Novel structural annotation and functional expression analysis of GTP_EFTU conserved genes in pepper based on the PacBio sequencing data

Abstract

Genes containing GTP_EFTU domain mainly express elongation factors (EF), Small GTPases, and GTP-binding proteins, which are closely related to protein synthesis, extension and ATP synthesis. In this study, we identified 39 genes containing GTP_EFTU domains from peppers. The evolutionary trees constructed from capsicum, Arabidopsis, rice, and tomato are mainly divided into 7 subfamilies. Using PacBio (Pacific Biosciences) sequencing and assembly data, we extracted these 39 gene sequences, from which 25 genes had alternative splicing. Particularly, the Capana08g000545 had 16 alternative splicing processes. Accordingly, we performed promoter sequence analysis, subcellular location prediction, the expression analysis of different tissues and periods, and also the GO (Gene ontology) analysis of co-expressed genes. Lastly we did the qRT-PCR analysis in 5 stages of pepper fruit development. These analyses revealed important structural and functional information for the identified 39 genes that contain GTP_EFTU domains, providing important references for further follow-up experiments to verify the genes function on plants or their unique roles in peppers.

Keywords

• Capsicum
• GTP_EFTU
• PacBio
• Phylogenetic analysis
• Expression analysis
• GO analysis