Resequencing Analyses of Rough Lemon (Citrus jambhiri)

Rough lemon (Citrus jambhiri) is considered tolerant to Huanglongbing, the most devastating disease of citrus in the world. Understanding the genetic origin of rough lemon should be useful to elucidate its tolerance mechanism. A total of 118 million (X2) 100-bp Illumina paired-end reads were generated from rough lemon DNA.The genome was assembled using a reference-guided method, IMR/DENOM, which combines the alignment to the reference genome (C. clementina v1.0) with the de novo assembled contigs. The resulting 299.7-Mb rough lemon genome is slightly smaller than that of the Clementine genome (301.4 Mb).Compared with the Clementine genome, 2,782,239 single base variants and 731,203 indels were identified in rough lemon. More than half (59.22%) of the single base variants were ambiguous, suggesting a high degree of heterozygosity.Combining the recently published nuclear species-diagnostic SNP markers for citrus, the relative contributions of four ancestral species to rough lemon were calculated. Similar contributions from citron (43.4%) and mandarin (44.8%) were identified, with most of the citron and mandarin diagnostic markers in heterozygous configuration. No contribution of papeda was found, while the contribution of pummelo was 11.8%.Phylogenetic analysis using the chloroplast SNVs showed that rough lemon was closely clustered with mandarin. These results demonstrate that rough lemon originated from the interspecific hybridization of mandarin, citron and pummelo, and its chloroplast is probably derived from mandarin.