Complementary transcriptome and proteome profiling in the mature seeds of Camellia oleifera from Hainan Island

Abstract

Camellia oleifera Abel. (C. oleifera), as an important woody tree species producing edible oils in China, has attracted enormous attention due to its abundant unsaturated fatty acids and their associated benefits to human health. To reveal novel insights into the characters during the maturation period of this plant as well as the molecular basis of fatty acid biosynthesis and degradation, we conducted a conjoint analysis of the transcriptome and proteome of C. oleifera seeds from Hainan Island. Using RNA sequencing (RNA-seq) technology and shotgun proteomic method, 59,391 transcripts and 40,500 unigenes were obtained by TIGR Gene Indices Clustering Tools (TGICL), while 1691 protein species were identified from Mass Spectrometry (MS). Subsequently, all genes and proteins were employed in euKaryotic Orthologous Groups (KOG) classification, Gene Ontology (GO) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to investigate their essential functions. The results indicated that the most abundant pathways were biological metabolic processes. There were 946 unigenes associated with lipid metabolism at the transcriptome level, with 116 proteins at the proteome level; among these, 38 specific proteins were involved in protein-protein interactions, with the majority being related to fatty acid catabolic process. The expression levels of 21 candidate unigenes encoding target proteins were further detected by quantitative real-time polymerase chain reaction (qRT-PCR). Finally, Gas Chromatography Mass Spectrometry (GC-MS) was carried out to determine the fatty acid composition of C. oleifera oil. These findings not only deepened our understanding about the molecular mechanisms of fatty acid metabolism but also offered new evidence concerning the roles of relevant proteins in oilbearing crops. Furthermore, the lipid-associated proteins recognized in this research might be helpful in providing a reference for the synthetic regulation of C. oleifera oil quality by genetic engineering techniques, thus resulting in potential application in agriculture.

Shotgun proteomics of Brassica rapa seed proteins identifies vicilin as a major seed storage protein in the mature seed

“…From a total of 34016 spectra, 323 proteins were identified (Fig 2). This number is similar to protein numbers reported for shotgun seed proteomics of soybean and quinoa seeds, (243 and 352 respectively) [75,76], although less than the number of proteins identified in seeds from the tree Camellia oleifera (1691 proteins) [77], or from rice and barley grains (822 and 1168 proteins, respectively) [78,79].…”

Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera

“…However, information regarding the metabolic mechanisms underlying fatty acid biosynthesis in C. oleifera on Hainan Island is still limited. It needs to be stated that we have previously performed a comprehensive proteomic and transcriptomic analysis on the mature seeds of this plant by using a shotgun qualitative approach and RNA-seq technique (Illumina HiSeq X Ten platform) and preliminarily revealed the characteristics of fatty acids in seeds at the maturity stage 22 . On this basis, the present study further elucidated the dynamic changes in the functional protein profile and its mRNA transcriptional level during seed ripening of C. oleifera on Hainan Island via an iTRAQ-based quantitative method and RNA-seq technology (Illumina NovaSeq platform).…”

“…For the degradation of fatty acids in mitochondria, ACAT can facilitate the condensation of two acetyl-CoAs to yield acetoacetyl-CoA, a common starting substrate for metabolite production 65 . We have previously demonstrated that this protein is the central one in the interaction network due to its strong relationships with many other proteins involved in lipid metabolic processes 22 . Two DAPs and five DEGs whose expression levels changed significantly during seed maturation were also identified in this work.…”

“…Four developmental periods were sampled from August to November: the nutrition synthesis stage (S1), fat accumulation stage (S2), mature stage (S3), and late mature stage (S4). The growth conditions, selection criteria, and sampling method for the plants followed those previously described 22 . For each phase, uniform fruits were pooled and divided into quarters for transcriptome sequencing, proteome profiling, metabolite detection, and qRT-PCR verification.…”

“…In addition, the fatty acid composition was detected through a protocol that was set in accordance with Chinese Standard GB 5009.168-2016. The standard preparation, sample pretreatment, and gas chromatography-mass spectrometry (GC-MS) determination conditions were described in our previous paper 22 . All samples for metabolite identification were analyzed in triplicate, and the data are presented as the means ± standard deviation (SD).…”