Characterization of the Sweet Pitaya (Stenocereus thurberi) Fruit Peel Transcriptome: Analysis of Genes Playing a Role in Cuticle Biosynthesis and Identification of Reference Genes

Abstract

Background Cactus (Cactaceae) are plants distributed across arid regions of America with ecological and economic value. One trait that allows the cactus to survive in desert ecosystems is its cuticle, which limits water loss in dry conditions. Nevertheless, the mechanism of cuticle biosynthesis has yet to be described for cactus. Stenocereus thurberi is a cactus endemic from the Sonoran desert, which produces a fruit named sweet pitaya. Transcripts from S. thurberi published in databases are scarce, and no gene expression analysis has been carried out for this species. This study reports for first time the de novo assembly and characterization of the sweet pitaya peel transcriptome. Results Two hundred forty-three million of 80–150 base pairs reads with at least 25 of quality in the Phred score were used to get the assembly. The transcriptome includes 174,449 transcripts with an N50 value of 2,110 bp and 85.4% of completeness. Out of the total transcripts, 122,234 (70.07%) were classified as coding RNA, and 43,391 were classified as long non-coding RNA. Functional categorization analysis suggests a response to stress and an active cuticle biosynthesis in fruit pitaya peel. The genes elongation factor 1-alpha (StEF1a), α-tubulin (StTUA), and polyubiquitin 3 (StUBQ3) are reliable reference genes for accurate normalization of gene expression analysis in this specie through qRT-PCR. The cuticle biosynthesis transcripts cytochrome p450 family 77 subfamily A (StCYP77A), Gly-Asp-Ser-Leu motif lipase/esterase 1 (StGDSL1), and ATP binding cassette transporter family G member 11 (StABCG11) showed higher expression at the early stages of fruit development and ripening suggesting an active cuticle compound biosynthesis and transport. Conclusions This is the first transcriptome developed in the S. thurberi specie. Further, housekeeping genes suitable for gene expression analysis by qRT-PCR in this specie are reported for first time. The information generated will help to analyze the molecular mechanism of cuticle biosynthesis and another relevant metabolic pathway in S. thurberi and other cactus species. Understanding the role of cuticle in the adaptation to arid environments could help design technologies to ensure fleshy fruit production in the context of the increase in water scarcity for agriculture predicted for the following years.