Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms.

Caixia Zhang,Manjun Yang,Jiansong Chen,Lijun Xu,Jian Li,Ernesto Picardi

doi:10.1155/2022/4017654

Abstract

The fruiting bodies or mycelia of Hericium coralloides (H. coralloides) contain many physiologically active compounds that are used to treat various diseases, including cardiovascular disorders and cancers. However, the genome of H. coralloides has not been sequenced, which hinders further investigations into aspects, such as bioactivity or evolutionary events. The present study is aimed at (i) performing de novo sequencing of the assembled genome; (ii) mapping the reads from PE400 DNA into the assembled genome; (iii) identifying the full length of all the repeated sequences; and (iv) annotating protein-coding genes using GO, eggNOG, and KEGG databases. The assembled genome comprised 5,59,05,675 bp, including 307 contigs. The mapping rate of reads obtained from PE400 DNA in the assembled genome was 92.46%. We identified 2,525 repeated sequences of 14,23,274 bp length. We predicted ncRNAs of 48,895 bp and 11,736 genes encoding proteins that were annotated in the GO, eggNOG, and KEGG databases. We are the first to sequence the entire H. coralloides genome (NCBI; Assembly: ASM367540v1), which will serve as a reference for studying the evolutionary diversification of edible and medicinal mushrooms and facilitate the application of bioactivity in H. coralloides.

Highlights

Wild edible mushrooms are extensively consumed owing to their unique and delicate flavors, abundant polysaccharides, proteins, fibers, and amino acids, and low lipid content that is good for low-calorie diets [1,2,3]
We identified 169 single-copy orthogroups from H. coralloides and other fungal species and used corresponding amino acid sequences to construct a phylogenetic tree (Figure 6) in which H. coralloides was clustered with Hericium alpestre, which is another species of the same genus
The study sequenced the entire genome of H. coralloides (NCBI; Assembly: ASM367540v1), which is widely applied in traditional Chinese medicine (TCM)

Summary

Introduction

Wild edible mushrooms are extensively consumed owing to their unique and delicate flavors, abundant polysaccharides, proteins, fibers, and amino acids, and low lipid content that is good for low-calorie diets [1,2,3]. Except for the nutritional characteristics, mushrooms contain rich bioactive compounds with medicinal properties, such with antimicrobial, antioxidant, lipid-lowering, and antitumor activity [4,5,6]. Hericium coralloides (1794) is an edible and medicinal mushroom species. We aimed to detect H. coralloides bioactivity by sequencing its genome. As a result of its potential activity, investigation of its genome may be necessary

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Conclusion