De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification

Abstract

Background Coccinia grandis (ivy gourd), is a dioecious member of Cucurbitaceae having heteromorphic sex chromosomes. Chromosome constitution of male and female plants of C. grandis is 22A + XY and 22A + XX respectively. Earlier we showed that a unique gynomonoecious form of C. grandis (22A + XX) also exists in nature bearing morphologically hermaphrodite flowers (GyM-H). Additionally, application of silver nitrate (AgNO3) on female plants induces stamen development leading to the formation of morphologically hermaphrodite flowers (Ag-H) despite the absence of Y-chromosome. Due to the unavailability of genome sequence and the slow pace at which sex-linked genes are identified, sex expression and modification in C. grandis are not well understood.ResultsWe have carried out a comprehensive RNA-Seq study from early-staged male, female, GyM-H, and Ag-H as well as middle-staged male and GyM-H flower buds. A de novo transcriptome was assembled using Trinity and annotated by BLAST2GO and Trinotate pipelines. The assembled transcriptome consisted of 467,233 ‘Trinity Transcripts’ clustering into 378,860 ‘Trinity Genes’. Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, and GyM-H_Middle_vs_Male_Middle comparisons exhibited 35,694, 3574, and 14,954 differentially expressed transcripts respectively. Further, qRT-PCR analysis of selected candidate genes validated digital gene expression profiling results. Interestingly, ethylene response-related genes were found to be upregulated in female buds compared to male buds. Also, we observed that AgNO3 treatment suppressed ethylene responses in Ag-H flowers by downregulation of ethylene-responsive transcription factors leading to stamen development. Further, GO terms related to stamen development were enriched in early-staged male, GyM-H, and Ag-H buds compared to female buds supporting the fact that stamen growth gets arrested in female flowers.ConclusionsSuppression of ethylene responses in both male and Ag-H compared to female buds suggests a probable role of ethylene in stamen suppression similar to monoecious cucurbits such as melon and cucumber. Also, pollen fertility associated GO terms were depleted in middle-staged GyM-H buds compared to male buds indicating the necessity of Y-chromosome for pollen fertility. Overall, this study would enable identification of new sex-biased genes for further investigation of stamen arrest, pollen fertility, and AgNO3-mediated sex modification.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1187-z) contains supplementary material, which is available to authorized users.

Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System

“…We found that 4% of the genes expressed in C. grandis floral buds are sex-biased (Supplementary Table S4), with a total of 3273 sex-biased genes identified (2682 male-biased and 591 female-biased), in agreement with prior studies on sex-biased genes in C. grandis [43,44]. Our results support enrichment for pollen production-related functions in male-biased genes as previously found in C. grandis [43,44] and in other plant systems (reviewed in [5]). Female-biased genes, on the other hand, were significantly enriched for hormone-signaling functions.…”

“…Despite this heteromorphy, the species has been estimated to be only 3.1 Myr old based on a molecular-clock model applied to a phylogeny with all 25 species [42]. C. grandis males and females show no morphological differences except in their flowers, but between 2 and 8% of the genes appear to be differentially expressed between males and females [43,44]. The species is a promising system in which to study sex chromosome evolution because of its relatively small genome size (~1 Gb) and its phylogenetic proximity to Cucumis [45], which includes the fully sequenced Cucumis sativus and Cucumis melo genomes [46][47][48][49].…”

Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis

“…Similar transcriptomics studies have also been carried out in papaya and cucumber that has led to better understanding of sex determination [32–34]. It can be noted that recently, we have carried out a de novo transcriptome profiling from male, female, GyM-H and Ag-H flower buds of C. grandis and identified many sex-biased genes that can provide crucial insights in to stamen arrest, pollen fertility and sex modification mechanism [35] .…”

“…In order to decipher differences in protein abundances among flower buds of male, female, gynomonoecious and chemically masculinized female plants of C. grandis , total proteome profiling was carried out at early and middle stages of flower development. Proteins were identified using IDA (Information dependent acquisition)-derived data using in silico translated in-house C. grandis flower bud transcriptome [35] database followed by label-free quantification using SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) analysis. Differential protein abundance among various sex forms of C. grandis was studied to identify players potentially involved in sex expression and modification.…”

Transcriptome profiling of differentially expressed genes in cytoplasmic male-sterile line and its fertility restorer line in pigeon pea (Cajanus cajan L.)

“…Functional annotation of the assembled unigenes was achieved by BLASTX search against Nr (NCBI nonredundant protein sequences), Virdiplantae, GO (Gene ontology) and KEGG (Kyoto encyclopedia of genes and genomes) databases with a stringent cut-off E-value of 1e − 3 [147][148][149]. Unigenes annotation against Nr database was performed with the aid of Blast2GO tool version 3.1.3 (http://www.blast2go.org) [150] up to 10 qualified blast hits for each unigene.…”