Chloroplast genome structure in Ilex (Aquifoliaceae)

Xin Yao,Ying-Ying Liu,Yun-Hong Tan,Richard T Corlett,Yu Song,Jun-Bo Yang

doi:10.1038/srep28559

Abstract

Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.

Highlights

Aquifoliaceae is the largest family in the campanulid order Aquifoliales
Since numerous copies are present in each cell, useable fragments of the chloroplast genome are more likely to persist in dried herbarium specimens[18,19], which is an important consideration for Ilex in China where many species are only known from the type collection
For the seven Ilex species, 239,377 to 748,662 pairedend reads (90bp in average reads length) were produced by Illumina sequencing. 233,558 to 692,191 reads were mapped to the reference genome Camellia yunnanensis (GenBank accession number KF156838), after screening these paired-end reads by aligning them to the reference genome, on average reaching over 100 ×coverage of the cp genome

Summary

Introduction

Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. Despite the previous problems with using chloroplast sequences to construct a species-level phylogeny for Ilex, chloroplast sequences have advantages for species identification as a result of www.nature.com/scientificreports/. Their small size, uniparental inheritance, haploid nature, and highly conserved genomic structure[16]. Chloroplast genomes have been used to improve the resolution of the backbone of phylogenies built with nuclear markers[10]

Methods

Results

Discussion

Conclusion