title: RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds.
abstract: The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germination growth. Herein, we report transcriptomes of aleurone cells treated with the hormones abscisic acid, gibberellic acid, or both. Using a comprehensive approach, we identified hundreds of novel genes. To minimize the number of false positives, only transcripts that did not overlap with existing annotations, had a high level of expression, and showed a high level of uniqueness within the rice genome were considered to be novel genes. This approach led to the identification of 553 novel genes that encode proteins and/or microRNAs. The transcriptome data reported here will help to further improve the annotation of the rice genome.
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Watanabe
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Ringler
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
authors.forename: Lingkun
authors.initials: L
authors.lastname: Gu
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA. Electronic address: jeffery.shen@unlv.edu.
authors.forename: Qingxi J
authors.initials: QJ
authors.lastname: Shen
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D000465:Algorithms; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005875:Gibberellins / Q000494:pharmacology; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012275:Oryza / Q000187:drug effects / Q000235:genetics*; D010937:Plant Growth Regulators / Q000494:pharmacology; D012639:Seeds / Q000187:drug effects / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005875:Gibberellins; D035683:MicroRNAs; D010937:Plant Growth Regulators; D000040:Abscisic Acid; C007842:gibberellic acid
keywords: Abscisic acid; Aleurone; Gibberellic acid; MicroRNA; RNA-seq; Rice