Genomic insights into longan evolution from a chromosome-level genome assembly and population analysis of longan accessions [article]

Jing Wang, Jianguang Li, Zaiyuan Li, Bo Liu, Lili Zhang, Dongliang Guo, Shilian Huang, Wanqiang Qian, Li Guo
2021 bioRxiv   pre-print
Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and has been regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement
more » ... contiguity (contig N50=12.1 Mb, scaffold N50= 29.5 Mb) over a previous draft assembly. A total of 40,420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of 87 longan accessions identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.
doi:10.1101/2021.05.27.445741 fatcat:7tby4afn5vhfrmooiqgb67yafq