RNA-Sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars

Abstract

Background Guava ( Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has potential to set the stage for the functional genomics for traits of commerce. Results Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with N50 of 3,603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues and 68 genes among colored tissue comparisons. Mapping the differentially expressed transcripts over molecular pathways indicate significant hormonal changes during fruit development. Comparisons of red vs green peel in guava cv. Apple Colour, white pulp vs red pulp in Punjab pink and fruit maturation vs ripening in non-coloured Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. Conclusions Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting colour genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

“…Specifically, ethylene biosynthesis and signal transduction genes, 1-aminocyclopropane-1-carboxylate synthase (ACS), ACC oxidase 3, Ethylene receptor 2 (ETR2), ethylene response factor ERF-1, basic helix loop-helix (bHLH) TF and pyridoxine biosynthesis gene PDX1.2 , were found upregulated during the development of fruit. Around 40 transcription factor families belonging to MYB , MADS , HB , WRKY , ARF , bHLH , AP/EREBP , bZIP , NAC , AUX/IAA , B3 , Jumonji and Polycomb were found to be regulating the fruit development in guava [ 21 ]. The RAPD markers were widely used for molecular characterisation among different varieties of Psidium sp., and lately they were utilized for discriminating different fruit shapes such as ‘round’ and ‘pyriform’ using cluster analysis [ 22 ].…”

“…Reticulin o-methyltransferase was found to contribute to red colouration in peel and pulp tissues. Candidate genes whose expression correlated with red peel colour were glycerol-3-phosphate acyltransferase 5 ( GPAT5 ), peamaclein, CTP synthase-like, chloroplastic monodehydroascorbate ( MDA ), probable 2-oxoglutarate dependent dioxygenase AOP1 ( 2OG-AOP1 ), methionine synthase ( MS ), Secoisolariciresinol dehydrogenase ( SDH ) and BEL1-like homeodomain 1( BLH1 ) [ 21 ]. In Psidium cattleyanum , where red and yellow fruits are common, the peel transcriptome revealed the involvement of anthocyanidin synthase ( ANS ) and UDP-glucose: flavonoid-o-glucosyl transferase ( UFGT ) in red peeled fruits [ 135 ] ( Table 3 ).…”