Complete chloroplast genome of a Peruvian landrace of Cucurbita moschata, loche, and its comparative analysis with other relative species

Background Loche ( Cucurbita moschata ) is a pre-Columbian squash that is cultivated exclusively in the northern coast of Peru, Lambayeque. This crop is notable for the presence of warts in its skin and for its vegetative reproduction as it commonly lacks of seeds in fruits. Currently, loche may be considered a new product for international markets, recognizing the gastronomy of Lambayeque in the world and dynamizing the Peruvian agro-export area. However, genomic information about this squash is very limited. Results In this study, the complete chloroplast (cp) genome of loche from Lambayeque was sequenced and annotated. Clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete chloroplast (cp) genome of C. moschata has a 157,592 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (88,192 bp) and 18,181 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (25,613 bp). The annotation of C. moschata cp genome predicted 81 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 38 transfer RNA (tRNA) genes and 01 pseudogen. A total of 59 simple sequence repeats (SSR) of this cp genome were divided into mononucleotide (43), dinucleotide (7), trinucleotide (2), tetranucleotide (6), and hexanucleotide (1). The highest percentage of identity was observed for C. moschata and C. maxima (0.99) while the lowest for C. moschata and Cucumis sativus (0.68). Cucurbita pepo is the closest relative to loche. Conclusions The cp genome of loche is similar to other cucurbit species and possesses 127 genes in total. Moreover, a total of 59 SSR were identified in this cp genome. A higher percentage of identity is evidenced between C. moschata and C. maxima whereas higher divergence values with Cucumis sativus . This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of a Peruvian squash landrace, that is commonly cultivated in a restricted area in northern Peru , providing valuable information for genetic and evolutionary studies in the genus Cucurbita .