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

Shuilian He; Yang Yang; Ziwei Li; Xuejiao Wang; Yanbing Guo; Hongzhi Wu

doi:10.7717/peerj.9132

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

PeerJ. 2020 May 22:8:e9132. doi: 10.7717/peerj.9132. eCollection 2020.

Authors

Shuilian He^#¹, Yang Yang^#², Ziwei Li¹, Xuejiao Wang¹, Yanbing Guo¹, Hongzhi Wu³

Affiliations

¹ College of Horticulture and Landscape, Yunnan Agricuture University, Kunming, Yunnan, China.
² College of Science, Yunnan Agricuture University, Kunming, Yunnan, China.
³ College of horticulture and landscape, Yunnan Agricultural University, Kunming, Yunnan, China.

^# Contributed equally.

Abstract

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

Keywords: Chloroplast genome; Genome comparison; IR expansion; Phylogenetic analysis; SSR; Zantedeschia.

Grants and funding

This study was supported by grants from the National Natural Science Foundation of China (grant nos. 31960610; 31660581 and 31500459). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.