Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka

Abstract

Cinnamomumspecies have gained worldwide attention because of their economic benefits. Among them,C.verum(synonymous withC.zeylanicumBlume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species,C.capparu-coronde,C.citriodorum,C.dubium,C.litseifolium,C.ovalifolium,C.rivulorumandC.sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding usingrbcL,matK, andtrnH-psbA regions could not also resolve the identification ofCinnamomumspecies in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and aC.verumsample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, theC.verum(Sri Lanka) is sister to previously sequencedC.verum(NC_035236.1, KY635878.1),C.dubiumandC.rivulorum. TheC.verumsample from India is sister toC.litseifoliumandC.ovalifolium. According to the ITS regions studied,C.verum(Sri Lanka) is sister toC.verum(NC_035236.1),C.dubiumandC.rivulorum.Cinnamomum verum(India) shares an identical ITS region withC.ovalifolium,C.litseifolium,C.citriodorum, andC.capparu-coronde. According to the Skmer analysisC.verum(Sri Lanka) is sister toC.dubiumandC.rivulorum, whereas C.verum(India) is sister toC.ovalifolium, andC.litseifolium. The chloroplast geneycf1was identified as a chloroplast barcode for the identification ofCinnamomumspecies. We identified an 18 bp indel region in theycf1gene, that could differentiateC.verum(India) andC.verum(Sri Lanka) samples tested.