Integrated Transcriptome and Proteome Analysis Provides Insight into the Ribosome Inactivating Proteins in Plukenetia volubilis Seeds

Abstract

Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome profiles of seeds at two developmental stages (Pv-1 and Pv-2) using RNA-Seq and iTRAQ technologies. A total of 53,224 unigenes and 6026 proteins were identified, with functional enrichment analyses, including GO, KEGG, and KOG annotations. At two development stages of P. volubilis seeds, 8815 unique differentially expressed genes (DEGs) and 4983 unique differentially abundant proteins (DAPs) were identified. Omics-based association analysis showed that ribosome-inactivating protein (RIP) transcripts had the highest expression and abundance levels in Pv-2, and those DEGs/DAPs of RIPs in the GO category were involved in hydrolase activity. Furthermore, 21 RIP genes and their corresponding amino acid sequences were obtained from libraries produced with transcriptome analysis. The analysis of physicochemical properties showed that 21 RIPs of P. volubilis contained ricin, the ricin_B_lectin domain, or RIP domains and could be divided into three subfamilies, with the largest number for type II RIPs. The expression patterns of 10 RIP genes indicated that they were mostly highly expressed in Pv-2 and 4 transcripts encoding ricin_B_like lectins had very low expression levels during the seed development of P. volubilis. This finding would represent valuable evidence for the safety of oil production from P. volubilis for human consumption. It is also notable that the expression level of the Unigene0030485 encoding type I RIP was the highest in roots, which would be related to the antiviral activity of RIPs. This study provides a comprehensive analysis of the physicochemical properties and expression patterns of RIPs in different organs of P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in P. volubilis.

Molecular Genetics Enhances Plant Breeding

“…On the other hand, Xiao et al [ 29 ] validated SbDOF21 as a key regulator for starch biosynthesis in sorghum, and Guo et al [ 30 ] characterized a new SPR -repressor Q allele ( Q c5 ) for compact spikes and bread quality in wheat. The other studies which stand out are those by Mažeikienė et al [ 27 ] and Liu et al [ 28 ], who brought RNA-seq technology to the new promissory crops Ribes nigrum and Sacha Inchi ( Plukenetia volubilis ). Each team was able to provide transcriptomic resources to breed for tolerance to the BRV virus [ 27 ] and better comprehend the expression profiles of seeds at two different developmental stages [ 28 ].…”

“…The other studies which stand out are those by Mažeikienė et al [ 27 ] and Liu et al [ 28 ], who brought RNA-seq technology to the new promissory crops Ribes nigrum and Sacha Inchi ( Plukenetia volubilis ). Each team was able to provide transcriptomic resources to breed for tolerance to the BRV virus [ 27 ] and better comprehend the expression profiles of seeds at two different developmental stages [ 28 ].…”

“…For original datasets, please refer to the published articles [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ] within the second Special Issue of IJMS on “Molecular Genetics and Plant Breeding 2.0” ( , as accessed on 6 June 2023).…”