Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)

Xueqin Wang,Zhenhua Guo,Huifu Zhuang,Dezhu Li,Xiaying Ye,Lei Zhao

doi:10.1038/s41598-017-11367-x

Abstract

The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defined from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for differences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group.

Highlights

The temperate bamboos are a clade of diverse taxa containing 32 genera and about 600 species[1,2,3,4]
With the development of high-throughput sequencing technologies, reduced-representation methods have revolutionized the fields of phylogeography, population genomics, and phylogenomics by providing high-resolution genomic data for non-model organisms at a reasonable cost[23,24,25], such as restriction site-associated DNA sequencing (RAD-seq)[26]
RAD sequencing reads are aligned to a reference genome and genotyped using standard tools, such as BWA36 and Stampy[37], and the output alignments are supported by several generic single nucleotide polymorphism (SNP) callers such as Genome Analysis Tool Kit[38] (GATK) and SAMtools[39]

Summary

Introduction

The temperate bamboos (tribe Arundinarieae, Bambusoideae, Poaceae) are a clade of diverse taxa containing 32 genera and about 600 species[1,2,3,4]. According to biogeographic analyses[13], Arundinarieae diversified during the middle to late Miocene, and followed by a rapid radiation especially within the clades containing largest genera and species. Such recent origin might make the temperate bamboos undergo very little molecular variation[14] and result in the intricate phylogenetic relationships within Arundinarieae. While in phylogeny based on nuclear DNA marker GBSSI18, 13 lineages were resolved and incongruence was revealed between the plastid and nuclear trees, indicating different evolutionary trajectories. To date, there has been no comparison of the performance of mapping and grouping in terms of the variants obtained and downstream phylogenetic analysis of RAD sequencing data

Methods

Results

Conclusion