For decades, transposable elements have been known to produce a wide variety of changes
in plant gene expression and function. This has led to the idea that transposable element …

Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

The genus Oryza is a model system for the study of molecular evolution over time scales
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …

De novo gene birth is the process by which new genes evolve from DNA sequences that
were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be …

Pigeonpea is an important legume food crop grown primarily by smallholder farmers in
many semi-arid tropical regions of the world. We used the Illumina next-generation …

Deep transcriptome sequencing has revealed the existence of many transcripts that lack
long or conserved open reading frames (ORFs) and which have been termed long non …

We have optimized and extended the widely used annotation engine MAKER in order to
better support plant genome annotation efforts. New features include better parallelization …

Comparisons of genomes of different species are used to identify lineage-specific genes,
those genes that appear unique to one species or clade. Lineage-specific genes are often …

The families of the plant-specific transcription factors (TFs) are defined by their characteristic
DNA-binding domains (DBDs), such as AP2/ERF, B3, NAC, SBP, and WRKY. Recently …

Although considered an extremely unlikely event, many genes emerge from previously
noncoding genomic regions. This review covers the entire life cycle of such de novo genes …