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Chromium sequencing: The doors open for genomics of obligate plant pathogens

McTaggart, A. R., Duong, T. A., Le, V. Q., Shuey, L. S., Smidt, W., Naidoo, S., Wingfield, M. J. and Wingfield, B. D. (2018) Chromium sequencing: The doors open for genomics of obligate plant pathogens. BioTechniques, 65 (5). pp. 253-257. ISSN 07366205 (ISSN)

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Article Link(s): https://doi.org/10.2144/btn-2018-0019

Abstract

It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor. © 2018 Future Science. All rights reserved.

Item Type:Article
Business groups:Horticulture and Forestry Science
Additional Information:Open access
Keywords:Chromium 10X Fungal genomes Myrtle rust Rust fungi chromium fungal DNA Basidiomycetes chemistry DNA sequence fungal genome gene library genetics genomics microbiology Myrtaceae plant disease procedures Basidiomycota DNA, Fungal Genome, Fungal Plant Diseases Sequence Analysis, DNA
Subjects:Science > Botany > Genetics
Plant pests and diseases > Plant pathology
Forestry > Research. Experimentation
Deposited On:09 Mar 2021 03:48
Last Modified:09 Mar 2021 03:48

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