Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia.
Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkab006.
Ascochyta lentis causes ascochyta blight in lentil (Lens culinaris Medik.) and yield loss can be as high as 50%. With careful agronomic management practices, fungicide use, and advances in breeding resistant lentil varieties, disease severity and impact to farmers have been largely controlled. However, evidence from major lentil producing countries, Canada and Australia, suggests that A. lentis isolates can change their virulence profile and level of aggressiveness over time and under different selection pressures. In this paper, we describe the first genome assembly for A. lentis for the Australian isolate Al4, through the integration of data from Illumina and PacBio SMRT sequencing. The Al4 reference genome assembly is almost 42 Mb in size and encodes 11,638 predicted genes. The Al4 genome comprises 21 full-length and gapless chromosomal contigs and two partial chromosome contigs each with one telomere. We predicted 31 secondary metabolite clusters, and 38 putative protein effectors, many of which were classified as having an unknown function. Comparison of A. lentis genome features with the recently published reference assembly for closely related A. rabiei show that genome synteny between these species is highly conserved. However, there are several translocations and inversions of genome sequence. The location of secondary metabolite clusters near transposable element and repeat-rich genomic regions was common for A. lentis as has been reported for other fungal plant pathogens.
长喙壳菌（Ascochyta lentis）引起菜豆（Lens culinaris Medik.）的长喙壳叶斑病，减产可达 50%。通过精细的农业管理措施、杀菌剂的使用以及培育抗菜豆品种的进展，已经在很大程度上控制了病害的严重程度和对农民的影响。然而，来自加拿大和澳大利亚这两个主要的菜豆生产国的证据表明，A. lentis 分离株的毒力谱和侵袭力会随时间和不同的选择压力而发生变化。本文描述了第一个通过整合 Illumina 和 PacBio SMRT 测序数据得到的澳大利亚分离株 Al4 的长喙壳菌基因组组装。Al4 参考基因组组装大小接近 42Mb，编码 11638 个预测基因。Al4 基因组由 21 个全长无缺口的染色体连续体和两个各有一个端粒的部分染色体连续体组成。我们预测了 31 个次生代谢物簇和 38 个可能的蛋白效应子，其中许多被归类为具有未知功能。与最近发表的密切相关的长喙壳菌 A. rabiei 的参考基因组组装相比，A. lentis 的基因组特征表明这些物种之间的基因组同线性高度保守。然而，也有几个基因组序列的易位和倒位。次生代谢物簇位于转座子和重复丰富的基因组区域附近的位置，这在 A. lentis 中很常见，也有报道称其他真菌植物病原体中也存在这种情况。
