1. The Construction of the Tree of Life
1) Phylogenetics and phylogenomics of the Bambusoideae (Gramineae).

The bamboo subfamily (Bambusoideae), the rice subfamily (the Erhartoideae) and the Pooideae (to which wheat belongs) are closely related and compose the BEP clade in the grass family. The Bambusoideae includes three major tribes, the woody Bambuseae from the pantropics, the herbaceous Olyreae mainly from the neotropics and the temperate Arundinarieae mainly from the Old World. There are about 392 species of 23 genera in Arundinarieae in China, and 142 species of 11 genera in Bambuseae in the Old World tropics of China. our group conducted study on how to use chloroplast phylogenomics to resolve the phylogenetic relationships within the temperate woody bamboos. This study clarifies the phylogeny of temperate woody bamboos, providing a basis for understanding of the bamboo species diversity and evolutionary history of this group. In addition, it also provides an important case study for chloroplast phylogenomic in reconstruction of challenging plant groups (Systematic Biology 2014, 63(6):933-950). The group also used multiple chloroplast DNA loci to investigate the biogeography of the temperate woody bamboos with densely-sampled phylogenetic tree of Bambusoideae. Biogeographic analyses revealed that temperate woody bamboos diversified from ca. 12~14 Mya, and this was followed by rapid radiation (Molecular Phylogenetics and Evolution 2016, 96:118-129). With respect to the evolution of chloroplast genome in Bambusoideae, they found horizontal transfer of mitochondrial DNA to the chloroplast genome in the herbaceous bamboo genus Pariana (Scientific Reports 2015, 5:11608). In addition to the chloroplast genome, they also explored the nuclear DNA information to clarify the phylogenetic relationships for the temperate woody bamboos. They identified 74 nuclear genes as potential markers for the phylogeny of temperate woody bamboos (Molecular Ecology Resources 2014, 14:988-999).

2) The Early Diverging Monocot Order Alismatale
The predominantly aquatic order Alismatales, which includes approximately 4500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. They have undergone extensive diversification, displaying all major aquatic life-forms, and have exceptionally high diversity of flower morphology and development. In addition, these plants play an important ecological role in both freshwater and coastal ecosystem. The near-basal phylogenetic position of the Alismatales order in monocots makes it potentially important in inferring the evolution of early diverging monocots.
Our group explored the evolution of early diverging monocots based on plastid phylogenomics. They sequenced the complete plastid genomes of several representive taxa from Tofieldiaceae, Potamogetonaceae and Alismataceae, which were first reported in each family. The result showed that the monophyly of Alismatales was confirmed and the family Tofieldiaceae was resolved as the most basal lineage within Alismatales ( Genome Biology and Evolution 2016, 8(3):932–945). This study not only clarifies the phylogeny and evolution of early diverging monocots, but also provides an important case study for plastid phylogenomic reconstruction of key nodes within plant groups.

3) Complete Plastid Genome Sequencing of Tilia (Malvaceae)
Tilia is an ecologically and economically important genus in the family Malvaceae. The taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report the complete plastid genome sequences of four Tilia species for the first time. The results showed that the gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low (PLOS ONE 2015, | DOI:10.1371/journal.pone.0142705).
        
2. Plant DNA barcoding and iFlora of China 
Prof Li initiated and led the Chinese plant DNA barcode plan, and put forward the new standard barcode (Proceedings of the National Academy of Sciences of the United States of America 2011,108 (49): 19641-19646). International peers commented that "this study represents a DNA sequence into the level of plant species is an important step in the classification and identification".The further study of Li’group revealed that phylogenomics based on organelle genome sequencing can light the species identification—organelle-scale “barcodes”, and developed the research connotation of organelles barcode and key technology（BMC Evolutionary Biology 2013, 13:84）. Based on plant classification and the practice of flora compile and research, integrateing into the latest molecular sequencing technology, DNA barcode, geographic distribution information and computer information technology, Li put forward "a new generation of intelligent flora (iFlora)" concept (Plant Diversity 2012, 34 (6): 525-531), and promoted the research plan. His team built the information platform which can support iFlora data gathering and application, and initially built the framework of the intelligent identification system of iFlora of important taxa of vascular plants in China (http://www.iflora.cn/).