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

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A Correction to this article was published on 27 November 2021

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Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for the organoleptic and nutraceutical properties of the juice and for the quality of the essential oils in the peel.

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, which agree well with an estimated genome size of 312 Mb. The analysis of the transposable element (TE) allowed the identification of 2878 regions on the primary and 2897 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 Citrus 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 35,020 and 34,577 predicted transcripts on primary and alternative assemblies respectively. To further characterize the annotated transcripts based on their function, a gene ontology and a gene orthology analysis with other Citrus and Citrus-related species were carried out.

The availability of a reference genome is an important prerequisite both for the setup of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.

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Projects ‘Development of Resistance Inductor against Citrus Vascular Pathogens’ (Sviluppo di Induttori di Resistenza a Patogeni Vascolari negli Agrumi, S.I.R.P.A.,, 08CT7211000254) and ‘Fruit Crops Resilience to Climate Change in the Mediterranean Basin’ (FREECLIMB,  and ‘Valutazione di genotipi di agrumi per l’individuazione di fonti di resistenza a stress biotici e abiotici’ (Linea 2 del Piano della Ricerca di Ateneo 2020, University of Catania) are supporting the proposed work related to new biotechnological approaches carried out to unlock genetic basis of mal secco resistance and to obtain new tolerant genotypes. The APC was funded by Fondi di Ateneo 2020–2022, University of Catania, linea Open Access. Mario Di Guardo took part on this work in the frame of the PON ‘AIM: Attrazione e Mobilità Internazionale’, project number 1848200–2.

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Authors and Affiliations



MDG: conceptualization, investigation, writing—original draft; MM: conceptualization, formal analysis, investigation, writing—original draft; MM: conceptualization, formal analysis, investigation, writing—original draft; CC: investigation; TM: conceptualization; DZ: investigation; CA: investigation; CM: investigation, writing—review and editing; DG: investigation, writing—review and editing, funding acquisition; LMS: conceptualization, writing—review and editing, funding acquisition; BL: conceptualization, formal analysis, investigation, writing—original draft; GA: conceptualization, writing—review and editing, funding acquisition.

Corresponding authors

Correspondence to Gaetano Distefano or Luca Bianco.

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The authors declare no competing interests.

Data archiving statement

The genome assembly sequences and gene predictions have been submitted to the citrus genome database ( where they can be downloaded and accessed through the genome browser and BLAST services. Raw data have been submitted to NCBI’s SRA under the bioproject id PRJNA732837.

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Communicated by D. Chagné

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Mario Di Guardo, Marco Moretto and Mirko Moser contributed equally to this work and share first authorship.

The original online version of this article was revised: The Author names and contribution text are modified in the original proof.

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Guardo, M.D., Moretto, M., Moser, M. et al. The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.). Tree Genetics & Genomes 17, 46 (2021).

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