Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes

Abstract

Pleurotus placentodes (PPL) and Pleurotus cystidiosus (PCY) are economically valuable species. PPL grows on conifers, while PCY grows on broad-leaved trees. To reveal the genetic mechanism behind PPL's adaptability to conifers, we performed de novo genome sequencing and comparative analysis of PPL and PCY. We determined the size of the genomes for PPL and PCY to be 36.12 and 42.74 Mb, respectively, and found that they contain 10,851 and 15,673 protein-coding genes, accounting for 59.34% and 53.70% of their respective genome sizes. Evolution analysis showed PPL was closely related to P. ostreatus with the divergence time of 62.7 MYA, while PCY was distantly related to other Pleurotus species with the divergence time of 111.7 MYA. Comparative analysis of carbohydrate-active enzymes (CAZYmes) in PPL and PCY showed that the increase number of CAZYmes related to pectin and cellulose degradation (e.g., AA9, PL1) in PPL may be important for the degradation and colonization of conifers. In addition, geraniol degradation and peroxisome pathways identified by comparative genomes should be another factors for PPL's tolerance to conifer substrate. Our research provides valuable genomes for Pleurotus species and sheds light on the genetic mechanism of PPL's conifer adaptability, which could aid in breeding new Pleurotus varieties for coniferous utilization.

Keywords: Pleurotus placentodes; adaption; coniferous utilization; evolution; genome sequencing.

FIGURE 1

The genome of PPL and PCY. (A) The genome information of PPL. (B) The genome information of PCY. Outside to inside of concentric circles show assembly contig number and GC content, gene density, all repeat content, LTR content, LINE content, DNA repeat content. (C) Genome assembly result of PPL and PCY.

FIGURE 2

Genome annotation result of PPL and PCY. (A) Function annotation of PPL and PCY. Yellow columns represent the same function, green columns represent unique functions in PCY, and brown columns represent unique functions in PPL. (B) Genome components of PPL and PCY.

FIGURE 3

Comparison of CAZYmes annotated by PPL and PCY. From left to right, show GHs, GTs, CBMs, AAs, CEs, and PLs. White numbers represent the number of annotated genes. The chromaticity bar at the bottom represents the gene number of different colors, corresponding to the figure above.

FIGURE 4

Genome collinearity analysis of PPL and PCY. Note: The contig/utg number is not continuous due to subsequent assembly optimization.

FIGURE 5

Comparative genome analysis of PPL and PCY. (A) Expansion and contraction of gene families in 12 species genomes. The numbers of gene families that expanded (blue) or contracted (red) in each lineage after classification are down on the corresponding branch. MRCA, the most recent common ancestor. The time shown in the bars represents the estimated divergence time. (B) Analysis of common unique gene families. The different color represent different orthologs. (C) KEGG enrichment of positively selected genes in PPL. (D) KEGG enrichment of expansion genes in PPL. The bottom color bar represents different KEGG pathway classifications.