Phylogenomic analyses of Alternaria section Alternaria: A high-resolution, genome-wide study of lineage sorting and gene tree discordance

Abstract

The genus Alternaria contains a diversity of saprobic and pathogenic species that can be found in a wide range of environments. Alternaria is currently divided into 26 subgeneric sections, and the "small-spored" Alternaria section Alternaria includes many species that are economically important agricultural pathogens. Recognizing that a stable framework for systematics and species identification is essential for management and regulation purposes, this section has experienced much taxonomic debate and systematic revision in recent years. Molecular phylogenetic studies have challenged the reliability of using morphological characteristics to differentiate Alternaria species but have also suggested that commonly used molecular markers for fungal phylogenetics may not be sufficiently informative at this taxonomic level. To allow the assessment of molecular variation and evolutionary history at a genome-wide scale, we present an overview and analysis of phylogenomic resources for Alternaria section Alternaria. We review the currently available genomic resources and report five newly sequenced genomes. We then perform multiple comparative genomic analyses, including macrosynteny assessment and inference of phylogenetic relationships using a variety of data sets and analysis methods. Fine-scale, genome-wide phylogenetic reconstruction revealed incomplete lineage sorting and the genomic distribution of gene/species tree discordance. Based on these patterns, we propose a list of candidate genes that may be developed into informative markers that are diagnostic for the main lineages. This overview identifies gaps in knowledge and can guide future genome sequencing efforts for this important group of plant pathogenic fungi.

Untargeted metabolomics screening reveals unique secondary metabolite production from Alternaria section Alternaria

“…NCBI accession numbers for the newly generated assemblies are as follows: DET2035 = JAERPI000000000; KAS5321 = JAERNY000000000; KAS5743 = JAERND000000000. The resulting assemblies had an average sequence coverage of 125X and quality statistics were similar to previous Alternaria assemblies (Dettman & Eggertson 2021). The genome sizes ranged from 33.0 to 34.1 Mb, with a mean N50 of 897.8 Kb, and BUSCO analyses indicated the assemblies were over 99% complete (for whole-genome assembly statistics refer to Supplementary Section 7).…”

“…Strains were grown on potato dextrose agar (PDA) plates at 25°C for 14 days. Genomic DNA extraction and short-read sequencing were performed as described in Dettman & Eggertson (2021) . In brief, genomic DNA samples were sheared to approximately 350 bp fragment lengths using a Covaris M220 sonicator (Covaris, Massachusetts), PCR-free libraries were constructed with a NxSeq AmpFREE Low DNA Library Kit (Lucigen, Wisconsin) and sequenced with paired-end reads (2 × 150bp) on a Illumina NextSeq500 instrument (Illumina, California) using a NextSeq High Output Reagent Kit.…”

“…Genome assembly from short-read data was performed as described in Dettman & Eggertson (2021) . In brief, raw reads were clipped of adapters and quality trimmed with TRIMMOMATIC (0.38, Bolger et al, 2014 ) and assembled with SPADES (3.12, Bankevich et al, 2012 ).…”

“…Gene prediction and annotation were performed using FUNANNOTATE (1.8.7; https://github.com/nextgenusfs/funannotate ; Palmer and Stajich., 2020 ) with methods described in Dettman and Eggertson, 2021 . A modification made here was that evidence from SNAP and CodingQuarry were excluded during the EvidenceModeler step.…”

“…Chromosome 8 was identified via whole chromosome alignments against the A. solani NL03003 genome assembly, performed with progressiveMAUVE (2.4; Darling et al, 2004). funannotate; Palmer and Stajich., 2020) with methods described in Dettman and Eggertson, 2021. A modification made here was that evidence from SNAP and CodingQuarry were excluded during the EvidenceModeler step.…”