Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.

Lei Zhao,Peng-Fei Ma,Qi Liu,Ning Zhang,De-Zhu Li,Zhen-Hua Guo

doi:10.1371/journal.pone.0064642

Lei Zhao, Peng-Fei Ma + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0064642

Copy DOI

Abstract

BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.

Highlights

Traditional phylogenetic studies were mainly based on ribosomal, chloroplast DNA, mitochondrial genes and several nuclear gene fragments [1,2]
We found genes evolving under positive selection from 314 and 173 one-to-one orthologous groups (OGs) in two bamboo species and 14 grass species that might be involved in response to environment stress, development and reproduction, signal transduction, biosynthesis and metabolism, for example, PM5, homologous-pairing protein Meu13, OsClp8, gammaglutamyl hydrolase precursor protein, RNA-recognition-motif (RRM) protein, and DNA-directed RNA polymerase II in the grass family
For the phylogenomic analyses of concatenation, the identical trees were inferred with strong support, and the BEP clade was recovered as a monophyletic group (Figure1) with three methods maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI)

Summary

Introduction

Traditional phylogenetic studies were mainly based on ribosomal (rDNA), chloroplast DNA (cpDNA), mitochondrial genes and several nuclear gene fragments [1,2]. They are susceptible to random or stochastic error (limited genes and taxa sampling) [3,4] and horizontal gene transfer [5], when inferring phylogenetic and evolutionary relationships. The increasing capacity of DNA sequencing technologies has made vast amount of nuclear sequence information possible, mainly including expressed sequence tags (ESTs), transcriptome (RNA-Seq reads) and whole genome sequences from a growing number of species [6].

Objectives

Methods

Results

Discussion

Conclusion