Reference genome sequence of the model plant Setaria
Key Points
- To establish a high-quality reference genome assembly for foxtail millet (Setaria italica) and investigate genetic diversity, adaptation, and genome evolution in related grass species.
- Assembled the ~400-Mb genome of Setaria italica and anchored it to a 992-locus genetic map, annotating sequences with >1.3 million expressed sequence tag reads and >580 million RNA-Seq reads.
- Sequenced Setaria viridis, the wild ancestor of S. italica, to map single-nucleotide polymorphism density, transposable element distribution, small RNAs, and chromosomal rearrangements.
- Compared five sequenced grass genomes and evaluated the genome assembly of polyploid switchgrass (Panicum virgatum) against the diploid Setaria reference.
- The Setaria italica assembly spans approximately 80% of the entire genome and captures over 95% of the gene space.
- Comparative sequencing between S. italica and S. viridis resolved distinct patterns of single-nucleotide polymorphism density, transposable element shifts, small RNA contents, chromosomal rearrangements, and segregation distortion.
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Implication
Comparative genomic analysis reveals the reference genome architecture in Setaria grasses, highlighting mechanisms of environmental adaptation and polyploid evolution.
Cite This Study
Bennetzen et al. (2012) studied this question.