Comparative de novo flower transcriptome analysis of polygamodioecious tree Garcinia indica

Abstract

To extend our understanding of molecular mechanism of sex determination in agro-economically important, polygamodioecious tree Garcinia indica (Kokum), high-throughput, next-generation flower transcriptome sequencing (NGS), and comparative analyses were performed to investigate differentially expressed gene in bisexual, female, and male flowers. A total of 49414 unigenes in BS, 45944 unigenes in FL, and 49028 unigenes in ML flowers were annotated. KO annotations revealed that 25 functional categories were large number of genes which were annotated to 'signal transduction'. We identified 33 genes for 'auxin response factor' and 50 for 'ethylene-responsive factor' whose expression changed significantly in all the three paired library combinations. Furthermore, key regulators of floral development such as FLC, SVP, AP1, AP2, AP3, AG, AGL2, AGL4, AGL9, and PI were identified. A total of 327 differentially expressed MADS-box genes were identified in G. indica transcriptome. Analysis of MADS-box genes identified five genes such as MADS AGL11, CRS2-associated factor chloroplastic, conserved hypothetical protein, uncharacterized protein LOC104422218, and MADS-box JOINTLESSlike isoform X3 significantly expressed in only FL flower. In addition, number of DEGs like dynamin 2A, auxin response factor, and spermidine synthase involved in sex expression and reproduction were discovered. The expression patterns of selected genes matched well with the expression levels of unigenes by transcriptome sequencing. Our large-scale comparative analyses may provide valuable hints for the next insights into the molecular mechanism of sex determination in G. indica.

Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock

“…Among the additional interesting CDVd-responsive stem genes whose differential expression was verified by RT-qPCR (Figure 5A), several were found including the plant defense receptor-like protein 9DC3 (LOC102630240) [70]; the MADS-box transcription factor 23-like (LOC102630220) [71], which is part of the transcription factor (TF) families (WRKY, MADS-box and MYB) that activate unique abiotic and biotic stress-responsive strategies considered as key determinants for defense and developmental processes in most eukaryotic plants [72]; the phospholipase A1-Ibeta2 (LOC102609966) [73], the chloroplast import protein TIC 55 (LOC102614849), the chloroplast import protein [74]; the chloroplast pentatricopeptide repeat-containing protein ortholog of At1g08070 (LOC102619843), which is involved in RNA editing events within the chloroplast [75]; the transcription factor MYB13 (LOC102616893), which regulates meristem function by being a component of a regulatory network controlling the establishment and/or development of the shoot system in Arabidopsis [76]; protein IQ-DOMAIN 1, transcript variant X1 (LOC102628194) which plays a role with calmodulins or calmodulin-like proteins as well as involved in scaffolding in cellular signaling and trafficking [77,78]; hydroxyproline O-galactosyltransferase GALT3, transcript variant X3 (LOC102626136), which commits arabinogalactan proteins to the first step in arabinogalactan polysaccharide addition. AGP glycans play essential roles in both vegetative and reproductive plant growth [79]; cytochrome P450 82C4-like, which is involved in the early Fe deficiency response in Arabidopsis [80]; LOC102622795; thaumatinlike protein 1 (LOC102619709), involved in local responses of roots to colonization by non-pathogenic plant growth-promoting rhizobacteria [81].…”