• Title/Summary/Keyword: NGS

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Current status of sweetpotato genomics research (고구마 유전체 연구현황 및 전망)

  • Yoon, Ung-Han;Jeong, Jae Cheol;Kwak, Sang-Soo;Yang, Jung-Wook;Kim, Tae-Ho;Lee, Hyeong-Un;Nam, Sang-Sik;Hahn, Jang-Ho
    • Journal of Plant Biotechnology
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    • v.42 no.3
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    • pp.161-167
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    • 2015
  • Sweetpotato [Ipomoea batatas (L.) Lam] grows well in harsh environmental conditions, and is cultivated as one of the top seven food crops in the world. Recently, sweetpotato is drawing interest from people as a healthy food because it is high in dietary fiber, vitamins, carotenoids and overall nutrition value. However, few studies have been conducted on sweetpotato genome sequencing in spite of its importance. This review is aimed at increasing the efficiency of sweetpotato genome sequencing research as well as establishing a base for gene utilization in order to control useful traits. Recently, animal and plant genome sequencing projects increased significantly. However, sweetpotato genome sequencing has not been performed due to polyploidy and heterogeneity problems in its genome. Meanwhile research on its transcriptome has been conducted actively. Recently, a draft of the diploid sweetpotato genome was reported in 2015 by Japanese researchers. In addition, the Korea-China-Japan Trilateral Research Association of Sweetpotato (TRAS) has conducted research on gene map construction and genome sequencing of the hexaploid sweetpotato Xushu 18 since 2014. The Bill & Melinda Gates Foundation launched the 'sweetpotato genomic sequencing to develop genomic tools for Sub-Sahara Africa breeding program'. The chloroplast genome sequence acquired during sweetpotato genome sequencing is used in evolutionary analyses. In this review, the trend of research in the sweetpotato genome sequencing was analyzed. Research trend analysis like this will provide researchers working toward sweetpotato productivity and nutrient improvement with information on the status of sweetpotato genome research. This will contribute to solving world food, energy and environmental problems.

Comparative Analysis of Gut Microbiota among Broiler Chickens, Pigs, and Cattle through Next-generation Sequencing (차세대염기서열 분석을 이용한 소, 돼지, 닭의 장내 미생물 군집 분석 및 비교)

  • Jeong, Ho Jin;Ha, Gwangsu;Shin, Su-Jin;Jeong, Su-Ji;Ryu, Myeong Seon;Yang, Hee-Jong;Jeong, Do-Youn
    • Journal of Life Science
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    • v.31 no.12
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    • pp.1079-1087
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    • 2021
  • To analyze gut microbiota of livestock in Korea and compare taxonomic differences, we conducted 16S rRNA metagenomic analysis through next-generation sequencing. Fecal samples from broiler chickens, pigs, and cattle were collected from domestic feedlots randomly. α-diversity results showed that significant differences in estimated species richness estimates (Chao1 and ACE, Abundance-based coverage estimators) and species richness index (OUTs, Operational taxonomic units) were identified among the three groups. However, NPShannon, Shannon, and Simpson indices revealed that abundance and evenness of the species were statistically significant only for poultry (broiler chickens) and mammals (pigs and cattle). Firmicutes was the most predominant phylum in the three groups of fecal samples. Linear discriminant (LDA) effect size (LEfSe) analysis was conducted to reveal the ranking order of abundant taxa in each of the fecal samples. A size-effect over 2.0 on the logarithmic LDA score was used as a discriminative functional biomarker. As shown by the fecal analysis at the genus level, broiler chickens were characterized by the presence of Weissella and Lactobacillus, as well as pigs were characterized by the presence of provetella and cattele were characterized by the presence of Acinetobacter. A permutational multivariate analysis of variance (PERMANOVA) showed that differences of microbial clusters among three groups were significant at the confidence level. (p=0.001). This study provides basic data that could be useful in future research on microorganisms associated with performance growth, as well as in studies on the livestock gut microbiome to increase productivity in the domestic livestock industry.

Imputation Accuracy from 770K SNP Chips to Next Generation Sequencing Data in a Hanwoo (Korean Native Cattle) Population using Minimac3 and Beagle (Minimac3와 Beagle 프로그램을 이용한 한우 770K chip 데이터에서 차세대 염기서열분석 데이터로의 결측치 대치의 정확도 분석)

  • An, Na-Rae;Son, Ju-Hwan;Park, Jong-Eun;Chai, Han-Ha;Jang, Gul-Won;Lim, Dajeong
    • Journal of Life Science
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    • v.28 no.11
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    • pp.1255-1261
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    • 2018
  • Whole genome analysis have been made possible with the development of DNA sequencing technologies and discovery of many single nucleotide polymorphisms (SNPs). Large number of SNP can be analyzed with SNP chips, since SNPs of human as well as livestock genomes are available. Among the various missing nucleotide imputation programs, Minimac3 software is suggested to be highly accurate, with a simplified workflow and relatively fast. In the present study, we used Minimac3 program to perform genomic missing value substitution 1,226 animals 770K SNP chip and imputing missing SNPs with next generation sequencing data from 311 animals. The accuracy on each chromosome was about 94~96%, and individual sample accuracy was about 92~98%. After imputation of the genotypes, SNPs with R Square ($R^2$) values for three conditions were 0.4, 0.6, and 0.8 and the percentage of SNPs were 91%, 84%, and 70% respectively. The differences in the Minor Allele Frequency gave $R^2$ values corresponding to seven intervals (0, 0.025), (0.025, 0.05), (0.05, 0.1), (0.1, 0.2), (0.2, 0.3). (0.3, 0.4) and (0.4, 0.5) of 64~88%. The total analysis time was about 12 hr. In future SNP chip studies, as the size and complexity of the genomic datasets increase, we expect that genomic imputation using Minimac3 can improve the reliability of chip data for Hanwoo discrimination.

Chronic Hereditary Tyrosinemia Type I with Novel Mutation in FAH Gene (FAH gene novel mutation을 가진 만성형 Hereditary tyrosinemia 1형)

  • Yang, Sungmin;Choi, Hyo Won;Kang, Yun Koo;Lee, Jin-Sung;Namgoong, Mee Kyung
    • Journal of The Korean Society of Inherited Metabolic disease
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    • v.20 no.2
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    • pp.55-62
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    • 2020
  • A 22-month-old girl who had taken iron supplements due to iron deficiency anemia, presented bloody mucoid stool for one month. She had a bruise at the right periorbital area due to minor trauma and hepatosplenomegaly. Laboratory studies showed anemia, thrombocytopenia, elevated alkaline phosphatase (ALP), hypophosphatemia, decreased haptoglobin, hypocomplementemia, negative direct/indirect Coomb's test, normal vitamin D3 level and high PTHi. Wrist x-ray showed no signs of rickets. The abdominal ultrasound showed only accessory spleen. Tandem mass spectrometry was normal. During follow up, bloody stool regressed after seven days of withdrawal of iron supplement and cow milk, and the total CO2 level had been within 15-20 mEq/L with normal anion gap. NGS (next generation sequencing) panel test for evaluation of renal tubular acidosis showed negative results. After low dose steroid and vitamin D supplements under the impression of hypocomplementemic vasculitis, thrombocytopenia, C3/C4, decreased haptoglobin, and elevated ALP level became normal. At 57 months of age, laboratory findings showed elevated liver enzyme, ALP and gamma-glutamyl transferase again. And liver cirrhosis with splenomegaly and diffuse renal disease were reported with abdomen CT scan. Liver biopsy reported macro- and micronodular cirrhosis. Urine organic acid profile showed elevated succinylacetone level. Whole exome sequencing revealed novel compound heterozygous mutations (NM_00137.2:c.107T>C, NM_00137, 2:c.614T>C) in FAH gene and confirmed by Sanger sequencing. Consequently, the patient was diagnosed as chronic hereditary tyrosinemia type I. She started low phenylalanine/tyrosine diet and nitisinone treatment. Our case had presented symptoms very slowly, which is the first case of chronic tyrosinemia type I in South Korea.

A Study on the Usage of Miào(廟) and Gōng(宮) in Zhou Dynasty through the Mentions to Them in the Scripture Sentences of 『Chūn-qiū(春秋)』 - In the Process of Investigating the Existence of Zhou Dynasty's System to Regulate the Number of Zōng-miào(宗廟) 【1/2】 (『춘추』 경문에서의 묘(廟)·궁(宮) 언급을 통한 주대(周代)의 그 쓰임 사례 일고찰 - 주대의 묘수제(廟數制) 실재 여부에 대한 궁구 과정에서 【1/2】-)

  • Seo, Jeong-Hwa
    • The Journal of Korean Philosophical History
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    • no.57
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    • pp.57-90
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    • 2018
  • In this discussion, as a way to verify the existence of the system to regulate Zhou dynasty's $z{\bar{o}}ng-mi{\grave{a}}o$(宗廟) numbers, the discussion was focused on '$mi{\grave{a}}o$ (廟)' and '$g{\bar{o}}ng$(宮)' in the records of "$Ch{\bar{u}}n-qi{\bar{u}}$(春秋)". As for the parts where the contents of scripture sentences were not specific, the context of the case was investigated through the writings in "$Zu{\breve{o}}-zhu{\grave{a}}n$(左傳)" and other materials. In the cases of the usage of the letter, '$mi{\grave{a}}o$(廟 : a ruler's house, a nation's royal court)', in the scripture sentences in "$Ch{\bar{u}}n-qi{\bar{u}}$(春秋)", the followings need to be noticed. In $t{\grave{a}}i-mi{\grave{a}}o$(太廟) of State $L{\check{u}}$(魯), nationwide events and a ruler's political ancestral rite, $d{\grave{i}}$(?) ritual, were performed, and fancy tools for ancestral rites used in those rituals were equipped. As for the $z{\bar{o}}ng-mi{\grave{a}}o$(宗廟) of a ruler of those times, a ritual of royal court, $ch{\acute{a}}o$(朝) rite, was performed. The usage case of the letter, '$g{\bar{o}}ng$(宮 : house)', is as the following. In $g{\bar{o}}ng$(宮) where a ruler's personal family lived was a family ancestral rite for them carried out. The record about the ornate decorating for the $hu{\acute{a}}n-g{\bar{o}}ng$ house(桓宮), which can be said to have been the political base of $s{\bar{a}}n-hu{\acute{a}}n-sh{\grave{i}}$(三桓氏), three politically noble families of State $L{\check{u}}$(魯), is outstanding. The $x{\bar{i}}-g{\bar{o}}ng$ house(西宮) during $X{\bar{i}}-g{\bar{o}}ng$(魯 僖公)'s reign and a $x{\bar{i}}n-g{\bar{o}}ng$ house(新宮 : a newly built house) destroyed by fire at the third year of $Ch{\acute{e}}ng-g{\bar{o}}ng$(魯 成公), are assumed to have been a ruler's another house, such as the $ch{\check{u}}-g{\bar{o}}ng$ house(楚宮) in which $Xi{\bar{a}}ng-g{\bar{o}}ng$(魯 襄公) used to enjoy staying, which is different from the viewpoint that it might be a $m{\acute{i}}-g{\bar{o}}ng$ shrine(?宮 : a house constructed as a shrine for the deceased father or the deceased grand father) that had been formed since Han dynasty. It has been discussed that, regarding the records that the '$w{\check{u}}-g{\bar{o}}ng$ house(武宮) was built' and that the '$y{\acute{a}}ng-g{\bar{o}}ng$ house(煬宮) was built', certain buildings were established with the symbols of '$w{\check{u}}$(武 : martial arts and force of arms)' and '$y{\acute{a}}ng$(煬 : to burn and get rid of everything)', and the events that a lord stood as its lord continued. Therefore, its main goal was not the performance of a dutiful ancestral rite by a ruler of those times for deceased rulers, for instance, $W{\check{u}}-g{\bar{o}}ng$(魯 武公) or $Y{\acute{a}}ng-g{\bar{o}}ng$(魯 煬公), but display of certain political symbolism through the ritual. This symbolism is most obvious with the $hu{\acute{a}}n-g{\bar{o}}ng$ house(桓宮) and the $x{\bar{i}}-g{\bar{o}}ng$ house(僖宮). As a consequence, all $mi{\grave{a}}os$(廟) and $g{\bar{o}}ngs$(宮) in scripture sentences had the functions of a shrine in some part, but it has been verified that they were not the buildings set up as a shrine to follow '$z{\bar{o}}ng-mi{\grave{a}}o$(宗廟)'s number regulation system' of '$ti{\bar{a}}nz{\check{i}}-7-mi{\grave{a}}o$(天子七廟 : an emperor owns seven $mi{\grave{a}}os$(廟))' or '$zh{\bar{u}}h{\acute{o}}u-5-mi{\grave{a}}o$(諸侯五廟 : a lord owns five $mi{\grave{a}}os$(廟))'.