The first nuclear genome assembly of quina (Cinchona officinalis), Peru’s national tree and historical source of quinine

Cinchona officinalis L. is an endemic Andean tree of major historical, pharmacological, and cultural significance, recognized as the national tree of Peru and the primary natural source of quinine, the principal antimalarial alkaloid of the pre-synthetic era. Despite its importance, genomic resources for the species remain extremely limited, constraining research on alkaloid biosynthesis, comparative genomics, and conservation genetics. Here we report the first draft nuclear genome assembly and genome-wide simple sequence repeat (SSR) survey for C. officinalis , generated from a specimen collected in the Cajamarca region of Peru. Paired-end sequencing on the Illumina HiSeq 2500 platform produced 347.6 million reads representing 52.1 Gbp of data. K-mer frequency analysis estimated a haploid genome size of ~ 1,081 Mbp, with a genome-wide heterozygosity of ~ 1.10% and a repeat content of ~ 13.8%. De novo assembly yielded 293,692 nuclear contigs spanning 791.2 Mbp, with a contig N50 of 10,657 bp and 75.2% BUSCO completeness. Reference-guided scaffolding against the chromosome-level genome of C. calisaya increased scaffold N50 to 39.9 Mbp and improved BUSCO completeness to 98.6%, comparable to other published Rubiaceae assemblies. Repeat annotation revealed that 62.63% of the genome is composed of repetitive elements, dominated by LTR retrotransposons, consistent with patterns reported across the family. A total of 457,680 SSR loci were identified, revealing interspecific differences in abundance and motif composition relative to C. calisaya and C. pubescens . This assembly establishes the first nuclear genomic resource for Peru's national tree and provides a foundation for future investigations into quinine biosynthesis pathways, population genetics, and conservation-oriented management of threatened Cinchona populations.