Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

Abstract

Summary The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines worldwide. A conditionally dispensable chromosome (CDC), which harbours the host‐selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we isolated and sequenced the CDCs of the A. alternata Z7 strain and analysed the function and evolution of their genes. The A. alternata Z7 strain has two CDCs (~1.1 and ~0.8 Mb, respectively), and the longer Z7 CDC contains all but one contig of the shorter one. Z7 CDCs contain 254 predicted protein‐coding genes, which are enriched in functional categories associated with ‘metabolic process’ (55 genes, P = 0.037). Relatively few of the CDC genes can be classified as carbohydrate‐active enzymes (CAZymes) (4) and transporters (19) and none as kinases. Evolutionary analysis of the 254 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes, likely due to fewer selective constraints. Interestingly, phylogenetic analysis suggested that four of the 25 genes responsible for the ACT toxin production were likely transferred from Colletotrichum (Sordariomycetes). Functional experiments showed that two of them are essential for the virulence of the tangerine pathotype of A. alternata. These results provide new insights into the function and evolution of CDC genes in Alternaria.

Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit

“…OrthoMCL 16 was used to explore single-copy homologous proteins by retrieving the protein data of eight genomes, including A. alternata (Y784-BC03), A. alternata SRC1lrK2f (GCA_001642055.1) isolated from effluent of coal mine drainage ( Zeiner et al, 2016 ), A. alternata Z7 (GCA_001572055.1) isolated from tangerine ( Wang et al, 2019 ), A. tenuissima FERA_1177 (GCA_004154755.1) and A. tenuissima FERA 1164 (GCA_004156015.1) from apple, A. tenuissima FERA 23450 (GCA_004154735.1), A. arborescens RGR 97.0013 (GCA_004155955.1), and A. arborescens strain RGR 97.0016 (GCA_004154815.1; Supplementary Table S1 ; Armitage et al, 2020 ). Single-copy orthologous genes shared by all eight genomes were further aligned using MUSCLE (version 3.8.31; Edgar, 2010 ).…”

Histone acetyltransferases and deacetylases are required for virulence, conidiation, DNA damage repair, and multiple stresses resistance of Alternaria alternata

“…The transcription of all ACT toxin synthesis-related genes did not change significantly in ΔGcn5 and ΔHos2 compared to wild-type. However, AALT_g11758 (CYP450), located in the ACT toxin gene cluster and required for pathogenicity but plays no role for ACT toxin synthesis (50), was significantly down-regulated in both ΔGcn5 (FC = -25) and ΔHos2 (FC = -6).…”

Critical Role of MetR/MetB/MetC/MetX in Cysteine and Methionine Metabolism, Fungal Development, and Virulence of Alternaria alternata

“…In contrast, the rough lemon pathotype is known to produce ACRL ( A lternaria c itri r ough l emon) toxin, which is toxic to rough lemon but not tangerine ( 2 – 4 ). The pathogenicity of A. alternata tangerine pathotype mainly relies on the host-selective ACT toxin, which is regulated by multiple copies of ACTT gene clusters located on less than 2.0 Mb of conditionally dispensable chromosome (CDC) ( 5 , 6 ). Intriguingly, genetic inactivation of any ACTT gene will block the biosynthesis of ACT toxin and lead to complete loss of pathogenicity but will not affect fungal growth and conidiation ( 5 – 7 ).…”

“…The pathogenicity of A. alternata tangerine pathotype mainly relies on the host-selective ACT toxin, which is regulated by multiple copies of ACTT gene clusters located on less than 2.0 Mb of conditionally dispensable chromosome (CDC) ( 5 , 6 ). Intriguingly, genetic inactivation of any ACTT gene will block the biosynthesis of ACT toxin and lead to complete loss of pathogenicity but will not affect fungal growth and conidiation ( 5 – 7 ). In addition to HST biosynthesis, the ability to detoxify host-generating reactive oxygen species (ROS) regulated by AaYap1 , AaHog1 , and AaSsn7 is essential for the full virulence of A. alternata ( 8 – 11 ).…”