title: The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.
abstract: 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 woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events.
  
  
  
  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. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers.
  
  
  
  Instances 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.
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL, 60115-2861, USA. wwysoc2@gmail.com.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Escuela Nacional de Estudios Superiores Unidad Morelia (UNAM), Antigua Carretera a Pátzcuaro 8701, Col. Ex Hacienda de San José de la Huerta, Morelia, Michoacán, 58190, Mexico.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Ruiz-Sanchez
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL, 60115-2861, USA.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL, 60115-2861, USA.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
mesh_terms: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D059467:Transcriptome
keywords: Bambusoideae; MADS-box; RNA-Seq; Transcriptome; Woody bamboos