Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Abstract

Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.

Keywords: Morchella crassipes; heterothallism; mating type; mitochondrial ORF; mitochondrial genome; nuclear genome.

Figure 1

The phylogenetic trees and gene family comparative analysis of 22 species. The number of phylogenetic tree nodes indicated the divergence time, Mya (million years); the bubble diagram on the right represented the expansion (red) and contraction (green) of the gene family among species; and the diameter of the bubble represented the number of genes that expanded and contracted.

Figure 2

Self-repetition in the mitochondrial genome of M. crassipes.From the inner circle to the outer circle, the six histograms in the inner circle showed the position and length of repetitive sequences with different lengths (red histograms, repeat sequence length > 800 bp; lavender histograms, repeat sequence length between 600–800 bp; orange histograms, repeat sequence length between 400–600 bp; dark brown histograms, repeat sequence length between 200–400 bp; light brown histograms, repeat sequence length between 100–200 bp; light gray histograms, repeat sequence length less than 100 bp); the outer second red circle showed the position information overlapping all repetitive sequences; and the outer blue bars showed the position information of genes without considering the direction.

Figure 3

Collinearity analysis of Mat1-1 loci of M. crassipes and M. importuna. The diagonal line showed the Mat1-1 loci collinear region between M. crassipes (a) and M. importuna (GenBank accession number: MK527108) (b) by Mauve software, and the peak graph on the coordinate axis represented the degree of similarity of the collinear region. The gene order of the Mat1-1 locus of M. crassipes was shown (c). Electrophoresis maps represented the amplification of Mat1-1-1 (d) and Mat1-2 (e) genes in monosporic populations of M. crassipes (M, DM2000 molecular marker; P, M10 tissue isolation parent strain; 37 monosporic populations isolated from M10 ascocarp was used for mating structure detection).

Figure 4

Comparative analysis of mitochondria between M. crassipes and M. importuna.On the upper right side, the mitochondrial genome of M. importuna with a size of 272 kb (GenBank accession number: MK527108) can been, and on the left, the mitochondrial genome of M. crassipes with a size of 531 kb (GenBank accession number: MN542893) can be seen. The red and blue bars of the outer track marked the location and direction of the genes (outward was the sense strand, and inward was the antisense strand), and the name of the gene was displayed in the outer circle with links; from the outside to the inside, the second circle was the GC percentage content; the third circle was the expression level of the genes in the mycelial and sclerotial stages; the inner circle was the connection of repeated sequences between M. crassipes and M. importuna, with the lines from light to deep color reflecting the length of the repeat sequence that increased.