Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species.

Sang-Chul Kim,Joo-Hwan Kim,Jung Sung Kim

doi:10.1093/aobpla/plw015

Abstract

Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, atrnI-CAU gene duplication event was reported fromParis verticillata, a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of twoTrilliumspecies representing two subgenera:TrilliumandPhyllantherum InTrillium tschonoskii(subgenusTrillium), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence ofT. maculatum(subgenusPhyllantherum) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that ofT. tschonoskii The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome ofT. maculatumcontained a 3.4-kb inverted sequence betweenndhCandrbcLin the LSC region, and it was a unique feature for subgeneraPhyllantherum In addition, we found three different types of gene duplication in the intergenic spacer betweenrpl23andycf2containingtrnI-CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excludingT. govanianum These genomic features provide informative molecular markers for identifying the infrageneric taxa ofTrilliumand improve our understanding of the evolution patterns of Parideae in Melanthiaceae.

Highlights

The chloroplast that characterizes all green plants (Viridiplantae) originated from an endosymbiotic event between independent living cyanobacteria and a nonphotosynthetic host (Dyall et al 2004)
60 805 and 246 240 reads were identified as the chloroplast genome sequences for T. tschonoskii and T. maculatum, respectively
The chloroplast genome of T. tschonoskii was composed of 156 852 bp in length (AT content 62.5 %), and it comprised a large single-copy (LSC) region (83 981 bp), a small single-copy (SSC) region (19 869 bp) and two inverted repeat (IR) regions (26 501 bp), while T. maculatum was 157 359 bp in length (AT content 62.5 %, 86 340 bp of LSC, 19 949 bp of SSC and 25 535 bp of IRs)

Summary

Introduction

The chloroplast that characterizes all green plants (Viridiplantae) originated from an endosymbiotic event between independent living cyanobacteria and a nonphotosynthetic host (Dyall et al 2004). Chloroplast genomes of flowering plants are typically circular doublestranded DNA molecules, and usually contain two inverted repeat (IR) regions (IRA and IRB) separated by Published by Oxford University Press on behalf of the Annals of Botany Company. The plastid genome is mostly stable in structure, gene content and gene order across land plant lineages (Jansen et al 2005). Complete chloroplast DNA genome sequence data have been released in GenBank’s Organelle Genome Resources (http://www.ncbi.nlm.nih.gov/genome)

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