Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions.
Jing Wang, Jianguang Li, Zaiyuan Li, Bo Liu, Lili Zhang, Dongliang Guo, Shilian Huang, Wanqiang Qian, Li Guo
Author Information
Jing Wang: Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China.
Jianguang Li: Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China.
Zaiyuan Li: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Bo Liu: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Lili Zhang: Weifang Institute of Technology, Weifang, China.
Dongliang Guo: Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China.
Shilian Huang: Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China.
Wanqiang Qian: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Li Guo: Peking University Institute of Advanced Agricultural Sciences, Weifang, China.
Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and 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 of 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 longan cultivars 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. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. 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.
