, were amplified by RT-PCR and then individually cloned into a plant expression vector. The requirement of these two genes for anthocyanin pigmentation was pre-confirmed via an in vivo assay using tobacco agro-infiltration. The mPAP1 and B-Peru vectors were further stably co-transformed into tobacco plants using Agrobacterium tumefaciens strain LBA4404. Tobacco plants harboring both genes could be readily selected through the manifestation of a red color due to anthocyanin accumulation in the whole plant body. The T1 segregants showed red or green phenotypes depending on the genotype. The need for both the mPAP1 and B-Peru genes for a red color phenotype due to anthocyanin pigmentation was further confirmed by genotyping of the T1 generation by genomic PCR analysis and an in vivo assay using agro-infiltration. From these results, we conclude that co-transformation with two individual vectors harboring a critical anthocyanin transcriptional factor has potential utility as an alternative visible selectable marker system for transgenic progeny selection in plants.

The Effect of Cucumber mosaic virus 2b Protein to Transient Expression and Transgene Silencing Mediated by Agro-infiltration

The transient and rapid expression system of a foreign protein in planta is a very useful technique in biotechnology application. We have investigated optimum condition of Agrobacterium-infiltration technique in which expression level of foreign proteins were maximized without detrimental effects on plants using GFP and Cucumber mosaic virus 2b protein, which is known as an enhancer of gene expression and a suppressor of post-transcriptional gene silencing(PTGS). The optimum expression level of both RNA and protein of GFP with minimum leaf impairment was obtained at

Complete chloroplast genomic sequence of Citrus platymamma determined by combined analysis of Sanger and NGS data

Citrus platymamma (Byeonggyul) of the family Rutacease is one of the most important genetic resources of Korean Citrus. To characterize the chloroplast (cp) genetic makeup of this species, the cp genome was sequenced by both Sanger and next generation sequencing (NGS) methods. The characterized cp genome is 160,121 bp in size: the large single copy (LSC) region is 87,732 bp, the inverted repeat (IR) is 26,998 bp, and the small single copy (SSC) region is 18,393 bp. The cp genome contains 114 genes and 21 introns, including 80 protein-coding genes, four RNA genes, 30 tRNA genes, 19 group II introns, and one group I intron. Based on phylogenetic analysis with six known cp genomes from the Sapindales order, to which the Rutaceae belongs, the cp genome of C. platymamma is closest to that of Citrus sinensis. When directly comparing the cp genomes of C. platymamma and C. sinenesis, we detected size variation in the psbC and rps4 genes, four SNPs, and eight 1-bp simple sequence repeats (SSRs). Additionally, we found that the cp genomic structures of C. platymamma and C. sinensis are identical in regards to the junction sequences of LSC-IRs and SSC-IRs, and provide evidence that the junction sequences of the SSC-IRs originated from the common ancestor of C. platymamma, C. sinensis, and C. aurantifolia. Further study of other species will provide enhanced understanding of cp genome evolution in the Citrus genus.

Aberrant promoter methylation occurred from multicopy transgene and SU(VAR)3–9 homolog 9 (SUVH9) gene in transgenic Nicotiana benthamiana

The chemical modification of DNA by methylation is a heritable trait and can be subsequently reversed without altering the original DNA sequence. Methylation can reduce or silence gene expression and is a component of a hosts defence response to foreign nucleic acids. In our study, we employed a plant transformation strategy using Nicotiana benthamiana Domin to study the heritable stability of the introduced transgenes. Through the introduction of the cauliflower mosaic virus (CaMV) 35S promoter and the green fluorescent protein (GFP) reporter gene, we demonstrated that this introduced promoter often triggers a homology-dependent gene-silencing (HDGS) response. These spontaneous transgene-silencing phenomena are due to methylation of the CaMV 35S promoter CAAT box during transgenic plant growth. This process is catalysed by SU(VAR)3-9 homologue 9 (SUVH9), histone deacetylase 1 (HDA1) and domains rearranged methylase 2 (DRM2). In particular, we showed from our data that SUVH9 is the key regulator of methylation activity in epigenetically silenced GFP transgenic lines; therefore, our findings demonstrate that an introduced viral promoter and transgene can be subject to a homology-dependent gene-silencing mechanism that can downregulate its expression and negatively influence the heritable stability of the transgene.

Interaction Study of Soybean mosaic virus Proteins with Soybean Proteins using the Yeast-Two Hybrid System

Interactions between viral proteins and host proteins are essential for virus replication. Especially, translation of viral genes completely depends on the host machinery. In potyviruses, interactions of genome-linked viral protein (VPg) with host translation factors including eIF4E, eIF(iso)4E, and poly(A)-binding protein (PABP) has previously been characterized. In this study, we investigated interactions between Soybean mosaic virus (SMV) viral proteins and host translation factors by yeast two-hybrid system. SMV VPg interacted with eIF4E, eIF(iso)4E, and PABP in yeast two-hybrid system, while SMV helper component proteinase (HC-pro) interacted with neither of those proteins. The interaction between SMV NIb and PABP was also detected. These results are consistent with those reported previously in other potyviruses. Interestingly, we found reproducible and specific interactions between SMV coat protein (CP) and PABP. Deletion analysis showed that the region of CP comprising amino acids 116 to 206 and the region of PABP comprising amino acids 520 to 580 are involved in CP/PABP interactions. Soybean library screening with SMV NIb by yeast two-hybrid assay also identified several soybean proteins including chlorophyll a/b binding preprotein, photo-system I-N subunit, ribulose 1,5-biphosphate carboxylase, ST-LSI protein, translation initiation factor 1, TIR-NBS type R protein, RNA binding protein, ubiquitin, and LRR protein kinase. Altogether, these results suggest that potyviral replicase may comprise a multi-protein complex with PABP, CP, and other host factors.

Construction of a draft reference transcripts of onion (Allium cepa) using long-read sequencing

To obtain intact and full-length RNA transcripts of onion (Allium cepa), long-read sequencing technology was first applied. Total RNAs extracted from four tissues; flowers, leaves, bulbs and roots, of red–purple and yellow-colored onions (A. cepa) were sequenced using long-read sequencing (RSII platform, P4-C2 chemistry). The 99,247 polished high-quality isoforms were produced by sequence correction processes of consensus calling, quality filtering, orientation verification, misread-nucleotide correction and dot-matrix view. The dot-matrix view was subsequently used to remove artificial inverted repeats (IRs), and resultantly 421 IRs were removed. The remaining 98,826 isoforms were condensed to 35,505 through the removal process of redundant isoforms. To assess the completeness of the 35,505 isoforms, the ratio of full-length isoforms, short-read mapping to the isoforms, and differentially expressed genes among the four tissues were analyzed along with the gene ontology across the tissues. As a result, the 35,505 isoforms were verified as a collection of isoforms with high completeness, and designated as draft reference transcripts (DRTs, ver 1.0) constructed by long-read sequencing.

Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild Chrysanthemum species

AbstractKey messageComparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species.AbstractPlants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.

Efficiency of microspore embryogenesis in Brassica rapa using different genotypes and culture conditions

Abstract Total of fifty accessions of Brassica rapa with various morphological characteristics were used for production of double haploid plants though microspore culture in Brassica rapa . Among them, only 30 accessions induced embryos from microspores. The highest efficiency of embryo induction of 1.194 per bud was obtained from IT135449 of turnip type, while 3 accessions of sarson (winter oil) type did not generate embryo. The effect of heat shock periods for embryogenesis was also investigated with 4 accessions (IT135449; Turnip type, IT199710; Chinese cabbage type, IT212886; Pak choi type, IT218043; Summer oil type). The high productions of embryos were observed in IT135449, IT199710 and IT212886 when microspores were pre-cultured to 32˚C for 2 days. In IT218043, high embryogenesis was observed at the 3 days of heat shock treatment. The optimal condition of shoot regeneration for IT199710 was observed in MS medium supplemented with NAA 0.5 mg·L -1 and BAP 1 mg·L -1 . In contrast, the IT135449 and IT212886 were observed high regeneration frequency in MS medium without plant growth regulators. All the plantlets regenerated from microspore-derived embryos have been successfully transplanted to soil, and bud self-pollinated seeds were produced from doubled haploid plants. This indicated that double-haploid genotype was likely generated naturally during embryogenesis process.