Developing bioinformatics methods and computational tools to analyze large-scale datasets from high throughput technologies to understand the massive amounts of information at system level incuding genome, transcriptome and proteome. Application of next-generation sequencing technologies and bioinformatics on several major species (including Bamboo, China fir and Populus trichocarpa) to infer gene regulatory networks by integrating omics data. Investigation of the interplay between different post-transcription regulations to provide theoretical basis for improving production of important species.

Research focus1: interplay between small RNAs and alternative splicing regulation

Small RNAs and alternative splicing are important post-transcriptional regulation mechanisms in most eukaryotes. In both animal and plant, mature small RNAs have been recognized and extensively studied. The phenomena of alternative splicing have been emerged in higher plants. However the interplay between small RNAs and splicing regulation is largely unknown in planta. Thus we will focus on the regulation of alternative splicing and miRNA.

We are pleasure to release out first version of ASmiRdb: the interplay between miRNA and alternative splicing in plant. The database was accompanied by easy-to-use web query interfaces for data visualization and downstream analysis. Especially, the forest genomics community also can submit own dataset to the web service to search for the small RNA target sites locating at AS region.

Research focus2: the mechanism of post-transcriptional regulation

Phyllostachys edulis, moso bamboo, or mao zhu (Chinese name: 毛竹) is a temperate species of giant timber bamboo. This bamboo can reach heights of up to 28 m. This particular species of bamboo is the most common species used in the bamboo textile industry of China. Phyllostchys edulis spreads using both asexual and sexual reproduction. The most common and well known for this plant is asexual reproduction. This occurs when the plant sends up new culms from underground rhizomes. Lateral buds on rhizome form new shoots which grow rapidly after emerging from soil and complete average culm height of 13 meters within 38 days in moso bamboo (Li et al., 1998, Song et al., 2016). The fast growth of the new shoots is entirely dependent on the well-developed rhizome-root system, which can horizontally spread widely and connect the young culms with other mature bamboos (Li et al., 2000, Embaye et al., 2005, Zhou et al., 2005, Song et al., 2016). The rhizome system has important function on energy storage, transportation and vegetative reproduction (Li et al., 1998).

moso bamboo PacBio database

However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore combined single-molecule long-read sequencing technology and SGS (RNA-seq and PAS-seq) to genome-wide identify and quantify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. Taken together, our results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.