De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction

Abstract

A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L−1 (T1) or 2.40 mL·L−1 ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple.

Comparative Analyses of the Transcriptome and Proteome of Comte de Paris and Smooth Cayenne to Improve the Understanding of Ethephon-Induced Floral Transition in Pineapple

“…These results indicated that carbohydrate metabolism and plant hormone signal transduction and metabolism were commonly involved in the floral transition process induced by ethephon. Similar results have been reported previously [18]. However, more carbohydrate metabolism, plant hormone signal transduction and metabolism-associated GO terms and KEGG metabolic pathways with more DEGs were enriched in the CP-T and CP-CK comparison group than in the SC-T and SC-CK comparison group.…”

“…A higher concentration of ethephon might be perceived as one type of stress encountered by pineapple plants, which results in the increased expression of TFs after ethephon treatment [17][18]. In addition to the previously mentioned ERFs, other TFs, including MYBs, WRKYs, NACs and bHLHs, were shown to be upregulated in response to ethephon treatment.…”

“…After floral initiation in response to ethylene induction, the process of FMI and floral morphogenesis, which requires the action of several FMI and floral development genes such as FT, LFY, PI, CAL and AG, is initiated [12,18,[26][27][42][43]. TFLs prevent flowers from developing on the inflorescence apex, suppress the FMI genes LFY and AP1 and maintain the inflorescence meristem [44][45].…”

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

“…These unigenes were used for BLASTX-algorithm based searches and annotations against the protein databases Nr, SwissPort, COG, KEGG, and GO. In total, 24,911 unigenes (34.62%) were annotated in sugar apple, which is much smaller than other fruit trees, such as pineapple (58.33%), mango (85%), and loquat (70.57%), and similar to the number annotated in manchurian walnut (39.92%) and “Bartlett” pears (32.8%) (Gong et al, 2015; Nham et al, 2015; Sherman et al, 2015; Hu et al, 2016; Liu and Fan, 2016). This indicated that the functions of a large portion of the genes of sugar apple have not yet been identified.…”

Peer Review #2 of "Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study (v0.2)"

“…We obtained a comprehensive and high-quality fruit transcriptome for pineapple fruit Although extensive RNA sequencing data for pineapple exists on public repositories such as NCBI SRA, only a few of these were produced from fruit (Ong, Voo & Kumar, 2012;Ma et al, 2015;Ming et al, 2015;Chen et al, 2016;Liu & Fan, 2016;Redwan, Saidin & Vijay Kumar, 2016). No data is available for the different tissues present in the pineapple collective fruit, and this fact hinders studies of pineapple fruit development.…”