Abstract
BackgroundGuava (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 a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel.ResultsDevelopment 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 a N50 of 3603 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. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways.ConclusionsBenchmarking 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 color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.
Highlights
Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world
In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits
To identify inducible genes resulting into apple color development in colored genotypes, we compared red vs green skin of Apple Color (AC) and mature fruit of Allahabad Safeda (AS) to Punjab Pink (PP)
Summary
Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Guava (Psidium guajava L.) fruit is a berry with edible pericarp tissue as flesh and has excellent antioxidant properties [1]. Guava popularly known as ‘Apple of the Tropics’ is a native of tropical America from where it was distributed in all tropical and subtropical areas of the world [4, 5]. Guava flowers are hermaphrodite and carry 160–400 bilobed anthers and an ovary which is inferior, syncarpous with axile placentation and subulate terminal style [6]. There are more than 400 guava cultivars grown around the world with variation in fruit pulp and peel color. Fruit pulp color ranges from white to deep pink and fruit skin turns green to yellow or red upon ripening and this character varies among cultivars and depends upon the season [7]
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