Abstract
BackgroundNext-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 woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events.ResultsTranscriptomes 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. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers.ConclusionsInstances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2707-1) contains supplementary material, which is available to authorized users.
Highlights
Next-generation sequencing allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses
Open reading frame (ORF) detection followed by a coding potential filtering step in the de novo assembly yielded over 78,000 putative coding transcripts (PCTs) in O. acuminata and between 37,000 and 48,000 PCTs in the three remaining species
If the putative orthologues from each taxon originated from different progenitor woody bamboo genomes, we might expect the support for nodes within the woody bamboo clade to reflect this. This marks the first study that compared transcriptomes across Bambusoideae and the first transcriptome generated from an herbaceous bamboo
Summary
Next-generation sequencing allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Despite the uncertainty of their phylogenetic relationships [2, 3, 5,6,7,8,9], the two woody bamboo lineages share aspects of phenology and sexual systems suggestive of common ancestry. Their phenological patterns can be especially striking as they can exhibit extremely long intervals between flowering periods (3—120 years), which may be synchronized between disjunct populations [10]. The subsequent die-off following a flowering event can result in sudden ecological consequences such as lower shade levels in former bamboo forests
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