Alternative Splicing in Wood Formation of Populus trichocarpa

Wood of forest trees is the major sink for carbon sequestration and the potential source of lignocellulosic material for ethanol production; its derived products are also inseparable part of our daily life. Wood is mostly secondary xylems, the walls are composed of three major components: cellulose, hemicelluloses, and lignin. Cellulose and hemi-cellulose consists of about 70 to 80 % of the dry weight and make up the framework of the cell wall. The majority of the remaining portion is lignin, a phenolic polymer that functions as a major barrier for pathogens defense and water diffusion. Trees are constantly challenged by mechanical perturbations in nature. The formation of reaction wood is one of the most critical defense systems of trees to counteract mechanical stress/load for their long-term adaptation. Tension wood is the reaction wood developed by woody angiosperm. Tension wood contains elevated cellulose and decreased xylan, lignin and vessel cells. A distinct structure feature of tension wood is the gelatinous-layer (G-layer) in lumen of the fiber cell. The G-layer contains essentially pure cellulose. Due to these characteristics, tension wood is highly desirable for ethanol production and its developmental processes has been a major research topic. To understand the underlying regulatory networks associated with the mechanical stress response and the control cellulose, hemicelluloses and lignin biosynthesis, we carried out comparative analyses of transcriptome and small RNA profiles of tension and normal wood in Populus trichocarpa. The functional categories of the differential expressed gene  agreed with previous sudies. The Genome-wide alterative splicing analysis using RSEM revealed 100 genes with transcript isoforms differentially expressed in tension woods. GO enrichment analysis results of these 100 genes did not show preferential functional categories. The functions of these genes scatter across transcription factors, cell wall biosynthesis and cytoskeletal frameworks that may be associated with the g-layer formation and other tension wood characteristics. The gene differential expression patterns were also cross-referenced with the small RNA profiles.