Chromosome-scale assembly of theSparassis latifoliagenome obtained using long-read and Hi-C sequencing

Abstract

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low quality genome of S. latifolia was obtained by Illumina HiSeq 2500 sequencing. These limitations in the available genome have constrained genetic and genomic studies in this mushroom resource. Herein, an updated draft genome sequence of S. latifolia was generated by Oxford Nanopore sequencing and the Hi-C technique. A total of 8.24 Gb of Oxford Nanopore long reads representing ~198.08X coverage of the S. latifolia genome were generated. Subsequently, a high-quality genome of 41.41 Mb, with scaffold and contig N50 sizes of 3.31 Mb and 1.51 Mb, respectively, was assembled. Hi-C scaffolding of the genome resulted in 12 pseudochromosomes containing 93.56% of the bases in the assembled genome. Genome annotation further revealed that 17.47% of the genome was composed of repetitive sequences. In addition, 13,103 protein-coding genes were predicted, among which 98.72% were functionally annotated. BUSCO assay results further revealed that there were 92.07% complete BUSCOs. The improved chromosome-scale assembly and genome features described here will aid further molecular elucidation of various traits, breeding of S. latifolia, and evolutionary studies with related taxa.ImportanceSparassis latifolia Y.C. Dai et Z. Wang (Sparassidaceae, Polyporales, Agaricomycetes), collections from Asian Sparassis (Dai et al., 2006) exhibits diverse biological and pharmacologic activities. To date, total fresh fruit production in Chinese factories is over 20 tons/d. Despite the significant economic and medical value of S. latifolia, the assembly level of genome was under chromosome-scale. This study assembles a high-quality chromosome-scale reference genome of S. latifolia using Oxford Nanopore sequencing combined with Hi-C (High-through chromosome conformation capture) scaffolding. The improved reference genome will facilitate molecular breeding of S. latifolia and advance our understanding of its genetics and evolution.

A High-quality Genome Assembly and Annotation of Quercus Acutissima Carruth

“…The contig N50 sizes of Q. lobata was 18,900 bp just using Illumina sequencing [10], which is much shorter than contig N50 length of our genome. Thus, the assemble length of contig N50 sizes can represent the genome assembling quality [21], consequently, our genome has high assembly contiguity. High heterozygosity and repetition rates are responsible for the inability to assemble high-quality genomes [22,23].…”

Comparative transcriptome reveals unique pine wood decay strategies in the Sparassis latifolia

“…Clean reads were generated after raw sequences were processed. These clean reads were mapped to the reference genome sequence of S. latifolia (15) by Hisat2 tools (version 2.0.4) (16). Reads were aligned to the reference genome and then assembled into transcripts by StringTie (version 1.3.3b) using default parameters (version 2.0.6) (17).…”