Apr 5, 2016

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

BioRxiv : the Preprint Server for Biology
Chia-Yi ChengChristopher D Town


The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, noncoding RNA, and small RNA. The most recent annotation update (TAIR10) released more than five years ago had a profound impact on Arabidopsis research. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-seq libraries from 113 datasets and constructed 48,359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of noncoding RNA including small RNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and microRNA using published datasets and in-house analytic results. Altogether, we identified 738 novel protein-coding genes, 508 novel transcribed regions, 5,051 non-coding genes, and 35,846 small-RNA loci that formerly eluded annotation. Analysis on the splicing events and RNA-seq based expression profile revealed the landscapes of gene structures, untranslated regions,...Continue Reading

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Mentioned in this Paper

Small Nuclear RNA
Untranslated Regions
RNA, Untranslated
Small Nuclear RNA Location
Protein Splicing
Nuclear mRNA Cis Splicing, via Spliceosome

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