Journalartikel

Jahr der Veröffentlichung: 2021

Seiten: 240-250

Zeitschrift: Plant Biotechnology Journal

Bandnummer: 19

Heftnummer: 2

ISSN: 1467-7644

eISSN: 1467-7652

Open Access Status: Gold

DOI Link: https://doi.org/10.1111/pbi.13456

Verlag: Wiley

Abstract: 
Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single-nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small- (30-10 000 bp) to mid-scale (10 000-30 000 bp) SV and their impact on evolution and adaptation-related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here, we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small- to mid-scale SV in a major allopolyploid crop species,Brassica napus. We found that up to 10% of all genes were affected by small- to mid-scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short-read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

Harvard-Zitierstil: Chawla, H., Lee, H., Gabur, I., Vollrath, P., Tamilselvan-Nattar-Amutha, S., Obermeier, C., et al. (2021) Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant, Plant Biotechnology Journal, 19(2), pp. 240-250. https://doi.org/10.1111/pbi.13456

APA-Zitierstil: Chawla, H., Lee, H., Gabur, I., Vollrath, P., Tamilselvan-Nattar-Amutha, S., Obermeier, C., Schiessl, S., Song, J., Liu, K., Guo, L., Parkin, I., & Snowdon, R. (2021). Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant. Plant Biotechnology Journal. 19(2), 240-250. https://doi.org/10.1111/pbi.13456