State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
Nanjing Forestry University, Nanjing, China.
Genome Biol Evol. 2021 Mar 1;13(3). doi: 10.1093/gbe/evab026.
The novel DSE Laburnicola rhizohalophila (Pleosporales, Ascomycota) is frequently found in the halophytic seepweed (Suaeda salsa). In this article, we report a near-chromosome-level hybrid assembly of this fungus using a combination of short-read Illumina data to polish assemblies generated from long-read Nanopore data. The reference genome for L. rhizohalophila was assembled into 26 scaffolds with a total length of 64.0 Mb and a N50 length of 3.15 Mb. Of them, 17 scaffolds approached the length of intact chromosomes, and 5 had telomeres at one end only. A total of 10,891 gene models were predicted. Intriguingly, 27.5 Mb of repeat sequences that accounted for 42.97% of the genome was identified, and long terminal repeat retrotransposons were the most frequent known transposable elements, indicating that transposable element proliferation contributes to its increased genome size. BUSCO analyses using the Fungi_odb10 data set showed that 95.0% of genes were complete. In addition, 292 carbohydrate active enzymes, 33 secondary metabolite clusters, and 84 putative effectors were identified in silico. The resulting high-quality assembly and genome features are not only an important resource for further research on understanding the mechanism of root-fungi symbiotic interactions but will also contribute to comparative analyses of genome biology and evolution within Pleosporalean species.
新型 DSE 植物内生放线菌（Laburnicola rhizohalophila）（ Pleosporales，子囊菌门）常存在于盐生植物獐毛（Suaeda salsa）中。在本文中，我们报道了一种使用短读 Illumina 数据与长读 Nanopore 数据相结合的方法对该真菌进行近染色体水平的混合组装。L. rhizohalophila 的参考基因组被组装成 26 个支架，总长度为 64.0Mb，N50 长度为 3.15Mb。其中 17 个支架接近完整染色体的长度，5 个支架只有一端有端粒。总共预测了 10891 个基因模型。有趣的是，鉴定出了 27.5Mb 的重复序列，占基因组的 42.97%，长末端重复反转录转座子是最常见的已知转座元件，表明转座元件的增殖导致了其基因组大小的增加。使用 Fungi_odb10 数据集进行 BUSCO 分析表明，95.0%的基因是完整的。此外，还在计算机上鉴定出了 292 个碳水化合物活性酶、33 个次级代谢物簇和 84 个推测的效应物。所得的高质量组装和基因组特征不仅是进一步研究理解根菌共生相互作用机制的重要资源，而且将有助于 Pleosporalean 物种内的基因组生物学和进化的比较分析。
