RESUMO
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
Assuntos
Genoma de Planta , Anotação de Sequência Molecular , Zea mays/genética , Centrômero/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Metilação de DNA , Resistência à Doença/genética , Genes de Plantas , Variação Genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Herança Multifatorial/genética , Fenótipo , Doenças das Plantas , Polimorfismo de Nucleotídeo Único , Sequências Reguladoras de Ácido Nucleico , Análise de Sequência de DNA , Tetraploidia , Transcriptoma , Sequenciamento Completo do GenomaRESUMO
OBJECTIVES: We sought to document the mucin gene profile in normal human laryngeal epithelium and compare it with that in patients with reflux-attributed laryngeal injury or disease. We also investigated the effect of low pH with or without pepsin on mucin messenger RNA levels in vitro. METHODS: Laryngeal biopsy specimens were obtained from 3 patients with clinically diagnosed laryngopharyngeal reflux and from 2 control subjects who had no signs or symptoms of reflux. Signs and symptoms were assessed by the Reflux Finding Score and the Reflux Symptom Index, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) was performed to establish the mucin gene profile. Human hypopharyngeal epithelial cells were exposed to pH 7, 5, 4, and 2 with and without pepsin (0.1 mg/mL) for 20 minutes at 37 degrees C, and expression of selected mucins was analyzed via real-time RT-PCR. RESULTS: Mucin 1-5, 7, 9, 13, 15, 16, and 18-20 transcripts were detected in normal laryngeal epithelium, whereas mucin 6, 8, and 17 transcripts were not. Mucins 2, 3, and 5 were expressed at reduced levels in patients with reflux-attributed laryngeal injury or disease. These mucin genes were up-regulated after exposure to low pH in vitro (p < 0.005). Pepsin inhibited this up-regulation (p <0.001). CONCLUSIONS: Reflux laryngitis is associated with down-regulation of mucin gene expression.