A global view of transcriptome dynamics during flower development in Capsicum annuum L.

An analysis of genome-wide gene expression profiles during floral organ development can provide important clues about the molecular basis of gene functions and developmental processes.In this study,we analyzed the transcriptome data of 36 samples obtained during floral organ development from pepper‘6421’and detected 30016 genes that were expressed in at least one sample.K-means clustering analysis was used to classify the data into 16 clusters based on the similarities between the dynamic expression profiles of genes.Of these,15 clusters exhibited notable up-regulation or down-regulation trends in different developmental stages or tissues of floral organs.We identified transcription factors expressed at the early,medium,and late stages of bud development(F1,F5,F9).Transcription factor families such as AP2-ERF,MADS-box,MYB,bHLH,and NAC showed significant levels of enrichment.In comparison with genes expressed in vegetative tissues at different stages,certain genes were specifically up-regulated during flower development;among these,the number of genes specifically up-regulated during the stamen(Sta10)and bud tetrad development(F4)stages was the highest.Through extensive studies of the ABCDE model of flower development in Arabidopsis,we identified 17 ABCDE model candidate genes in pepper,most of which were up-regulated at specific stages of flower bud development.The expression data provided in this study is the most comprehensive dataset available for pepper to date and will serve as a resource for identifying the functions of many specific genes involved in flower development in pepper and other Solanaceae plants.

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

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,fromwhich 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 qRTPCR 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.