Chromosome-Scale Assembly of the Sparassis latifolia Genome Obtained Using Long-Read and Hi-C Sequencing

Summary

This research provided the first complete genetic blueprint of the edible mushroom Sparassis latifolia. Using advanced DNA sequencing technologies, scientists mapped out all the genes and chromosomes of this commercially important mushroom species. This improved understanding of the mushroom’s genetics will help develop better cultivation methods and varieties. Impacts on everyday life: • Better mushroom varieties could be developed for commercial farming • More efficient cultivation methods may lead to increased availability and lower costs • Understanding the mushroom’s genetics could help enhance its nutritional and medicinal properties • This knowledge may lead to improved preservation and storage methods • The research advances our ability to study and utilize beneficial compounds found in mushrooms

Background

Sparassis latifolia is a valuable edible mushroom cultivated in China with diverse biological and pharmacologic activities. In 2018, an incomplete and low-quality genome of S. latifolia was reported, which constrained genetic and genomic studies of this important mushroom resource.

Objective

This study aimed to assemble a high-quality chromosome-scale reference genome of S. latifolia using Oxford Nanopore sequencing combined with high-through chromosome conformation capture (Hi-C) scaffolding to facilitate molecular breeding and advance understanding of its genetics and evolution.

Results

The sequencing generated 8.24 Gb of Oxford Nanopore long reads representing ~198.08X coverage. A high-quality genome of 41.41 Mb was assembled, with scaffold and contig N50 sizes of 3.31 and 1.51 Mb respectively. Hi-C scaffolding resulted in 12 pseudochromosomes containing 93.56% of the assembled genome. The genome contained 17.47% repetitive sequences and 13,103 protein-coding genes, with 98.72% being functionally annotated. BUSCO assay revealed 92.07% complete BUSCOs.

Conclusion

The study successfully produced an improved chromosome-scale assembly of the S. latifolia genome, which will aid further molecular elucidation of various traits, breeding efforts, and evolutionary studies with related taxa.
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