The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternaria have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. Alternaria are supported by molecular data, whole-genome sequencing of nine Alternaria morphospecies supplemented with transcriptome sequencing of 12 Alternaria morphospecies as well as multi-gene sequencing of 168 Alternaria isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. Alternaria and from 32.0–39.1 Mb for all Alternaria genomes. The number of repetitive sequences differed significantly between the different Alternaria genomes; ranging from 1.4–16.5 %. The repeat content within sect. Alternaria was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. Alternaria isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the A. alternata reference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. Alternaria, while the percentage of SNPs found in isolates from different sections compared to the A. alternata reference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. Alternaria (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. Alternaria was tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPG and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria more effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternaria sect. Alternaria, this manuscript provides a clear and stable species classification in this section.

世界性真菌链格孢属由多种腐生和致病物种组成。根据系统发育和形态学研究，该属目前分为26个科。链格孢属。链格孢属包含大多数具有串联分生孢子的小孢子链格孢属物种，包括重要的植物、人类和采后病原体。教派内的物种。链格孢属主要是根据形态和/或宿主特异性来描述的，但它们之间的分子变异很小。调查所描述的形态种是否属于教派。链格孢得到分子数据的支持，对 9 个链格孢形态种进行了全基因组测序，辅以 12 个链格孢形态种的转录组测序，以及对 168 个链格孢分离株进行了多基因测序。组内组装的基因组大小范围为 33.3–35.2 Mb。链格孢属 (Alternaria)以及所有链格孢属(Alternaria)基因组的 32.0–39.1 Mb。不同链格孢属基因组之间重复序列的数量存在显着差异；范围为 1.4–16.5%。章节内的重复内容。链格孢属相对较低，重复率仅为 1.4-2.7%。全基因组比对揭示了不同教派之间 96.7-98.2% 的基因组同一性。链格孢分离株，相比之下，其他部分的分离株与链格孢参考基因组的基因组同一性为 85.1–89.3%。同样，1.4–2.8% 和 0.8–1。在来自该组的分离株之间的基因组和转录组序列中分别观察到 8% 的单核苷酸多态性 (SNP)。链格孢 (Alternaria) ，而与链格孢参考基因组相比，不同切片的分离株中发现的 SNP 百分比要高得多； 8.0–10.3% 和 6.1–8.5%。基于全基因组和转录组读数的系统发育树的拓扑结构与基于常用基因区域的多基因系统发育一致。根据基因组和转录组数据，提取了一组核心蛋白，并针对组内保守程度相对较低的两个基因区域设计了引物。链格孢属（保护率分别为 96.8% 和 97.3%）。他们在教派内潜在的歧视性权力。链格孢属在该科的九个常用基因区域旁边进行了测试。链格孢属，即 SSU、LSU、ITS、 gapdh 、 rpb2 、 tef1 、 Alt a 1 、 endoPG和 OPA10-2 基因区域。来自保守性相对较低的两个基因区域 KOG1058 和 KOG1077 的系统发育无法区分所描述的组内形态种。与基于链格孢属常用基因区域的系统发育相比，链格孢属更有效。基于基因组和转录组比较以及分子系统发育，链格孢属（ Alternaria sect）。链格孢属仅由 11 个系统发育物种和一个物种复合体组成。无法根据多基因系统发育来区分的 35 个形态种在A. alternata下同义。 为链格孢属系统发育物种的命名和鉴定提供指南。链格孢属，本手稿在本节中提供了清晰且稳定的物种分类。