Whole-Genome Resequencing and Evolutionary Analysis of Wild Morel Mushroom <i>Morchella</i> sp.

Morels (<i>Morchella</i> sp.) are important edible fungi cultivated mainly in China. Although the relevant culture technology for <i>Morchella</i> is now fundamentally mature, it is limited to the Elata and Rufobrunnea clades, and the artificial culture technology for the Esculenta clade, which also has economic value, has not been extensively studied. In this study, we selected a wild morel belonging to the Esculenta clade as the research material and performed de novo sequencing and assembly of the <i>Morchella</i> sp. (<i>Mosp</i>) genome using second- and third-generation sequencing. The whole-genome size of <i>Mosp</i> was 55.17 Mb with a contig N50 of 1.89 Mb, and the GC content was 47.49%. A total of 10,896 protein-coding genes were identified. The non-coding RNA prediction results showed that there were 329 tRNAs, 65 rRNAs, and 37 snRNAs in the <i>Mosp</i> genome. The functional annotation of the <i>Mosp</i> genes showed that most of the genes were related to the reproductive and metabolic processes of the cells and participated in nutrient digestion, absorption, utilization, and catabolism in morels. There was a high degree of repetition (21.58%) in the <i>Mosp</i> genome, and the sizes of the DNA transposons and the long terminal repeats were 0.55 Mb and 5.85 Mb, respectively. The phylogeny analysis showed that <i>Mosp</i> clusters together with four other <i>Morchella</i> species: <i>Morchella importuna</i>, <i>Morchella conica</i>, <i>Morchella sextelata</i>, and <i>Morchella snyderi</i>. Molecular dating indicated that the differentiation of <i>Mosp</i> and the black morels group occurred about 147.0 million years ago (MYA). In addition, the evolutionary analysis showed that 296 gene families were contracted and 96 gene families were expanded in <i>Mosp</i> versus the related morel species. The results of this study provide new insights into the genome evolution of <i>Mosp</i> and lay the foundation for future in-depth research into the molecular biology and breeding of the genus <i>Morchella</i>.