Supporting data for "Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano and Hi-C analysis"

<i>Juglans sigillata</i> (NCBI: txid224355), belonging to Juglandales order, is an economically important tree species in Asia, especially in Yunnan province of China. However, little research has been conducted on <i>J. sigillata</i> at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to the plateau environment. To address these issues, a high-quality reference genome of <i>J. sigillata</i> would be a very useful resource.<br>To construct a high-quality reference genome for <i>J. sigillata</i>, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50 Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored approximately 93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated the divergence time between <i>J. sigillata</i> and <i>J.regia</i> was estimated to be 49 million years ago (Mya) based on single-copy orthologous genes.<br> We provide the first chromosome-level genome for <i>J. sigillata</i>. The genome will lay a valuable foundation for future research on genetic improvement of <i>J. sigillata</i>.