Features

Douglas Allen, Ph.D.

 

Doug’s research is dedicated to understanding the metabolic networks of oilseed plants to enhance biomass composition using experimental and computational methods. These investigations give insight to plant metabolism, important for designing crops to meet future nutritional and chemical feedstock needs.

Welcome to the online resource for supplemental information for the Mockler lab’s genome-wide mapping of alternative splicing in Arabidopsis thaliana.

Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ∼42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in non-consensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts.

The data underlying these discoveries is available for download via the link below:

Take me to the files

How should I cite these resources?

In your publication, you can cite the original paper that presented these resources:

Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC Genome-wide mapping of alternative splicing in Arabidopsis thaliana.  Genome Res. 2010 Jan;20(1):45-58. Epub 2009 Oct 26. PMID: 19858364