The Draft Genome of Lychee (Litchi chinensis Sonn) Revealed Independent Domestication Events of Early and Late Mature Cultivars

Lychee is an exotic and nutritious fruit that has been domesticated thousands of years ago, and cultivated in tropical regions worldwide. We reports a high-quality draft genome of the domesticated litchi (Litchi chinensisSonn.), which is the first genome sequence of Sapindaceae family and perennial tropical fruit trees. The assembled genome size (987 Mb) is twice that determined by flow cytometry and were separated into two haplotypes spanning ~430 Mb (haplotype A, HA) and ~443 Mb (haplotype B, HB), respectively. Of the totally predicted 65,076 gene models of all the assembly, HA and HB contains 30,371 and 31,209 genes respectively. We identified 28,174 pair allelic genes between the two haplotypes and the mean identity of the allele pairs was about 96.90%, and 24.42% of them were selectively expressed in 15 transcriptome samples. The lychee genome has no whole genome duplication event after the “gamma” triplication event shared by all eudicots. Re-sequencing of 64 litchi accessions, including 31 wild and 33 cultivated, resulted in identification of selective sweeps, candidate genes for fruit maturation, and independent domestication events of early and late mature cultivars. The early mature lychee cultivars were domesticated in Yunnan province while the late mature cultivars in Hannan Island, southern China.