A global view of gene activity at the flowering transition phase in precocious trifoliate orange and its wild-type [Poncirus trifoliata (L.) Raf.] by transcriptome and proteome analysis

• Published in: Gene 2012-11, Vol.510 (1), p.47-58
• Main Authors: Ai, Xiao-Yan, Lin, Guang, Sun, Lei-Ming, Hu, Chun-Gen, Guo, Wen-Wu, Deng, Xiu-Xin, Zhang, Jin-Zhi
• Format: Article
• Language: English
• Subjects: Alternative splicing; Base Sequence; Citrus; Electrophoresis, Polyacrylamide Gel; Flowering; Flowering time; Flowers - genetics; Flowers - metabolism; Fruits; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Plant; Genotypes; iTRAQ; Mass Spectrometry; Molecular modelling; Molecular Sequence Data; mRNA; Mutation; Oligonucleotide Array Sequence Analysis; Plant Proteins - analysis; Plant Proteins - genetics; Polymorphism, Single Nucleotide; Poncirus - genetics; Poncirus - metabolism; Poncirus trifoliata; Post-transcription; Precocious trifoliate orange; Proteome - analysis; Proteomics - methods; Reverse Transcriptase Polymerase Chain Reaction; RNA Splicing; RNA-Seq; Sequence Homology, Nucleic Acid; Shoots; Splice junctions; Transcription; Transcriptome - genetics
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2012.07.090

Most of what we know about the molecular genetics of flowering time regulation comes from studies in the model plants. However, little is known about the regulation of flowering transition in perennial species or in species with particular growth habits compared with model plants. Here comparative transcriptome and proteome profiling of spring shoots was performed on an early flowering trifoliate orange mutant (precocious trifoliate orange, Poncirus trifoliata) and its wild-type. A total of 19,215 read-mapped genes were observed in two genotypes by RNA-Seq. Of these, 1450 and 1159 genes were specifically observed in the mutant and wild-type libraries, respectively. There were 355 genes that were expressed differently in the two genotypes. A total of 1664 proteins were identified by the iTRAQ technique, and transcript and protein profiles were parallel across the time course for 50% of the comparisons made, but divergent patterns were also observed, indicative of post-transcriptional events. In addition, a global survey of messenger RNA splicing events identified 16,343 splice junctions among 12,688 genes and showed that alternative 3′ splice is the most prevalent form of alternative splicing. We further identify 5698 novel transcribed regions that are not overlapping with annotated citrus transcriptome in two genotypes. Understanding of the regulation of flowering transition in citrus can help in the development of new genetic or management strategies to improve fruit production. ► Comparative transcriptome and proteome analysis was performed in two trifoliate orange. ► A total of 19,215 genes and 1664 proteins were isolated in two genotypes. ► 16,343 splice junctions were identified in two genotypes. ► 5698 novel transcripts were identified in trifoliate orange.