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

Pradeepa C G Bandaranayake; Nathasha Naranpanawa; C H W M R Bhagya Chandrasekara; Hiruna Samarakoon; S Lokuge; S Jayasundara; Asitha U Bandaranayake; D K N G Pushpakumara; D Siril A Wijesundara

doi:10.1371/journal.pone.0291763

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

PLoS One. 2023 Sep 20;18(9):e0291763. doi: 10.1371/journal.pone.0291763. eCollection 2023.

Authors

Pradeepa C G Bandaranayake¹, Nathasha Naranpanawa^{1

2}, C H W M R Bhagya Chandrasekara¹, Hiruna Samarakoon¹, S Lokuge¹, S Jayasundara¹, Asitha U Bandaranayake³, D K N G Pushpakumara⁴, D Siril A Wijesundara⁵

Affiliations

¹ Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka.
² Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka.
³ Faculty of Engineering, Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka.
⁴ Faculty of Agriculture, Department of Crop Science, University of Peradeniya, Peradeniya, Sri Lanka.
⁵ National Institute of Fundamental Studies, Kandy, Sri Lanka.

Abstract

Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), 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. rivulorum and C. 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 using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (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, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.

Copyright: © 2023 Bandaranayake et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bayes Theorem
Cinnamomum zeylanicum
Cinnamomum* / genetics
Genome, Chloroplast*
Genome, Mitochondrial*
Sri Lanka

Grants and funding

PCG is the PI of the grant NSF SP/CIN/2016/01 funded by the Ministry of Primary Industries and Social Empowerment through the National Science Foundation of Sri Lanka (http://www.nsf.ac.lk/) under the special Cinnamon project –Molecular And Biochemical Characterizations Of Sri Lankan Cinnamon And Their Wild Relatives And Expression Analysis Of Major Biochemical Genes Under Different Environmental Conditions And Plant Parts To Enhance Utilization Value Of Cinnamon In Sri Lanka. Grant No: NSF SP/CIN/2016/01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.