Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N₅₀ of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.

Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

由链格孢引起的链格孢褐斑病（ABS）是世界范围内柑橘属重要的经济真菌病害。ABS 病原体A. alternata tangerine 病理型可产生宿主特异性 ACT 毒素，该毒素受位于条件可有可无的染色体 (CDC) 中的 ACT 毒素基因簇调控。以前，我们已经组装了A. alternata tangerine 致病型菌株 Z7 的基因组草图，其中包含 165 个重叠群。在这项研究中，我们通过牛津纳米孔测序和 Illumina 测序技术的结合报告了A. alternata Z7的染色体水平基因组组装。A. alternata Z7的组装总大小为 34.28 Mb，GC 含量为 51.01%，contig N_{50 个}，共 3.08 Mb。基因组包含 12,067 个蛋白质编码基因、34 个核糖体 RNA 和 107 个转移 RNA。有趣的是，A. alternata Z7由10条必需染色体和2条CDCs组成，这与脉冲场凝胶电泳的实验证据一致。据我们所知，这是A. alternata的第一次染色体水平基因组组装。此外，还建立了柑橘相关链格孢基因组数据库，为链格孢属的序列、注释和比较基因组数据提供公共资源。在染色体水平上改进的基因组序列和注释是朝着更好地了解致病性的重要一步。A. 交替。每当新分离的链格孢属的基因组出现时，该数据库将定期更新。可用。柑橘相关链格孢基因组数据库可通过柑橘真菌病数据库开放访问。

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