The Hypoxylaceae (Xylariales, Ascomycota) is a diverse family of mainly saprotrophic fungi, which commonly occur in angiosperm-dominated forests around the world. Despite their importance in forest and plant ecology as well as a prolific source of secondary metabolites and enzymes, genome sequences of related taxa are scarce and usually derived from environmental isolates. To address this lack of knowledge thirteen taxonomically well-defined representatives of the family and one member of the closely related Xylariaceae were genome sequenced using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing. The workflow leads to high quality draft genome sequences with an average N50 of 3.0 Mbp. A backbone phylogenomic tree was calculated based on the amino acid sequences of 4912 core genes reflecting the current accepted taxonomic concept of the Hypoxylaceae. A Percentage of Conserved Proteins (POCP) analysis revealed that 70% of the proteins are conserved within the family, a value with potential application for the definition of family boundaries within the order Xylariales. Also, Hypomontagnella spongiphila is proposed as a new marine derived lineage of Hypom. monticulosa based on in-depth genomic comparison and morphological differences of the cultures. The results showed that both species share 95% of their genes corresponding to more than 700 strain-specific proteins. This difference is not reflected by standard taxonomic assessments (morphology of sexual and asexual morph, chemotaxonomy, phylogeny), preventing species delimitation based on traditional concepts. Genetic changes are likely to be the result of environmental adaptations and selective pressure, the driving force of speciation. These data provide an important starting point for the establishment of a stable phylogeny of the Xylariales; they enable studies on evolution, ecological behavior and biosynthesis of natural products; and they significantly advance the taxonomy of fungi.

hyperoxylaceae（Xylariales，Ascomycota）是一个主要由腐生真菌组成的多样化家族，常见于世界被子植物为主的森林中。尽管它们在森林和植物生态学中非常重要，并且是次级代谢产物和酶的丰富来源，但相关分类单元的基因组序列却很少，通常来自环境分离株。为了解决这一知识匮乏的问题，使用Illumina和Oxford纳米孔技术或PacBio测序技术对13个生物分类学定义明确的家族代表和近缘木糖科的一名成员进行了基因组测序。该工作流程可产生高质量的基因组草图序列，平均N50为3.0 Mbp。基于反映当前公认的hypoxylaceae概念的4912个核心基因的氨基酸序列，计算了骨架系统树。保守蛋白百分比（POCP）分析显示，该家族中70％的蛋白是保守的，该值在Xylariales家族中定义家族边界具有潜在价值。也，海绵状小单胞菌被建议作为一种新的海洋来源的Hypom血统。蒙提科洛萨基于深入的基因组比较和培养物的形态差异。结果表明，这两个物种共享其基因的95％，对应于700多个菌株特异性蛋白质。标准分类学评估（有性和无性形态，化学分类学，系统发育）没有反映出这种差异，从而防止了基于传统概念的物种划界。遗传变化可能是环境适应和选择压力（物种形成的驱动力）的结果。这些数据为建立木糖稳定的系统发育提供了重要的起点。它们使人们能够研究天然产物的进化，生态行为和生物合成；他们大大提高了真菌的分类学。