Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).

Domitille Chalopin,Lynn G Clark,Melvin R Duvall,Minkyu Park,William P Wysocki,Jeffrey L Bennetzen

doi:10.3389/fpls.2021.725728

Abstract

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

Highlights

The bamboos (Poaceae: Bambusoideae), with ∼1700 species, are the third largest grass subfamily and represent the only major clade of grasses to diversify primarily in association with forests (Clark et al, 2015; Soreng et al, 2017; Clark and Oliveira, 2018)
Of the 51 bambusoid taxa, Arundinarieae is represented by 17 species from six of the 12 numbered lineages representing three of five subtribes, Bambuseae is represented by 19 Paleotropical species representing four of eight subtribes and by nine Neotropical species representing all three subtribes, while Olyreae is represented by six species representing two of the three subtribes (Table 1)
In both Bayesian inference (BI) and Maximum likelihood (ML) analyses, Bambusoideae and each of the three tribes were fully supported as monophyletic (PP 1.00, MLBS 100, hereafter in this order) (Figure 2)

Summary

Introduction

The bamboos (Poaceae: Bambusoideae), with ∼1700 species, are the third largest grass subfamily and represent the only major clade of grasses to diversify primarily in association with forests (Clark et al, 2015; Soreng et al, 2017; Clark and Oliveira, 2018). Within Olyreae, the monotypic New Guinean endemic Buergersiochloa is strongly supported as sister to the wholly Neotropical subtribes Parianinae and Olyrinae (with the exception of one weedy species that occurs in Africa) (Kelchner and Bamboo Phylogeny Group, 2013; Oliveira et al, 2014; Clark et al, 2015; Wysocki et al, 2015; Zhang et al, 2016). The Olyreae are fundamentally diploid, and instances of polyploidy appear to be of relatively recent origin (Judziewicz et al, 1999; Triplett et al, 2014)

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Conclusion