Four species of bamboo (Bambusoideae; Poaceae). Guadua inermis, Otatea acuminata, Lithachne pauciflora, Phyllostachys aurea raw sequence reads

Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are a woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events. Floral transcriptomes were sequenced using RNA-Seq in four species, which represented the three main bamboo lineages. Transcriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Instances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Lastly, putative nuclear orthologues were identified in bamboos to use as phylogenetic markers. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis.