Comparative analysis of four <i>Zantedeschia</i> chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

Abstract

The horticulturally important genus <i>Zantedeschia</i> (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of <i>Zantedeschia</i> (<i>Z. aethiopica</i>, <i>Z. odorata</i>, <i>Z. elliottiana</i>, and <i>Z. rehmannii</i>) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of <i>Zantedeschia</i> ranges in size from 169,065 bp (<i>Z. aethiopica</i>) to 175,906 bp (<i>Z. elliottiana</i>). 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 the <i>Zantedeschia</i> cp genomes may result from inverted repeats (IR) region expansion. The sampled <i>Zantedeschia</i> species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in <i>Zantedeschia</i> are 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 four <i>Zantedeschia</i> species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of <i>Zantedeschia</i> suggested that high genetic diversity (<i>I</i> = 0.934; <i>Ne</i> = 2.371) is present in the <i>Zantedeschia</i> cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of <i>Zantedeschia</i> varieties.