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.

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Arundinarieae (temperate woody bamboos) is a taxonomically challenging group and the taxa in this tribe show a low level of DNA sequence variation, especially for plastid markers. As a result of the scarcity of flowering collections, species identification mainly depends on vegetative features, and leaf epidermal micromorphology has proven to be useful in bamboo taxonomy. In this study, we used scanning electron microscopy to investigate the abaxial leaf epidermal micromorphology of 94 species in 24 genera of Arundinarieae and three species of Bambuseae. Leaf epidermal characteristics differed mainly in the number and distribution pattern of papillae. Seven papilla forms were assigned, which had little taxonomic value at the generic and subtribal levels. However, the papilla patterns combined with other leaf epidermal features were useful in the discrimination of several species. Most papilla types were shared between tribes Arundinarieae and Bambuseae. We assessed the phylogenetic implications of the leaf epidermal micromorphology based on recently published molecular phylogenetic analyses. With one exception, none of the papilla types corresponded to a particular clade in the plastid or nuclear phylogenetic trees. Based on these results, the papilla patterns have limited phylogenetic value.