Reference genome sequence of the model plant Setaria

By Jeffrey Bennetzen, J. Schmutz, Ryan J. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, Liang Feng, Justin N. Vaughn, J. Grimwood, J. Jenkins and 23 more. Nature Biotechnology, 2012

836 citations recorded by the source corpus.

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

View Paper: https://www.semanticscholar.org/paper/ab21e67dbbce4f23058783eb18c897ac9a3e2202

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Citations in the corpus

Initiation of Setaria as a model plant (2014, background): “C3 species, such as rice and Brachypodium, share the primary carbon shuttle enzymes with C4 species of Setaria, sorghum and maize, albeit the amino acid identity of those enzymes between C4 and C3 might be low, and it is deduced those enzymes were recently recruited into the C4 pathway from ancestra”
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol (2013, background): “These SNPs comprise the framework maps, which were ordered based on the strong synteny between the two species [33].”
PLAZA 3.0: an access point for plant comparative genomics (2014, background): “0 are Musa acuminata (banana) (42), Setaria italica (foxtail millet) (43) and Hordeum vulgare (barley) (44).”