title: Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis.
abstract: BACKGROUND
  Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.
  
  
  RESULTS
  Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.
  
  
  CONCLUSIONS
  Phylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, 60115-2861, IL, USA. wwysoc2@gmail.com.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, 50011-1020, IA, USA. lgclark@iastate.edu.
authors.forename: Lynn G
authors.initials: LG
authors.lastname: Clark
authors.affiliation: Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, 50011-1020, IA, USA. lakshmi@iastate.edu.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Attigala
authors.affiliation: Instituto de Ecología AC, Centro Regional del Bajío, Biodiversidad y Sistemática, Av. Lázaro Cárdenas 253, Pátzcuaro, 61600, Michoacán, Mexico. ruizsanchez.eduardo@gmail.com.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Ruiz-Sanchez
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, 60115-2861, IL, USA. mel-duvall@niu.edu.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
mesh_terms: D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics; D020869:Gene Expression Profiling; D054628:Genome, Chloroplast; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000166:cytology / Q000235:genetics*