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Title: Expanding and vetting Sorghum bicolor gene annotations through transcriptome and methylome sequencing

item OLSON, ANDREW - Cold Spring Harbor Laboratory
item Klein, Robert - Bob
item Dugas, Diana
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item KLEIN, PATRICIA - Texas A&M University
item Ware, Doreen

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2013
Publication Date: 7/1/2014
Citation: Olson, A.J., Klein, R.R., Dugas, D.V., Lu, Z., Regulski, M., Klein, P., Ware, D. 2014. Expanding and vetting Sorghum bicolor gene annotations through transcriptome and methylome sequencing. The Plant Genome. 7(2). Available:

Interpretive Summary: Major advancements in science hinge on the identification of genes controlling plant and animal traits that are critically important to agriculture. Genes are tiny packets of genetic blueprint material that are found inside the cells of all plants and animals; they control all of the physical characteristics of these organisms. Our work focuses on improving major grain and biofuel crops. With gene sequences, the genetic blueprint will be visible, and this information can make improving the plants more efficient. This study details the efforts to improve the annotation of the sorghum genome and the methylation pattern of active genes. This information will be used to develop a resource to understand the function of all genes across the genome. This refinement of the annotation of genes and gene methylation represents a bioinformatics resource for the entire cereal community, and will allow scientists to understand those key features of the genetic blueprint that make sorghum's physical appearance differ from that of other cereals. Information will be primarily used by fellow scientists, but the work should ultimately result in better adapted, higher producing crop varieties available to American farmers.

Technical Abstract: With the emergence and subsequent advancement of next generation sequence technology, detailed structural and functional characterization of genomes is readily attainable. Here, we have sampled the Sorghum bicolor methylome by shallow sequencing of bisulfite treated DNA derived from root samples. We used these data to identify methylation patterns associated with functional gene loci. We trained a decision tree classifier to predict high confidence gene models based on expression levels, methylation profiles, and gene sequence conservation and applied these to updated annotations. A phylogenetic analysis suggests that almost 800 genes are missing from annotation Sbi1.4 and over 400 gene models are split. We have expanded the transcriptome atlas sorghum by conducting RNAseq analysis on meristematic tissues, florets, and embryos, and we have utilized this information to develop a more complete annotation of the sorghum transcriptome. Using the GrameneEnsEMBL GeneBuilder and our classifier, we identified a set of 34,276 putative gene models in addition to the community annotations of Sbi1.4. Updated gene models most often have extended UTR annotations, but some show improvements in protein coding regions. Our new gene models include 30% of the phylogenetically conserved missing genes and resolve 50% of the split gene models.