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Kim, Seungill,Kim, Myung-Shin,Kim, Yong-Min,Yeom, Seon-In,Cheong, Kyeongchae,Kim, Ki-Tae,Jeon, Jongbum,Kim, Sunggil,Kim, Do-Sun,Sohn, Seong-Han,Lee, Yong-Hwan,Choi, Doil Oxford University Press 2015 DNA research Vol.22 No.1
<P>The onion (<I>Allium cepa</I> 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 <I>de novo</I> 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 <I>ab initio</I> 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 <I>de novo</I> transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in <I>Allium</I> spp.</P>
Bogyu Kim,Younguk Jeon,Hyebi Kim,Chulwoo Lee,JoonHyun Kang,Jongbum Kim,In Soo Kim,Young-Hwan Kim,Kwanil Lee,Young Duck Kim,Il Ki Han 한국진공학회 2021 한국진공학회 학술발표회초록집 Vol.2021 No.2
Potassium tantalate niobate (KTal-xNbxO3, KTN) is a ferroelectric material with an extremely high electro-optic (EO) coefficient suitable for integrated photonic device. In the K-Ta-Nb-O system, the perovskite structure KTN with the ferroelectric properties is generally hard to deposit due to high volatility of potassium(K). By controlling K contents in a KTN ceramic target, the crystal structure can be formed from pyrochlore to perovskite phase. In this presentation, we will analyze the effects of K-enriched targets on the phase-formation process in KTN films and its structural differences.
De novo assembly and phasing of a Korean human genome
Seo, Jeong-Sun,Rhie, Arang,Kim, Junsoo,Lee, Sangjin,Sohn, Min-Hwan,Kim, Chang-Uk,Hastie, Alex,Cao, Han,Yun, Ji-Young,Kim, Jihye,Kuk, Junho,Park, Gun Hwa,Kim, Juhyeok,Ryu, Hanna,Kim, Jongbum,Roh, Mira Nature Publishing Group, a division of Macmillan P 2016 Nature Vol.538 No.7624
<P>Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing(2), next-generation mapping(3), microfluidics-based linked reads(4), and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.</P>