Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

Abstract

The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e.g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.

Genome skimming reveals the complete chloroplast genome of Ampelocalamus naibunensis (Poaceae: Bambusoideae: Arundinarieae) with phylogenomic implication

“…Ampelocalamus naibunensis is distantly related to A. calcareus, the earliest divergent lineage (XI) of Arundinarieae (Zhang et al 2016b). The phylogenetic relationships of the 11 major lineages (I to XI) of Arundinarieae recovered here is congruent with Ma et al (2014 The short internodes connected by long branches in the ML tree suggested a probable recent rapid radiation of Arundinarieae (Zhang et al 2016b). …”

Herbarium genomics: skimming and plastomics from archival specimens

“…However, at the plant species-level plastome exons can be remarkably conserved (or even non-variant) causing sequence alignments to be non-informative. In addition, exon coding regions can be prone to selective and functional constraints that could cause a functional rather than historic signal to be tracked (Ma et al 2014;Rockenbach et al 2016), something to which non-coding regions will not be susceptible. Therefore, aiming for as complete as possible plastomes in genome-skimming phylogenetic projects will pay-off in the longer term.…”

V. Subfamily Bambusoideae Luerss. (1893)

“…"A". calcareus is in a position unrelated to other species of Ampelocalamus in the phylogenies of Yang et al (2013) and Ma et al (2014), and is thus placed in Clade XI of the Arundinarieae; in the latter phylogeny it is sister to all other species of the tribe. The species is poorly known and is not given a full description here, nor is it placed in the key pending more comprehensive analysis.…”

“…Culm internodes not alternating in length; bud prophylls triangular; culm leaf blades reflexed; spikelets not clustered 4 4 (3). Foliage leaves dimorphic, the blades of those on the main culm much larger than the ones on the lateral branches; leaf sheaths with fused fimbriae creating a This tribe includes all the temperate woody bamboos, and is monophyletic in all molecular phylogenies (Bamboo Phylogeny Group 2012; Burke et al 2012;Ma et al 2014;Zhang et al 2012. Leptomorph rhizomes may be a synapomorphy for this clade, but if so then the character has apparently reversed in some taxa.…”

“…Even with large amounts of molecular data, relationships within the tribe are poorly resolved (Burke et al 2012;Ma et al 2014). Most genera are para-or polyphyletic, and generic limits are thus highly likely to change in the near future.…”