• Title/Summary/Keyword: 게놈

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Current status and prospects to identify mutations responsible for mutant phenotypes by using NGS technology (NGS 기술 활용 돌연변이체 해석 및 연구현황)

  • Jung, Yu Jin;Ryu, Ho Jin;Cho, Yong-Gu;Kang, Kwon Kyoo
    • Journal of Plant Biotechnology
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    • v.43 no.4
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    • pp.411-416
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    • 2016
  • Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions absent in the reference cannot be identified by simple alignment. In this review, we report the current status and prospects in identification of genes in mutant phenotypes, by using the methods MutMap, MutMap-Gap, and MutMap+. These methods delineate a candidate region harboring a mutation of interest, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. These methods are likely to prove useful for cloning genes that exhibit significant structural variations, such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

Characterization of Rice black-streaked dwarf virus in Maize (옥수수에 발생하는 벼검은줄오갈병의 유전자 비교)

  • Lee, Bong-Choon;Yoon, Young-Nam;Hong, Sung-Jun;Hong, Yeon-Kyu;Hwang, Jae-Bok;Song, Sek-Bo;Kang, Hwang-Won;Lee, Key-Woon
    • Research in Plant Disease
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    • v.14 no.3
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    • pp.223-225
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    • 2008
  • This study was carried out to identify the Rice black-streaked dwarf virus that infected maize plants collected from Gochang-gun in Jeollabukdo in 2005. The genomic dsRNA from infected plants was extracted and the genome pattern was analyzed by polyacrylamide gel electrophoresis. Results of the electrophoresis revealed the already known to-segment genome and the difference of mobility was confirmed in isolates by collected areas. The RBSDV was identified from the result of RT-PCR using the template of extracted dsRNA and specific primer. The results of S10 cloned to pGEM-T vector and the conducted in sequence analysis consisted of 1,801nt and 559aa. This was of the same size as the RBSDV S10 identified in rice, and the change was confirmed in 18 base and displayed homology of 99%.

Complete Mitochondrial Genome of the Gypsy Moth, Lymantria dispar (Lepidoptera: Erebidae) (매미나방의 미토콘드리아 게놈 분석)

  • Na Ra, Jeong;Youngwoo, Nam;Wonhoon, Lee
    • Korean journal of applied entomology
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    • v.61 no.3
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    • pp.507-512
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    • 2022
  • The Gypsy moth, Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) is a serious pest that attacks forest as well as fruit trees. We sequenced the 15,548 bp long complete mitochondrial genome (mitogenome) of this species. It consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region. The orientation and gene order of the L. dispar mitogenome are identical to that of the ancestral type found in majority of the insects. Phylogenetic analyses using concatenated sequences of 13 PCGs and 2 rRNAs (13,568 bp including gaps) revealed that the L. dispar examined in our study, together with other geographical samples of L. dispar in a group forming the family Erebidae and consistently supported the monophyly of each family (Erebidae, Euteliidae, Noctuidae, Nolidae and Notodontidae), generally with the highest nodal supports.

The Specific Gene Characteristics of Chloroplast Genome in Viola (제비꽃종류에서 나타나는 엽록체 DNA 게놈의 특이 유전자 특징)

  • Ah-reum Go;Ki-Oug Yoo
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2023.04a
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    • pp.19-19
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    • 2023
  • 제비꽃속 34분류군의 61개체를 대상으로 엽록체 DNA 게놈 특이 유전자의 특징을 알아보고자 하였다. 61개체의 엽록체 게놈 전체 길이는 155,535~158,940 bp 로 모두 전형적인 사분할 구조였다. 지역별로는 LSC 지역이 84,826~87,250 bp, SSC 지역이 16,338~18,654 bp, 그리고 IR 지역이 26,029~27,192 bp 였다. 유전자 개수는 131개로 84개 protein coding-gene, 37개 tRNA 유전자, 8개 rRNA유전자, 그리고 2개의 유사유전자인 𝜓rps19, 𝜓ycf1으로 구성되어 있었다. LSC/IRa 경계에 위치한 rps19 유전자 길이는 279 bp로 모든 분류군에서 동일하였으며, 𝜓rps19의 길이는 다양했으나 유전자 개수에는 영향을 미치지 않았다. SSC/IRb 경계에 위치한 ycf1 유전자 길이는 약 5,600 bp 였으나, V. japonica (MZ151699) 1개체에서는 다른 종에 비해 약 1,000 bp 위치에서 발생한 점돌연변이로 인해 종결 코돈이 나타나는 특징을 보였다. 한편 13분류군의 23개체에서는 𝜓ycf1의 길이가 650 bp 정도 짧은 것을 확인하였는데, 이 종류들은 원예종인 V. tricolor (ON262802) 이외에는 모두 줄기가 없는 분류군들로 IR 지역의 확장과 SSC 지역의 수축에 의한 것으로 판단된다. ndhF는 대체로 SSC 지역에 위치하나, V. inconspicua (MZ065354), V. mongolica (MW802534, ON548135), V. yunnanfuensis (MW802541) 등 4개체에서는 IRa/SSC 경계에 위치하면서 유사유전자가 발생하였고, 그 결과 다른 제비꽃 종류에 비해 유전자 개수가 132개로 차이를 보였다. 또한, V. collina (OP271831), V. mirabilis (MH256000), V. tricolor (ON262802) 등 3분류군에서는 SSC 지역이 inversion 되어 엽록체 이성질체가 존재함을 확인하였다. 이상의 결과를 종합하면, 제비 꽃속 엽록체 게놈 61개체의 ycf1, 𝜓ycf1, ndhF, 𝜓ndhF 등은 유전자 길이와 개수 등에 차이를 보이는 것으로 나타났으며, 제비꽃속에서도 엽록체 이성질체가 존재함을 확인할 수 있었다.

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Complete genome sequence of Paenibacillus swuensis DY6T, a bacterium isolated from gamma-ray irradiated soil (감마선 조사된 토양에서 분리된 박테리아 Paenibacillus swuensis DY6T의 완전한 게놈 서열)

  • Kim, Myung Kyum;Lee, Seung-Yeol;Jung, Hee-Young;Srinivasan, Sathiyaraj
    • Korean Journal of Microbiology
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    • v.52 no.4
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    • pp.500-502
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    • 2016
  • Several bacterial species have been reported to be surviving after the ionizing radiation treatment due to the presence of sophisticated enzymes systems and some endospores producing bacterial strains can also resist, due to the presence of thick spore coat. In this study, we report the complete genome sequence of a bacterium Paenibacillus swuensis $DY6^T$, isolated from an irradiated soil sample. The genome comprised of 5,012,599 bp with the G+C content of 49.93%, the genome included 4,463 protein coding genes and 133 RNA genes.

Polydnavirus and Its Novel Application to Insect Pest Control (폴리드나바이러스와 새로운 해충방제 전략)

  • Kim, Yong-Gyun
    • Korean journal of applied entomology
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    • v.45 no.3 s.144
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    • pp.241-259
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    • 2006
  • Polydnavirus is a mutualistic DNA virus found in some braconid and ichneumonid wasps. Its genome is integrated into host chromosome as a provirus. Its replication occurs at ovarian calyx epithelium during host pupal stage to form episomal viral particles. The viral particles are delivered into hemocoel of the parasitized insect along with eggs during wasp oviposition. Several polydnaviral genomes, which are isolated from the episomal virus particles, have been sequenced and exhibit some gene families with speculative physiological functions. This review presents the viral characteristics in terms of Its parasitic physiology. For developing new insect pest control tactics, it also discusses several application strategies exploiting the viral genome to manipulate insect physiology.

Cloning and Characterization of Highly Repetitive Sequences in the Genome of Allium sativum L. (마늘(Allium sativum L.) 게놈의 고반복서열의 분이와 특성 조사)

  • 이동희
    • Journal of Plant Biology
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    • v.39 no.1
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    • pp.49-55
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    • 1996
  • We have studied the DNA of Allium sativum L. with respect to highly repetitive sequences. Fast reassociated DNA fragments expected to be highly repetitive sequences based on $C_{o}t$ curve were isolated and characterized. Their copy numbers were approximately $10^{5}~10^{7}$ per haploid genome. Nucleotide sequences analysis of six candidates reveals that their G/C content were low, 25-40% and typical patterns of repeating sequences exist. Repeat sequences were used as probes to access restriction fragment length polymorphism (RFLP) of genomic DNAs of four local clones, Tanyang, Mungyong, So san, and Uisong. The hybridization pattern were very similar among these four local clones.clones.

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Genomic Structure Analyses of Five Kinds of Human Sialyltransferase Gene (5종류의 인간유래 시알산전이효소 유전자들의 게놈구조 분석)

  • Kang Nam-Young;Kim Sang-Wan;Kim Cheorl-Ho;Lee Young-Choon
    • Journal of Life Science
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    • v.14 no.6 s.67
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    • pp.1009-1017
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    • 2004
  • Sialyltransferases cloned so far show the remarkable tissue-specific expression, which is correlated with the existence of cell type-specific sialylated sugar structure in glycoconjugates. In the previous studies, we found various mRNA isoforms of human sialyltransferases generated by alternative splicing and alternative promoter utilization. To understand the regulatory mechanisms for specific expression of human sialyltransferase genes and for production of their mRNA isoforms, in this study, we have isolated and characterized five kinds of human sialyltransferase genes: hST3Gal II, hST8Sia II, hST8Sia III, hST8Sia IV, and hST8Sia V. The hST3Gal II gene is composed of six exons, which span over 17kb, with exons ranging in size from 46 to over 1017 bp. The hST8Sia III gene comprises over 10 kb, and consists of only four exons, which is much smaller and simpler than other human sialyltransferase genes. In contrast, three genes (hST8Sia II, hST8Sia IV and hST8Sia V) span more than 70 kb, and comprise five or more exons. All exon-intron boundaries follow the GT-AG rule. In particular, the sialylmotif L, which is a highly conserved region in all cloned sialyltransferases, was found in one exon of hST8Sia III, whereas this motif is encoded by discrete exons in the other human sialyltransferases. Exon structures of these sialyltransferase genes show the structural diversity, as found in other human sialyltransferase genes reported so far. We determined the transcription start site of hST3Gal II gene by the 5'-RACE and cap site hunting experiments.