Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species.

Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.

Insights into identifying resistance genes for cold and disease stresses through chromosome-level reference genome analyses of Poncirus polyandra.

Poncirus polyandra, a plant species with extremely small populations in China, has become extinct in the wild. This study aimed to identify functional genes that improve tolerance to abiotic and biotic stresses. Here, we present a high-quality chromosome-scale reference genome of P. polyandra. The reference genome is 315.78 Mb in size, with an N50 scaffold size of 32.07 Mb, and contains nine chromosomes with 20,815 protein-coding genes, covering 97.82% of the estimated gene space. We identified 17 rapidly evolving nucleotide-binding-site (NBS) genes, three C-repeat-binding factors (CBF) genes, 19 citrus greening disease (Huanglongbing, HLB) tolerance genes, 11 citrus tristeza virus (CTV) genes, and one citrus nematode resistance gene. A divergence time of 1.96 million years ago was estimated between P. polyandra and P. trifoliata. This is the first genome-scale assembly and annotation of P. polyandra, which will be useful for genetic, genomic, and molecular research and provide guidance for the development of conservation strategies.