Supporting data for "A chromosome-level genome assembly of <i>Artocarpus nanchuanensis</i> (Moraceae), an extremely endangered fruit tree"

<i>Artocarpus nanchuanensis</i> (Moraceae), which is naturally distributed in China, is a representative and extremely endangered tree species. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation information for <i>A. nanchuanensis</i> using integrated approaches, including Illumina, Nanopore sequencing platform and Hi-C. A total of 128.71 gigabases (Gb) of raw Nanopore reads were generated from 20 kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34x coverage depth and a 17.48 kb average read length. The final assembled <i>A. nanchuanensis</i> genome was 769.44 Mb with a 2.09 Mb contig N50, and 99.62% (766.50 Mb) of the assembled data was assigned to 28 pseudochromosomes. 39,596 genes (95.10%, 39,596/41636) were successfully annotated, and 129 metabolic pathways were detected. Plants disease resistance/insect resistance genes, plant-pathogen interaction metabolic pathways, and abundant biosynthesis pathways of vitamins, flavonoid and gingerol were detected. Unigene reveals the basis of species-specific functions, and gene family in contraction and expansion generally implies strong functional differences in the evolution. Compared with other related species, a total of 512 unigenes, 309 gene families in contraction and 559 gene families in expansion were detected in <i>A. nanchuanensis</i>. This <i>A. nanchuanensis</i> genome information provides an important resource to expand our understanding of the unique biological processes, nutritional and medicinal benefits, and evolutionary relationship of this species. The study of gene function and metabolic pathway in <i>A. nanchuanensis</i> may reveal the theoretical basis of special trait in <i>A. nanchuanensis</i>, and promote the study and utilization of its rare medicinal value.