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DNA sequence variations between UVB-sensitive and tolerant soybean genotypes
Sangrea Shim,Moon Young Kim,Suk-Ha Lee 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
UVB radiation which causes dermatosis, cancroid, and necrosis in living organisms is mostly absorbed by ozone layer, resulting in transmission of only small UVB proportion to earth surface. Recently, however, rapid increases of pollutants like CFCs have accelerated depletion of stratospheric ozone layer. Increased UVB irradiation alters affects biomolecule interinity such as DNA, RNA and protein. To understand DNA mutation spectra in response to UVB, in the present study, we used two soybean cultivars, Buseok and Cheongja 3, which were screened as the most UVB tolerant and sensitive genotypes among 140 soybean germplasms, respectively. Whole genomes of Buseok and Cheongja were sequenced at low-coverage depth by illumina Hiseq2000, and we also sequenced 6 hr UVB irradiated genomes of two cultivars. Raw sequence reads were aligned to the soybean reference sequences (cv. Williams 82) by BWA aligner software. To identify DNA mutations induced by UV-B irradiation, multiple comparisons between non-irradiated and irradiated genomes in these two soybean genotypes were conducted using samtools and GenomeAnalyzerTK packages and homebrew python codes. A total, 13,992 and 17,078 single nucleotide polymorphisms (SNPs) were indentified between non-irradiated and irradiated genomes of Buseok and Cheongja 3, respectively. In addition, Buseok and Cheongja 3 have 423 and 465 insertions/deletions induced by UVB, respectively. Approximately 58% of the identified SNPs were C to T or CC to TT transversions, consistent with the previous studies. Chromosomal distributions of the SNPs likely showed differences in UV-B mutation positions depending on the soybean genotype
Shim, Sangrea,Lee, Hong Gil,Seo, Pil Joon Korean Society for Molecular and Cellular Biology 2021 Molecules and cells Vol.44 No.10
Plant somatic cells can be reprogrammed into a pluripotent cell mass, called callus, which can be subsequently used for de novo shoot regeneration through a two-step in vitro tissue culture method. MET1-dependent CG methylation has been implicated in plant regeneration in Arabidopsis, because the met1-3 mutant exhibits increased shoot regeneration compared with the wild-type. To understand the role of MET1 in de novo shoot regeneration, we compared the genome-wide DNA methylomes and transcriptomes of wildtype and met1-3 callus and leaf. The CG methylation patterns were largely unchanged during leaf-to-callus transition, suggesting that the altered regeneration phenotype of met1-3 was caused by the constitutively hypomethylated genes, independent of the tissue type. In particular, MET1-dependent CG methylation was observed at the blue light receptor genes, CRYPTOCHROME 1 (CRY1) and CRY2, which reduced their expression. Coexpression network analysis revealed that the CRY1 gene was closely linked to cytokinin signaling genes. Consistently, functional enrichment analysis of differentially expressed genes in met1-3 showed that gene ontology terms related to light and hormone signaling were overrepresented. Overall, our findings indicate that MET1-dependent repression of light and cytokinin signaling influences plant regeneration capacity and shoot identity establishment.
Ha, Jungmin,Shim, Sangrea,Lee, Taeyoung,Kang, Yang J.,Hwang, Won J.,Jeong, Haneul,Laosatit, Kularb,Lee, Jayern,Kim, Sue K.,Satyawan, Dani,Lestari, Puji,Yoon, Min Y.,Kim, Moon Y.,Chitikineni, Annapurna John Wiley and Sons Inc. 2019 Plant biotechnology journal Vol.17 No.2
<P><B>Summary</B></P><P><I>Jatropha curcas</I> (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 <I>J. curcas</I> 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 <I>Jatropha</I> 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.</P>
m6 A mRNA Modifcation as a New Layer of Gene Regulation in Plants
Ji Woo Kim,Sangrea Shim,Hongwoo Lee,서필준 한국식물학회 2020 Journal of Plant Biology Vol.63 No.2
N6 -methyladenosine (m6 A) is the most prevalent mRNA modifcation in higher eukaryotes. Technical advances in m6 A detection and mapping have allowed a comprehensive understanding of transcriptome-wide distribution of the RNA modifcation and its biological impacts especially in model plant systems. The m6 A modifcation is reversibly catalyzed by antagonistic actions of m6 A writers and erasers and the mRNA modifcation is biologically interpreted by m6 A readers. In this review, we summarized the recent understanding of molecular mechanisms underlying m6 A deposition and m6 A-regulated biological functions in diverse aspects of plant development. We also illustrated the evolutionary history of m6 A modifcation components and discussed future perspectives of mRNA modifcation in plants.
Translational genomics for plant breeding with the genome sequence explosion
Kang, Yang Jae,Lee, Taeyoung,Lee, Jayern,Shim, Sangrea,Jeong, Haneul,Satyawan, Dani,Kim, Moon Young,Lee, Suk‐,Ha BLACKWELL 2016 PLANT BIOTECHNOLOGY JOURNAL Vol.14 No.4
<P><B>Summary</B></P><P>The use of next‐generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.</P>