Genomic Sequences of Citrus limonia Reveal High Similarity to Citrus medica

Rangpur (Citrus limonia Osbeck) is a citrus hybrid originated in India. It is also known as Rangpur lime even though it does not share many similarities with true limes. Indeed its fruit resembles a mandarin and presents a very acidic juice content, allowing its use as a substitute for commercial lemons or limes. There are several varieties of this mandarin-like fruit with different characteristics but whose origin is somewhat controversial. It is hypothesized that Rangpur resulted from a cross of lemon (C. limon) and mandarin (C. reticulata), citron (C. medica) and a mandarin hybrid, rough lemon (C. jambhiri) and mandarin, or mandarin and citron. To get insights on the origin of this mandarin-like citrus, we have evaluated an assembly of 948,437,749 sequences  (99.95% Illumina and 0.05% 454) that resulted in 409,783,077 nucleotides (1.1 x coverage) in 513,098 contigs, which were compared to genomic sequences of C. clementina, C. sinensis, C. reticulata, C. medica, and C. maxima. Fragments larger than 1.5 Kb present in all the species were evaluated for the level of similarity among themselves. Around 60% of the Rangpur sequences were more similar to C. medica sequences while 30% of them showed higher similarity to the genome of C. clementina, being those, the species with higher similarities to the genome of C. limonia. The next species with highest level of similarity was C. sinensis (4%) and then C. reticulata (2%). The other sequences showed either higher similarity to the genome of C. maxima, or were not closely related to any species in particular. These results point to citron and a mandarin (or one of its hybrids) as the parental species of Rangpur. Clearly citron is the responsible for the majority of the Rangpur genome and interestingly, the C. reticulata variety used for the analysis, which is supposedly a hybrid of the true C. reticulata species that could be the putative parental is not, in fact, one of the closest genome.

Financial support: FAPESP (08/57909-2) and CNPq (573848/08-4).