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논문 기본 정보

자료유형
학술저널
저자정보
Lim, Jong-Sung (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) Choi, Beom-Soon (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) Lee, Jeong-Soo (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) Shin, Chan-Seok (Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University) Yang, Tae-Jin (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University) Rhee, Jae-Sung (Department of Chemistry, College of Natural Sciences, Hanyang University) Lee, Jae-Seong (Department of Chemistry, College of Natural Sciences, Hanyang University) Choi, Ik-Young (National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University)
저널정보
한국유전체학회 Genomics & informatics Genomics & informatics 제10권 제1호
발행연도
2012.1
수록면
1 - 8 (8page)

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Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.
#$de$ $novo$ assembly #expression profiling #multiplatform #NGS #resequencing #whole genome

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참고문헌 (41)

참고문헌 신청
Margulies M / 2005 / Genome sequencing in microfabricated high-density picolitre reactors / Nature 437:376~380 google schola Jiang Y / 2011 / A pilot study for channel catfish whole genome sequencing and de novo assembly / BMC Genomics 12:629 google schola Li J / 2012 / 6-10x pyrosequencing is a practical approach for whole prokaryote genome studies / Gene 494:57~64 google schola Cleary DF / 2012 / Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing / PLoS One 7:29380 google schola Hong PY / 2011 / Pyrosequencing-based analysis of the mucosal microbiota in healthy individuals reveals ubiquitous bacterial groups and micro-heterogeneity / PLoS One 6:25042 google schola

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