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Bamboo: a key lineage to our understanding of evolution of the grass family

Zhen-Hua Guo  Peng-Fei Ma  Guo-Qian Yang  Meng-Yuan Zhou  Cen Guo  Yu-Xiao Zhang  Xia-Ying Ye  Ying Guo  Jing-Xia Liu  De-Zhu Li  
【摘要】:Bamboo(the Bambusoideae),along with the Pooideae(incl.Triticum and Brachypodium),and the Oryzoideae(incl.Oryza) composes the BOP clade of the grass family(Poaceae) and is the only major grass lineage diversified in forests.However,the basal grasses,Anomochlooideae(incl.Anomochloa and Streptochaeta),Pharoideae(incl.Pharus) and Puelioideae(Puelia) were previously placed in Bambusoideae based on shared morphological and anatomical features.The Bambusoideae comprise four monophyletic clades: the herbaceous bamboos(Olyreae),the temperate woody bamboos(Arundinarieae),the paleotropical tropical woody bamboos and the neotropical woody bamboos(Bambuseae).The taxonomy of the temperate woody bamboos has long been debated.After nearly two decades of molecular phylogenetic studies,consensus on the high-level phylogeny of this tribe has remained elusive.Twelve clades based on plastid DNA sequences have been recognized,but many genera were resolved as polyphyly.Recently,we sampled more than 400 species from all of the recognized clades and genera of the tribe around the world for plastid genome and ddRAD sequencing.In ddRAD phylogeny,five major clades were identified,the basal Ampelocalamus calcareus(representing a new genus,Hsuehochloa),the ADH(Ampelocalamus-Drepanostachyum-Himalayacalamus) clade,Gaoligongshania,and the majority of the tribe falling into two clades,a pachymorph one(the alpine bamboos) and a leptomorph one.However,highly conflicting topologies were obtained between nuclear and plastid phylogenies.Using complete plastid sequences,five major clades were recognized in the paleotropical bamboos,i.e.,the Melocanninae,the Hickliinae,the Temburoungiinae,a Racemobambosinae plus Dinochloinae clade,and the Holttumochloinae plus Bambusinae,which is further divided into the basal grades and the BDG(BambusaDendrocalamus-Gigantochloa) complex.The phylogeny of the BDG complex is ongoing based on ddRAD data.The Poaceae is a long-standing model system in plant biology.However,bamboo genetics and genomics have been lagged behind and there had been a black box due to their extremely long life-cycle and unpredictable flowering.To fill in this notable gap,we generated four draft genomes of major bamboo lineages at all ploidy levels(diploid,tetraploid and hexaploid).We also constructed the first high-density genetic linkage map for a hexaploid bamboo,providing a linkage-map-based strategy for assembly and identification of subgenomes in polyploid genomes.Our results revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution by three independent allopolyploid events from four extinct diploid ancestors.Further analyses are ongoing to better understand their unique biological traits,such as long vegetative growth,fast growing,and gregarious flowering followed by death of the parent plants.

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