Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain.
URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.
BMC Genomics. 2017 Nov 16;18(1):883. doi: 10.1186/s12864-017-4243-z.
Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size.
In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years.
Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species.
Olivaceous Coniophora 是担子菌门的一种蕈类真菌，属于 Boletales 目，可导致针叶树枯木腐朽。Boletales 目包含了一个多样化的物种群体，包括腐生菌和外生菌根真菌，它们在基因组大小方面表现出重要的差异。
本研究报告了 Olivaceous Coniophora 的 39.07 兆碱基（Mb）基因组草图组装和注释。共注释了 14928 个基因，其中包括 470 个可能分泌的蛋白，这些蛋白富含木质纤维素降解功能。通过相似性聚类和蛋白质结构预测，我们鉴定了一个新的 10 个推定的溶菌多糖单加氧酶基因家族。这个家族在担子菌中是保守的，并且缺乏以前的功能注释。进一步的分析表明，Olivaceous Coniophora 具有低重复的基因组，重复序列为 2.91%，转座元件（TEs）含量有限。在四个相关的 Boletales 中对 TEs 的注释显示，重复序列含量存在重要差异，范围从基因组大小的 3.94%到 41.17%。LTR 反转录转座子插入年龄的分布表明，这些重复元件的差异扩张塑造了 Boletales 过去 6000 万年的基因组结构。
Olivaceous Coniophora 具有一个小而紧凑的基因组，与 Coniophora puteana 具有宏观同线性。功能注释揭示了典型褐腐的酶学特征。转座元件的注释和比较基因组学揭示了它们在 Coniophora 属中的特殊收缩，突出了它们在 Boletales 物种中发现的差异基因组扩张中的作用。
