Characterisation of the Cinnamomum parthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics

Cinnamomum parthenoxylon is an endemic and endangered species with significanteconomic and ecological value in Vietnam. A better understanding of the geneticarchitecture of the species will be useful when planning management and conservation.We aimed to characterize the transcriptome of C. parthenoxylon, develop novel molecularmarkers, and assess the genetic variability of the species. First, transcriptome sequencingof five trees (C. parthenoxylon) based on root, leaf, and stem tissues was performed forfunctional annotation analysis and development of novel molecular markers. Thetranscriptomes of C. parthenoxylon were analyzed via an Illumina HiSeq 4000 sequencing system. A total of 27,363,199 bases were generated for C. parthenoxylon. Denovo assembly indicated that a total of 160,435 unigenes were generated (average length= 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG,GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a totalof 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selectedfor testing, with 15 successfully amplified across nine populations of C. parthenoxylon. Weuncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P =94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variancewas 10% among populations and low genetic differentiation (Fst = 0.06) indicated low geneflow (Nm = 2.16). A reduction in the population size of C. parthenoxylon was detectedusing BOTTLENECK (VP population). The structure analysis suggested two optimalgenetic clusters related to gene flow among the populations. Analysis of molecularvariance (AMOVA) revealed higher genetic variation within populations (90%) than amongpopulations (10%). The UPGMA approach and DAPC divided the nine populations intothree main clusters. Our findings revealed a significant fraction of the transcriptomesequences and these newlydeveloped novel EST-SSR markers are a very efficient tool forgermplasm evaluation, genetic diversity and molecular marker-assisted selection in C. parthenoxylon. This study provides comprehensive genetic resources for the breeding andconservation of different varieties of C. parthenoxylon.