Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden.
Present Address: National Food Agency, P.O. Box 622, 75126, Uppsala, Sweden.
BMC Genomics. 2018 Jan 3;19(1):14. doi: 10.1186/s12864-017-4407-x.
Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.
The draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1-1-1 and MAT1-2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.
The established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.
芸薹属植物受到多种病原体的攻击；其中，具有土壤传播方式的病原体变得越来越重要。由长蠕孢菌引起的黄萎病就是一个例子。这种真菌物种被认为是杂交起源的，其基因组由命名为 A 和 D 的谱系组合组成。在这项研究中，我们报告了使用 Illumina 技术测序的 2 个长蠕孢菌田间分离株的基因组草案。进行了基因组特征和谱系组成的分析，以及选择基因分析，以促进对其基因组特征和潜在效应物类别的理解。
2 个长蠕孢菌单孢子分离株（VL1 和 VL2）的基因组草案估计无缺口大小约为 70Mb。在 VL1 中鉴定出的编码蛋白质基因总数为 20793 个，而在 VL2 中预测了 21072 个基因模型。预测的基因组大小、基因含量，包括编码碳水化合物活性酶的基因家族，几乎是长蠕孢菌和白腐菌的两倍。单核苷酸多态性（SNP）在两个基因组中频繁分布，但杂合性和深度的分布并不独立。对潜在亲本谱系的进一步分析表明，长蠕孢菌基因组由两部分组成，A1 和 D1，其中 A1 比亲本谱系基因组 D1 更古老，后者与长蠕孢菌更接近。在长蠕孢菌基因组中证实了交配型基因 MAT1-1-1 和 MAT1-2-1 的存在。然而，长蠕孢菌、白腐菌和长蠕孢菌中的 MAT 基因在核苷酸上经历了广泛的变化，至少部分解释了这些真菌物种目前的无性性质。
与其他研究的子囊菌相比，建立的长蠕孢菌基因组草案相对较大。因此，在两个长蠕孢菌基因组中预测了大量基因，其中包括许多分泌蛋白和碳水化合物活性酶（CAZy）编码基因。基因组由两部分组成，其中一个谱系比与长蠕孢菌更接近的部分更古老。鉴定出不同的交配型序列表明可能发生了古老的杂交事件。
