Comparative analysis of fourZantedeschiachloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

Abstract

The horticulturally important genusZantedeschia(Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species ofZantedeschia(Z. aethiopica,Z. odorata,Z. elliottiana, andZ. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome ofZantedeschiaranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of theZantedeschiacp genomes may result from inverted repeats (IR) region expansion. The sampledZantedeschiaspecies formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions inZantedeschiaare more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the fourZantedeschiaspecies studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars ofZantedeschiasuggested that high genetic diversity (I = 0.934;Ne = 2.371) is present in theZantedeschiacultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification ofZantedeschiavarieties.