BACKGROUND:Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources. OBJECTIVE:To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study. METHODS:In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level. RESULTS:The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis. CONCLUSION:This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

棉花(Gossypium hirsutum L.)是一种重要的经济作物,是世界上第二大的天然纺织纤维来源和重要的食用油来源.棉花对生物和非生物胁迫高度敏感,尤其是高温胁迫极易影响花粉的活力和花药的开裂.为了解析棉花在高温胁迫下基因转录水平的相应变化机制,开展了热敏和耐热2个棉花品种的全长转录组响应高温胁迫处理变化的研究.通过转录本的可变剪切分析发现,2个棉花品种在高温胁迫下可变剪切的总数显著增加.热敏品种Che61-72中发现了2900个差异表达基因,并且差异基因在加热前样本(R0)和加热12 h后的样本(R12)中分别识别到了13251个和25296个可变剪切事件,其中内含子保留事件增加得最多,有3837个.耐热品种新陆早36号中发现了2437个差异表达基因,在加热前样本(T0)和加热12 h后的样本(T12)中鉴定到了11248个和13769个可变剪切事件,外显子跳跃事件变化得最大,增加了4144个.富集分析发现,2个品种的差异基因都显著富集到了光系统Ⅰ的光捕获、叶绿体类囊体膜和光合作用-天线蛋白通路中,并筛选出5个关键基因(CPB3、A0 A1 U8 IZF2、A0 A1 U8 KCA2、A0A1 U8NDW4和A0A1 U8NI70),均被注释为叶绿素a/b结合蛋白,它们参与了调控棉花光合作用动态平衡.本研究为棉花在高温胁迫的调节机制的深入研究提供了理论依据,为后续耐高温的种质改良及新品种培育提供了数据支持.

Oncidium, an important tropical orchid, has high ornamental value due to its specific color and occupies a significant market position for the worldwide flower. Transcriptome analysis of flower and leaf color formation provides new sources for producing novel Oncidium hybridum cultivars. We sequenced 12 samples of flowers (yellow and white) and leaves (striped and regular) of O. hybridum and assembled 381,136 and 453,566 unigene sequences from RNA-seq data, respectively. Among unigenes, 662 and 1,324 differentially expressed genes were identified in flower and leaf samples, respectively. Gene ontology and pathway enrichment showed that secondary metabolite biosynthetic pathways were responsible for flower and leaf color formation. It was determined that UGT75C1, E2.4.1.115, CCD7, E2.1.1.76, and CCoAOMT are involved in regulating flower color, and UGT75C1, LHCB, UGT, RP-L18Ae, and ABCB1 play crucial roles in regulating leaf color. Kyoto Encyclopedia of Genes and Genomes analysis revealed that UGT75C1 was significantly enriched in the anthocyanin biosynthetic pathway, showing effects on flower and leaf colors. This study was the first detailed analysis of the molecular mechanisms of O. hybridum flower and leaf colors, and the results advanced the understanding of the genetic basis of flower and leaf colors; they also provided additional support for improving commercial value and producing novel cultivars of O. hybridum.