Characteristics and Significance of Intergenic Polyadenylated RNA Transcription in Arabidopsis    

Abstract

The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes.

Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes

“…In A. thaliana, rice, and S. cerevisiae, a paralogous pair for Ks analysis only (e.g., Figure 2A) was defined by identifying a gene and its top-scoring match in BLAST similarity searches (Altschul et al, 1990). Nucleotide diversity between 80 A. thaliana accessions was calculated according to an earlier study (Moghe et al, 2013). Genes with paralogs produced in the a or bg WGD events were identified by Bowers et al (2003).…”

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

“…Translation is also modulated by regulatory molecules, including auxin (22,23), gibberellins (24), and polyamines (25). Most of the recent studies documenting dynamics in mRNA translation were performed using microarrays, but the application of high-throughput mRNA sequencing (mRNA-seq) to evaluate translatomes has provided greater detail of RNAs associated with ribosomes (3,26). In yeast, the translatome is recognized as an accessible proxy of de novo protein synthesis (27).…”

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

“…A major challenge for these researchers is the generation and dissemination of high-quality gene structure annotations for downstream applications. This is especially true for plant genomics researchers, given that plant genomes can be difficult targets for annotation: they are unusually rich in transposable elements (Feschotte et al, 2002;Schnable et al, 2009;Kejnovsky et al, 2012), have high rates of pseudogenization Zou et al, 2009;Hua et al, 2011), and contain many novel protein-coding and noncoding RNA (ncRNA) genes as revealed through RNA-Seq and proteomics studies (Campbell et al, 2007;Hanada et al, 2007;Jiang et al, 2009;Yang et al, 2009;Li et al, 2010;Lin et al, 2010;Donoghue et al, 2011;Garg et al, 2011;Boerner and McGinnis, 2012;Moghe et al, 2013). Plant genomes are also relatively large compared with other eukaryotes, representing some of the largest genomes in existence (Pellicer et al, 2010;Birol et al, 2013;Nystedt et al, 2013), meaning that the time required to annotate a large plant genome can be measured in months rather than hours.…”