Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants
Yun Gyeong LeeChangsoo Kim

Abstract

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it 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 reading 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 used as a good reference. However, plant species have complex and large genomes when 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 for overcoming 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 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× cover...Continue Reading

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Citations

Jan 8, 2021·Plants·Alessio VallettaFrancesca Leonelli

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Datasets Mentioned

BETA
PRJNA544582

Methods Mentioned

BETA
Illumina sequencing
of DNA
electrophoresis
Ligation

Software Mentioned

Canu
MinKNOW
BWA
Mummer
Racon
BWA mem
Mosdepth
SAMtools
mummerplot
mem

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