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논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 발행연도
- 2017.1
- 수록면
- 128 - 135 (8page)
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As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.
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참고문헌 (33)
참고문헌 신청
Pierre Comizzoli / 2016 / Implications of the Nagoya Protocol for genome resource banks composed of biomaterials from rare and endangered species / Reproduction, Fertility and Development 28(8):1145
Schindel DE / 2014 / Biodiversity: reap the benefits of the Nagoya Protocol / Nature 515:37
Burton JN / 2013 / Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions / Nat Biotechnol 31:1119~1125
Muggli MD / 2015 / Misassembly detection using paired-end sequence reads and optical mapping data / Bioinformatics 31:i80~i88
Phillippy AM / 2008 / Genome assembly forensics:finding the elusive mis-assembly / Genome Biol 9:R55
Schindel DE / 2014 / Biodiversity: reap the benefits of the Nagoya Protocol / Nature 515:37
Burton JN / 2013 / Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions / Nat Biotechnol 31:1119~1125
Muggli MD / 2015 / Misassembly detection using paired-end sequence reads and optical mapping data / Bioinformatics 31:i80~i88
Phillippy AM / 2008 / Genome assembly forensics:finding the elusive mis-assembly / Genome Biol 9:R55
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