Genome of a citrus rootstock and global DNA demethylation caused by heterografting

Grafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years.Citrus plants,with a seed-to-seed cycle of 5–15 years,are among the fruit crops that were probably domesticated by grafting.Poncirus trifoliata,a widely used citrus rootstock,can promote early flowering,strengthen stress tolerance,and improve fruit quality via scion–rootstock interactions.Here,we report its genome assembly using PacBio sequencing.We obtained a final genome of 303 Mb with a contig N50 size of 1.17Mb and annotated 25,680 protein-coding genes.DNA methylome and transcriptome analyses indicated that the strong adaptability of P.trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes.Heterografting by using sweet orange as scion and P.trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock.Single-base methylome analysis indicated that P.trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs(sRNAs)in scions compared to the level observed with autografting,implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting.Taken together,the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.

NEW INSIGHTS INTO THE PHYLOGENY AND SPECIATION OF KUMQUAT (FORTUNELLA SPP.) BASED ON CHLOROPLAST SNP, NUCLEAR SSR AND WHOLE-GENOME SEQUENCING

Kumquat(Fortunella spp.)is a fruit and ornamental crop worldwide due to the palatable taste and high ornamental value of its fruit.Although Fortunella is classified into the economically important true citrus fruit tree group together with Citrus and Poncirus,few studies have been focused on its evolutionary scenario.In this study,analysis of five chloroplast loci and 47 nuclear microsatellites(nSSR)loci from 38 kumquat and 10 citrus accessions revealed the independent phylogeny of Fortunella among citrus taxa,and that Fortunella mainly comprises two populations:CUL,cultivated Fortunella spp.(F.margarita,F.crassifolia and F.japonica);and HK,wild Hong Kong kumquat(Fortunella hindsii).Genomic analysis based on whole-genome SNPs indicated that the allele frequency of both pupations deviated from the neutral selection model,suggesting directional selection was a force driving their evolutions.CUL exhibited lower genomic diversity and higher linkage strength than HK,suggesting artificial selection involved in its origin.A high level of genetic differentiation(Fst=0.364)was detected and obviously asynchronous demographic changes were observed between CUL and HK.Based on these results,a new hypothesis for the speciation of Fortunella is proposed.