title: Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance.
abstract: The diploid C4plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan.|Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan.|Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Tsai
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Mei-Yeh Jade
authors.initials: MJ
authors.lastname: Lu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Kai-Jung
authors.initials: KJ
authors.lastname: Yang
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Mengyun
authors.initials: M
authors.lastname: Li
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Yuchuan
authors.initials: Y
authors.lastname: Teng
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.
authors.forename: Shihmay
authors.initials: S
authors.lastname: Chen
authors.affiliation: Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004 Taiwan.|School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
authors.forename: Maurice S B
authors.initials: MS
authors.lastname: Ku
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan.|Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA.
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics*; D055864:Droughts; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation / Q000379:methods; D031782:Pennisetum / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D032983:Setaria Plant / Q000235:genetics*
chemical_list: D010940:Plant Proteins