Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae).

Yang Jae Kang,Myounghai Kwak,Jungho Lee,Hyosig Won,Soonok Kim,Gi-Heum Nam,Giuseppe Pellegrino

doi:10.1371/journal.pone.0241178

Abstract

Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris, is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea, have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup (Sisyrinchium angustifolium), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species.

Highlights

Genomic sequences of approximately 0.9–2.3 Gbps were generated from each species using the Illumina platform (Table 2)
Using the whole-plastid genome assemblies of 14 native Korean Iris species determined in our study, together with the previously published I. gatesii and I. sanguinea plastid genomes [20, 21], we performed pairwise Ks calculation and Bayesian inference (BI) phylogenetic tree construction with 57 nonredundant plastid genes to enable the observation of speciation among Korean-native Iris
From our BI phylogenetic tree, we observed that Series Chinenses species, which did not cocluster in with psbA-trnH and trnL-F-based phylogenetic trees calculated in a previous study

Summary

Introduction

The Iris genus is comprised of hundreds of species, making it one of the largest in the Iridaceae family. Identification of plastid genomic regions inferring species identity of 14 Korean-native Iris species landscape gardening, as well as many economically important medicinal plants. Iris species are distributed across Europe, Asia, and America, and display high levels of genome diversity and variable ploidy [2,3,4]. In Korea, several native Iris species are distributed across diverse environments, ranging from dry to wet regions. Some species are currently considered endangered (e.g. Iris laevigata, Iris ruthenica, and Iris koreana) and are subject to legal protection by the Korean government

Methods

Results

Conclusion