Chromosome-Level Genome Assembly and Annotation of the Highly Heterozygous <i>Phallus echinovolvatus</i> Provide New Insights into Its Genetics

Chromosome-Level Genome Assembly and Annotation of the Highly Heterozygous <i>Phallus echinovolvatus</i> Provide New Insights into Its Genetics

<i>Phallus echinovolvatus</i> is a well-known edible and medicinal fungus with significant economic value. However, the available whole-genome information is lacking for this species. The chromosome-scale reference genome (Monop) and two haploid genomes (Hap1 and Hap2) of <i>P. ech...

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Bibliographic Details
Main Authors: Mengya An, Ruoxi Liang, Yanliu Chen, Jinhua Zhang, Xiuqing Wang, Xing Li, Guohua Qu, Junfeng Liang
Format: Article
Language:English
Published: MDPI AG 2025-01-01
Series:Journal of Fungi
Subjects:
<i>Phallus echinovolvatus</i>
whole genome
dikaryon
comparative genomics
CAZymes
secondary metabolism
Online Access:https://www.mdpi.com/2309-608X/11/1/62
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Summary:<i>Phallus echinovolvatus</i> is a well-known edible and medicinal fungus with significant economic value. However, the available whole-genome information is lacking for this species. The chromosome-scale reference genome (Monop) and two haploid genomes (Hap1 and Hap2) of <i>P. echinovolvatus</i>, each assembled into 11 pseudochromosomes, were constructed using Illumina, PacBio-HiFi long-read sequencing, and Hi-C technology. The Monop had a size of 36.54 Mb, with 10,251 predicted protein-coding genes and including 433 carbohydrate-active enzyme genes, 385 cytochrome P450 enzyme genes, and 42 gene clusters related to secondary metabolite synthesis. Phylogenetic and collinearity analysis revealed a close evolutionary relationship between <i>P. echinovolvatus</i> and <i>Clathrus columnatus</i> in the core Phallales clade. Hap1 and Hap2 had sizes of 35.46 Mb and 36.11 Mb, respectively. Collinear relationships were not observed for 15.38% of the genes in the two haplotypes. Hap1 had 256 unique genes, and Hap2 had 370 unique genes. Our analysis of the <i>P. echinovolvatus</i> genome provides insights into the genetic basis of the mechanisms underlying the metabolic effects of bioactive substances and will aid ongoing breeding efforts and studies of genetic mechanisms.
ISSN:2309-608X

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