Genome Resources of Four Distinct Pathogenic Races Within Fusarium oxysporum f. sp. vasinfectum that Cause Vascular Wilt Disease of Cotton

Abstract

Whole Genome Sequence (WGS) based identifications are being increasingly used by regulatory and public health agencies to facilitate the detection, investigation, and control of pathogens and pests. Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant vascular wilt pathogen of cultivated cotton, and consists of several pathogenic races that are not each other’s closest phylogenetic relatives. We have developed WGS assemblies for isolates of race 1 (FOV1), race 4 (FOV4), race 5 (FOV5), and race 8 (FOV8) using a combination of Nanopore (MinION) and Illumina sequencing technology (Mi-Seq). This resulted in assembled contigs with more than 100X coverage for each of the FOV races and estimated genome sizes of FOV1 52 Mb, FOV4 68 Mb, FOV5 68 Mb and FOV8 55 Mb. The AUGUSTUS gene prediction program predicted 16,263 genes in FOV1, 20,259 genes in FOV4, 20,375 genes in FOV5 and 16,615 genes in FOV8. We were able to identify 525 genes unique to FOV1, 570 unique to FOV4, 1242 unique to FOV5 and 383 unique to FOV8. We expect that these findings will help in comparative genomics, and in the identification of unique genes as candidate targets for diagnostic marker and methods development to permit rapid differentiation of FOV subgroups.

The impact of pRAP vectors on plant genetic transformation and pathogenesis studies including an analysis of BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-mediated resistance

“…vasinfectum race 4 (FOV4) has become a major threat to cotton production. Recent studies have been undertaken to understand its epidemiology and identify resistance (Ulloa et al 2013;Wang et al 2018a;Abdelraheem et al 2020;Srivastava et al 2021). The transgenic analysis of charcoal rot presented by Lawaju et al (2018), through the use of the pRAP plasmids, provides a model for understanding and developing resistance for FOV4.…”

Studies of evaluation parameters for resistance to Fusarium wilt in cotton caused by Fusarium wilt race 4 (Fusarium oxysporumf. sp.vasinfectum)

“…After FOV4 was recently identified in far‐west Texas (Bell et al., 2019; Halpern et al., 2018; Zhu et al., 2019) and southern New Mexico (Zhang, Zhu et al., 2020; Zhu et al., 2020, Zhu, Abdelraheem, Lujan et al., 2021), research efforts have intensified. Studies include FOV4 identification and molecular characterization (Bell et al., 2019; Diaz et al., 2021; Liu & Wagner, 2022; Zhu et al., 2019; Zhu, Abdelraheem, Wheeler et al., 2021), genome sequencing of FOV4 (Seo et al., 2020; Srivastava et al., 2021), resistance evaluation methods (Parris et al., 2021; Zhang, Abdelraheem, Zhu, Wheeler, Dever, Nichols, & Wedegaertner, 2021), large scale germplasm screening for FOV4 resistance in the greenhouse (Zhang, Abdelraheem, Zhu, Wheeler, Dever, Frelichowski et al., 2020; Zhang, Abdelraheem, Zhu, Wheeler, Dever, Elkins‐Arce et al., 2020) and field (Zhang, Abdelraheem, Zhu, Wheeler, Dever, Elkins‐Arce et al., 2020), defense differences (Puckhaber et al., 2018), quantitative trait locus (QTL) mapping for FOV4 resistance (Abdelraheem, Elassbli et al., 2020; Zhu et al., unpublished data, 2022), and selection of cotton for FOV4 resistance in breeding programs (Ulloa et al., 2021; Zhang, Abdelraheem, Zhu, Wheeler, Dever, Elkins‐Arce et al., 2020). In collective efforts between New Mexico and Texas public researchers, we have screened numerous cotton germplasm lines for FOV4 resistance (Abdelraheem et al., 2021b; Zhang, Abdelraheem, Zhu, Wheeler, Dever, Frelichowski et al., 2020; Zhang, Abdelraheem, Zhu, Wheeler, Dever, Yu et al., 2021), studied the quantitative genetic basis of FOV4 resistance in a set of Pima cotton genotypes (Abdelraheem et al., 2021a), mapped QTL for FOV4 resistance (Abdelraheem, Wedegaertner et al., 2020; Zhang, Abdelraheem, Ma et al., 2022; Zhu et al., unpublished data, 2022), compared infection processes in the cotton root between susceptible and resistant Pima lines (Zhu et al., 2022), estimated experimental errors in the field (Zhang, Zhu, Abdelraheem et al., 2021), and investigated the effects of cotton cultivar and growth stage, root wounding, planting date, inoculum density, and temperature on the FOV4‐associated disease development (Zhang, Abdelraheem, Zhu, Wheeler, Dever, Nichols, & Wedegaertner, 2021; Zhang, Abdelraheem, Zhu et al., 2022; Zhu, Abdelraheem, Wheeler et al., 2021).…”

Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

“…We downloaded 490 nucleotide assemblies of FOSC publicly available on GenBank (including genomes from these studies: Ma et al 2010 , Thatcher et al 2012 , Guo et al 2014 , Kitts et al 2016 , Pu et al 2016 , van Dam et al 2016 , Williams et al 2016 , Singh et al 2017 , van Dam & Rep 2017 , Armitage et al 2018 , Ayhan et al 2018 , Lv et al 2018 , Urbaniak et al 2018 , Asai et al 2019 , Gebru et al 2019 , Henry et al 2019 , Seo et al 2019 , Taylor et al 2019 , Urbaniak et al 2019 , Achari et al 2020 , Batson et al 2020 , Fokkens et al 2020 , Henry et al 2020 , Hudson et al 2020 , Kanapin et al 2020 , Khayi et al 2020 , Kim et al 2020 , Krasnov et al 2020 , Li et al 2020 , Srivastava et al 2020 , Thangavelu et al 2020 , Wang et al 2020 , Yu et al 2020 , Zhang et al 2020 , Henry et al 2021 , Chang & Cook unpublished). Genes were predicted in Augustus using a model of F. graminearum ( Stanke & Morgenstern 2005 ).…”