Format: ORAL

Meng-Yuan Zhou1, Peng-Fei Ma1, Jing-Xia Liu1, Yun-Long Liu1, Cen Guo1, 2, De-Zhu Li1, *

1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. 2 Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 650201, China. * Correspondence: dzl@mail.kib.ac.cn

Bambusoideae is a typical legacy of complex reticulation. It has diverse ploidy levels (herbaceous bamboos, temperate and neotropical woody bamboos, and paleotropical woody bamboos being diploid, allotetraploid, and allohexaploid, respectively) and cytonuclear discordance is manifest, making it a difficult plant group in which phylogenetic relationships and taxonomy of some tribes, subtribes, genera and species remain controversial to varying degrees. Ancient hybridization, polyploidization, and complex reticulate evolution history have led to extensive cytonuclear discordance and difficulties in accurately identifying orthologous genes applicable to phylogenetic studies of allopolyploid plants. Also, great challenges have been encountered in elucidating the complex history of deep reticulation. In order to recover the phylogenetic framework of bamboo and explore its evolutionary history, we sampled 43 representative species across the 19 bamboo subtribes with reference to traditional taxonomy and previous molecular phylogenies based on plastomes and ddRAD data whenever available. Of the sampled 43 ingroups, there are 12 reference-level genomes and 31 assemblies generated from deep genome skimming data. We compared four different analysis strategies (i.e., single-copy gene, perfect-copy syntenic gene, RT ortholog group, and syntelog group) for identifying orthologs, and finally selected a large number of syntelog groups to carry out phylogenomic analyses and to resolve relationships at deep nodes for reconstructing the subtribal-level phylogeny of bamboos. Moreover, the evolutionary history was deciphered by integrating published bamboo transcriptome data and multiple lines of evidence such as the detection of potential hybridizations and introgressions, divergence time estimation, etc. Ultimately, this study offers a robust phylogenomic framework for further taxonomic studies of subtribal delimitations from a molecular biology point of view, and provides an example for tracing the origin and evolutionary history of deep reticulation in polyploid plants.