Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae

Abstract

Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.

Keywords: Sanguinoderma; Ganodermataceae; comparative genomic analyses; medicinal fungi; next-generation sequencing.

Fig. 1.

Circos of S. infundibulare. From inside to outside, the first circle is collinearity analyses, the second circle is a scaffold composition map, the third circle is a line chart of GC content, the fourth circle is a line chart of GC Skew, the fifth circle is a histogram of the repeat sequence, and the sixth circle is a heat map of gene density.

Fig. 2.

Collinearity analyses between S. infundibulare and S. rugosum, G. lucidum, and G. sinense.

Fig. 3.

Orthologous analyses between S. infundibulare, S. rugosum, G. lucidum, and G. sinense.

Fig. 4.

Annotation of S. infundibulare based on GO database.

Fig. 5.

Annotation of S. infundibulare based on KEGG database.

Fig. 6.

Porphyrin metabolism pathway of S. infundibulare (map00860) and the bold line part represent the siroheme biosynthesis pathway of S. infundibulare.

Fig. 7.

Annotation of S. infundibulare, S. rugosum, G. lucidum, and G. sinense based on CAZymes database.

Fig. 8.

a) Annotation of the genome and specific gene families of S. infundibulare and orthologroups of 4 species based on eggNOG database. b) Annotation of S. infundibulare, S. rugosum, G. lucidum, and G. sinense based on eggNOG database. Category functions: (A) RNA processing and modification; (B) chromatin structure and dynamics; (C) energy production and conversion; (D) cell cycle control, cell division, chromosome partitioning; (E) amino acid transport and metabolism; (F) nucleotide transport and metabolism; (G) carbohydrate transport and metabolism; (H) coenzyme transport and metabolism; (I) lipid transport and metabolism; (J) translation, ribosomal structure, and biogenesis; (K) transcription; (L) replication, recombination, and repair; (M) cell wall/membrane/envelope biogenesis; (N) cell motility; (O) posttranslational modification, protein turnover, and chaperones; (P) inorganic ion transport and metabolism; (Q) secondary metabolites biosynthesis, transport, and catabolism; (R) general function prediction only; (S) function unknown; (T) signal transduction mechanisms; (U) intracellular trafficking, secretion, and vesicular transport; (V) defense mechanisms; (W) extracellular structures; (Y) nuclear structure; and (Z) cytoskeleton.