Phylogeny And Chloroplast Genome Evolution Of Bambusoideae

The bamboo subfamily (Bambusoideae of Poaceae), a group of grasses with lignification stems which are economically important forest species, comprises an estimated 1,500 species worldwide. The taxonomy of this subfamily has been a long-standing dispute among taxonomists chiefly due to its heavily relying on vegetable morphology and alternative interpretation of morphological characters. This state has been improved as more and more taxa and molecular markers were applied in the phylogenetic analyses. However, the generic-level phylogenetic strcuture within Bambusoideae is far from nearly complete; frameworks below the generic level also lacked in some genera. Additionally, while accumulations of DNA data have greatly enhanced the bamboo phylogenetics, detailed characteristics of molecular evolution of bamboos have rarely been reported. In this study, we first reconstructed the phylogeny for Bambusoideae based on an extensive new molecular dataset, and then applied the genotypic fingerprinting method to decipher Bambusa phylogeny. Moreover, we investigated the evolution of bamboo chloroplast genomes by combining our new data and the public available data. The main results are summarized as follows:1. Phylogenetic reconstruction of Bambusuideae at generic levelA dataset of 23 DNA loci was phylogeneticly analysed using both maximum likelihood and bayesian methods for 241 bamboos. The results indicated that Bambusoideae was composed of three highly supported monophyletic subtribes (Olyreae, Bambuseae and Arundinarieae) that corresponded to herbaceous bamboos, tropical woody bamboos and temperate woody bamboos. Woody bamboos was a paraphyletic group in which paleotropical woody bamboos and herbaceous bamoos formed a sister group to temperate woody bamboos. Three monophyletic subtribes were identified in Olyreae; subtribe Buergersiochloinae was resolved as sister group to the other two subtribes (Olyrinae and Parianinae). The two-clades division within tropical bamboos (neotropical and paleotropical) showed strong biogeographic associations. The neotropical bamboos could be further divided into three subtribes in which closer relationships were found between subtribe Guaduinae and subtribe Arthrostylidiinae. Within paleotropical bamboos, subtribe Melocanninae was the first clade to separate out on the gene tree (the basal group), followd by subtribe Hickeliinae. Species of subtribe Racemobambosinae merged with that of subtribe Bambusinae greatly disagreed on the monophyletic circumscription of subtribe Bambusinae. Nine major lineages were detected in temperate bamboos but the relationships among them were still not clear. Extensive sampling of both bamboo species and DNA loci notably improved the support values for deeper nodes. However, many shallow branches collapsed as large amount of similar sequence data was introduced in the datamatrix.2. Phylogenetic relationships among species in gunus BambusaBambusa, the type genus of Bambusoideae, is an species-rich and difficult group both in taxonomical and phylogenetic studies. Given the low DNA sequence divergence, we applied AFLP molecular marker to construct the phylogenetic framwork within Bambusa. The potential efficiency and appropriateness of applying this method in bamboo phylogenetic research were also evaluated. The eight most highly polymorphic AFLP primer pairs amplified a total of 2,309 fragments and the Jaccard similarity coefficient between samples varied between 0.158-0.735. Four different analytic method (NJ, BI, PcoA and network) received almost the same results which denied the traditionally identified four-subgenera devision on the basis of morphorlogy. Instead, two major clades were recovered in our analyses. Existence of reticular relationship among species obliged for the low node values on the bifurcate tree.3. Pattern of chloroplast evolution of bamboosTo elucidate chloroplast genome evolution of species grown in different terrestrial environment, we fully characterized the chloroplast genome of the woody bamboo Guadua angustifolia and focused on comparative analyses among neotropical and paleotropical bamboos. This newly sequenced chloroplast genome (GenBank NO. KM365071) is 135,331 bp long and comprises of an 82,839-bp large single-copy (LSC) region, a 12.898-bp small single-copy (SSC) region, and a pair of 19,797-bp inverted repeats (IRs). Comparative cpDNA sequence analyses of G. angustifolia with other representative bamboo cpDNAs revealed overall conservative chloroplast genome structure, gene order and gene contents among bamboos. The patterns of bamboo plastome evolution greatly correlated to their geographic distribution, i.e. all the neotropical bamboos habored-4kb smaller plastome size than that of the paleotropical ones which were caused by large fragment deletions in the integenic spaces. The most intriguing differences could be discerned between bamboos with different life forms. The herbaceous bamboos differed from woody bamboos in IRb/SSC boundary, total gene number and molecular evolution rates. Divergence time estimation based on complete chloroplast molecular suggested that most bamboo genera divergerd after the Miocene and that speciation events of extant species occurred during or after the Pliocene.