Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development

Pepper
(Capsicum annuum L.) fruit development
is a complex and genetically programmed process. In this study, we
conducted integrative analysis of transcriptome and proteome profiles
during pepper fruit development. A total of 23 349 transcripts
and 5455 protein groups were identified in four fruit developmental
stages of two pepper varieties. The numbers of transcripts and proteins
identified were decreased gradually across fruit development, and
the most significant changes in transcript and protein levels happened
from the mature green (MG) to breaker (Br) stages. Poor correlation
between differentially expressed transcript and differentially expressed
protein profiles was observed during pepper fruit development. We
then analyzed expression profiles of transcripts and proteins involved
in cell wall metabolism, and capsanthin, tocopherol, and ascorbate
biosynthetic pathways during fruit development, and identified key
regulatory proteins in these pathways. We presented a dynamic picture
of pepper fruit development via comprehensive analysis of transcriptome
and proteome profiles at different fruit developmental stages and
in different varieties, revealing the temporal specificity of key
protein expression. Our report provides insight into the transcription
and translation dynamics of pepper fruit development and a reference
for other nonclimacteric species.