기본 정보
연구 분야
프로젝트
논문
구성원
preprint|
green
·인용수 4
·2019
Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology
Yun Gyeong Lee, Sang Chul Choi, Yuna Kang, Kyeong Min Kim, Chon-Sik Kang, Changsoo Kim
Preprints.org
초록

The whole genome sequencing (WGS) has become a crucial tool to understand genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on read length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be be used as a good reference. However, plant species have complex and large genomes compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool to overcome the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 using the MinION platform and obtained 895,678 reads and 17.9 gigabytes(Gb) (ca. 25X coverage of reference) from long-read sequence data. Through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome, a total of 6,124 contigs (covering 45.9%) were generated from Canu, and a total of 2,661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon pipeline. Our results provide a pipeline of long-read sequencing analysis for plant species using the MinION platform and a clue to determine the total sequencing scale for optimal coverage based on various genome sizes.

키워드
MinionNanopore sequencingContigGenomeHybrid genome assemblyReference genomeSequence assemblyBiologyWhole genome sequencingDNA sequencing
타입
preprint
IF / 인용수
- / 4
게재 연도
2019

주식회사 디써클

대표 장재우,이윤구서울특별시 강남구 역삼로 169, 명우빌딩 2층 (TIPS타운 S2)대표 전화 0507-1312-6417이메일 info@rndcircle.io사업자등록번호 458-87-03380호스팅제공자 구글 클라우드 플랫폼(GCP)

© 2026 RnDcircle. All Rights Reserved.