The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for their organoleptic and nutraceutical properties of the juice. Herein we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively. The analysis of the long terminal repeat (LTR) allowed the identification of 1921 regions on the primary and 1911 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in-silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of C. sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome. In parallel, total RNA was extracted from fruit, flower, leaf and root enabling the detection of 38,205 and 37,753 predicted transcripts on primary and alternative assemblies respectively. Among those, the highest and lowest number of tissue-specific transcripts were detected in flower (2.73% and 2.71% in primary and alternative assemblies respectively) and leaf (0.7% and 0.68%) while gene ontology analysis enables a more precise characterization of the expressed genes based on their function. The availability of a reference genome is an important prerequisite both for the set-up of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.