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× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.
Highlights
The whole genome sequencing (WGS) has become a crucial tool for understanding genome structure and genetic variation
Next-generation sequencing (NGS) technology, which has been actively used over the past decade, has revolutionized the genomic research of plants as well as animals and microorganisms, which leads to a high-throughput WGS [1,2]
MinION sequencing for each library was conducted while using the standard script that was provided in the MinKNOW software
Summary
The whole genome sequencing (WGS) has become a crucial tool for understanding genome structure and genetic variation. Next-generation sequencing (NGS) technology, which has been actively used over the past decade, has revolutionized the genomic research of plants as well as animals and microorganisms, which leads to a high-throughput WGS [1,2]. Most of the existing NGS techniques typically generate short-reads (35–700 bp) and the assembled sequences from these short-reads have resulted in an occurrence of gaps. This is because short-reads are not able to span repetitive sequences longer than their length due to the limitations of assembly completeness, which thereby causes an incomplete genome assembly [1,3].
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