ONT-Based Draft Genome Assembly and Annotation of Alternaria atra

Abstract

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

Evaluation of Dragon’s Head Iranian landraces for resistance to prevalent diseases in the field and glasshouse conditions

“…Landraces normally are very genetically heterogeneous, so; are considered valuable sources of resistance to abiotic and biotic stresses to be exploited in the breeding programs (Casañas et In this study, we identi ed two distinct Alternaria species A. tenussima and A.atra attacking L.iberica which based on the pieces of literature are new for this host (Farr and Rossman, 2020). Both of them mainly are regarded as a saprophyte or as an opportunist plant pathogen (Simmons, 2007;Bonthala et al, 2021). As a plant pathogen, they show different host ranges, where 376 and 5 host plant species were infected by A.tenuissima and A. atra, respectively, and no record was observed for L.iberica (Farr and Rossman, 2020).…”

“…Alternaria spp. are mainly saprophytes but some species obtaining pathogenic capacities changed to be very successful plant pathogens(Thomma, 2003;Bonthala et al, 2021).…”

Chitosan reduces naturally occurring plant pathogenic fungi and increases nematophagous fungusPurpureocilliumunder field soil conditions

“…We also found that the abundance of Alternaria atra and Fusarium falciforme decreased in soil treated with a chitosan solution. These two fungal species cause diseases in several crops worldwide (Bonthala et al, 2021; Trolinger et al, 2017). Therefore, soil treatment with chitosan could be a sustainable alternative for managing these fungal plant pathogens.…”

Alternaria diseases on potato and tomato

“…For the A. alternata isolate Z7, which causes brown spot of citrus, a high‐quality genome is available as well (Gai et al., 2021 ). A scaffold‐level genome assembly for Alternaria atra is available for an isolate that has been collected from a wild tomato plant (Bonthala et al., 2021 ). It has 43 scaffolds and a length of 39.6 Mb.…”