A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree

Abstract

Artocarpus nanchuanensis (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 A. nanchuanensis using integrated approaches, including Illumina, Nanopore sequencing platform, and Hi-C. A total of 128.71 Gb of raw Nanopore reads were generated from 20-kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34× coverage depth and a 17.48-kb average read length. The final assembled A. nanchuanensis 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. In total, 39,596 genes (95.10%, 39,596/41,636) 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 A. nanchuanensis. This A. nanchuanensis 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 A. nanchuanensis may reveal the theoretical basis of a special trait in A. nanchuanensis and promote the study and utilization of its rare medicinal value.

The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis

“…Raw data with adapter sequences or low-quality sequences were filtered using SOAPnuke with the following parameters: -n 0.01 -l 20 -q 0.3 -adaMR 0.25 -ada_trim -polyX 50 -minReadLen 150 (Chen et al, 2018). BWA-MEM (Li, 2013) and default parameters were used to map paired-end clean reads to the reference genome of A. nanchuanensis (He et al, 2022b). SAMtools (Danecek et al, 2021) and Picard (http:// picard.sourceforge.net/) were used to sort and delete duplicate reads, respectively.…”

“…For each individual, we calculated the number of homozygous LOF sites and the number of genes containing one or more homozygous LOF sites divided by the total number of protein-coding genes (PCGs). Finally, gene ontology (GO) analysis was applied to characterize the detected genes containing homozygous LOF sites based on the genome annotation results of recent studies by using TBtools (Chen et al, 2020;He et al, 2022a).…”

“…Clavati), which contains mostly Chinese species (Gardner et al, 2021). The fruit of A. nanchuanensis is rich in nutrients and can be used for brewing, processing jam and beverages (He, 2014;He et al, 2022a). Straight trunks are often used for shipbuilding and making furniture (He, 2014).…”

“…The recently reported genome assembly at the chromosome level of A. nanchuanensis provided an opportunity to resequence at the whole genome level (He et al, 2022a). To reveal the genetic structure and demographic history of A. nanchuaensis fully and accurately and provide meaningful guidance for its conservation, 101 individuals from 7 populations of A. nanchuanensis were resequenced in this study.…”