Chromium Sequencing: The Doors Open for Genomics of Obligate Plant Pathogens

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.

Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia vastatrix)

“…However, due to the complexity of these obligate plant pathogen genomes [15], there are only 24 genomic assemblies reported so far in the NCBI database. These genomes are part of Pucciniales order, and include Melampsora larici-populina (101 Mb), Puccinia graminis (89 Mb) [18], Puccinia triticina (~106 Mb) [19], Puccinia striiformis (~88 Mb) [20], and Austropuccinia psidii (1.2 Gb) [21], among others. For coffee leaf rust, there are two draft genome assemblies, one with a length of 201 Mb, released in 2014 [22], and the other with an assembly length of 543 Mb, as published in 2019 [23].…”

“…As a consequence, although there are studies at the RAD sequencing level [16,17], to date, only 19 genome assemblies (at the scaffold level (https:// www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=5258&utm_source=data-hub, accessed at 19 January 2022)) from these plant pathogens have been reported. These genome assemblies include: Melampsora larici-populina (101 Mb), Puccinia graminis (89 Mb) [18], Puccinia triticina (~106 Mb) [19], Puccinia striiformis (~88 Mb) [20], and Austropuccinia psidii (1.2 Gb), the largest assembled fungal genome to date [21]. For coffee leaf rust, there are currently two draft genome assemblies, one with a length of 201 Mb, released in 2014 [22], and the other with an assembly length of 543 Mb, as published in 2019 [23].…”

Exogenous double‐stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta

“…Published genomes of A. psidii (McTaggart et al, 2018 ), Cronartium quercuum f. sp. fusiforme (Coleosporiaceae) (Pendleton et al, 2014 ), H. vastatrix (Zaghouaniaceae) (Cristancho et al, 2014 ), Melampsora larici‐populina (Melampsoraceae) (Duplessis et al, 2011 ), Puccinia coronata f. sp.…”

Fungal genomes enhance our understanding of the pathogens affecting trees cultivated in Southern Hemisphere plantations

“…The genome size of most fungi falls within the 30-40 million bases (Mb) size range. However, genome sizes range from two to 1 200 Mb (Aylward et al 2017;McTaggart et al 2018), with the largest to date being that of the myrtle rust pathogen Austropuccinia psidii (McTaggart et al 2018). The average genome size of plant pathogenic Basidiomycota (53.7 Mb) is much larger than that of plant pathogenic Ascomycota (39.4 Mb) (Aylward et al 2017).…”

“…Compared to other genera in this family of fungi, Ceratocystis species have many more MGEs in their genomes (Fourie et al 2019) and they have most likely played an important role in the evolution of the MAT1 locus and the chromosome that harbours the locus in these fungi (Simpson et al 2018). Another interesting example is found in the myrtle rust pathogen A. psidii, which has been shown to be unusually large for a fungal genome (Tan et al 2014;McTaggart et al 2018). Some of the increase in genome size has been attributed to an enrichment of TEs (Tan et al 2014).…”