Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening

Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism

BACKGROUND

Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved.

RESULTS

We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening.

CONCLUSION

Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.

Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development

BACKGROUND

Fish scales are typical products of biomineralization and play an important role in the adaptation of fish to their environment. The Gymnocypris przewalskii scales are highly specialized, with scales embedded in only specific parts of the dermis, such as the areas around the anal fin and branchiostegite, making G. przewalskii an ideal material for biomineralization research. In this study, we aimed to unveil genes and pathways controlling scale formation through an integrated analysis of both transcriptome and proteome, of which G. przewalskii tissues of the dorsal skin (no scales) and the rump side skin (with scales) were sequenced. The sequencing results were further combined with cellular experiments to clarify the relationship between genes and signaling pathways.

RESULTS

The results indicated the following: (1) a total of 4,904 differentially expressed genes were screened out, including 3,294 upregulated genes and 1,610 downregulated genes (with a filtering threshold of |log2Fold-Change|> 1 and p-adjust < 0.05). The identified differentially expressed genes contained family members such as FGF, EDAR, Wnt10, and bmp. (2) A total of 535 differentially expressed proteins (DEPs) were filtered out from the proteome, with 204 DEPs downregulated and 331 DEPs upregulated (with a filtering threshold of |Fold-Change|> 1.5 and p < 0.05). (3) Integrated analyses of transcriptome and proteome revealed that emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were important genes contributing to scale development and that PI3K-AKT was the most important signaling pathway involved. (4) With the use of the constructed G. przewalskii fibroblast cell line, emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were confirmed to be positively regulated by the PI3K-AKT signaling pathway.

CONCLUSION

This study provides experimental evidence for PI3K-AKT controlled scale development in G. przewalskii and would benefit further study on stress adaptation, scale biomineralization, and the development of skin appendages.

CsTT8 regulates anthocyanin accumulation in blood orange through alternative splicing transcription

A homologous gene of basic-helix-loop-helix AtTT8 in Arabidopsis thaliana was identified in juice sac cells of pulp tissues from blood orange (Citrus sinensis cv 'Tarocco'), which was designated as CsTT8 in this study. Additionally, the mRNA levels of TT8 with the full-length open reading frame were significantly higher in 'Tarocco' than in mutant fruit lacking pigment in pulp or peel tissues. However, an alternative splicing transcript, Δ15-TT8, with the fourth exon skipped, was also identified from transcripts different in length from that in 'Tarocco'. The mRNA levels of Δ15-TT8 were higher in mutant fruit lacking pigment in pulp or peel tissues than in the wild type. Therefore, the TT8/Δ15-TT8 mRNA level ratio was found to be crucial for sufficient pigment in either pulp or peel tissues. TT8 from blood orange fruit demonstrated the capacity for nucleus localization and binding to other proteins. In contrast, Δ15-TT8, lacking the fourth exon, lost its ability to interact with RUBY1 and to localize at the nucleus. Using a dual luciferase reporter assay and transient overexpression in tobacco, we proved that two regulatory complexes formed by a functional TT8 with different MYB(v-myb avian myeloblastosis viral oncogene homolog)-type partners significantly promoted expression of an anthocyanin biosynthetic gene and a proton pumping gene, leading to anthocyanin and citrate production. Our findings suggest that TT8, rather than dysfunctional Δ15-TT8, is possibly involved in modulating anthocyanin biosynthesis and its transport into vacuoles by proton gradients. However, increased mRNA levels of the dysfunctional alternative splicing transcript may act as a negative feedback to downregulate TT8 expression and limit anthocyanin accumulation in blood oranges.

Comprehensive analyses of the citrus WRKY gene family involved in the metabolism of fruit sugars and organic acids

Sugars and organic acids are the main factors determining the flavor of citrus fruit. The WRKY transcription factor family plays a vital role in plant growth and development. However, there are still few studies about the regulation of citrus WRKY transcription factors (CsWRKYs) on sugars and organic acids in citrus fruit. In this work, a genome-wide analysis of CsWRKYs was carried out in the citrus genome, and a total of 81 CsWRKYs were identified, which contained conserved WRKY motifs. Cis-regulatory element analysis revealed that most of the CsWRKY promoters contained several kinds of hormone-responsive and abiotic-responsive cis-elements. Furthermore, gene expression analysis and fruit quality determination showed that multiple CsWRKYs were closely linked to fruit sugars and organic acids with the development of citrus fruit. Notably, transcriptome co-expression network analysis further indicated that three CsWRKYs, namely, CsWRKY3, CsWRKY47, and CsWRKY46, co-expressed with multiple genes involved in various pathways, such as Pyruvate metabolism and Citrate cycle. These CsWRKYs may participate in the metabolism of fruit sugars and organic acids by regulating carbohydrate metabolism genes in citrus fruit. These findings provide comprehensive knowledge of the CsWRKY family on the regulation of fruit quality.

Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality

Introduction

Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.

Methods

In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks.

Results and discussion

The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.

The potential of different ripeness of blood oranges (Citrus sinensis L. Osbeck) for sale in advance after low-temperature storage: Anthocyanin enhancements, volatile compounds, and taste attributes

To explore the optimal early harvest time similar to the ripe fruit qualities, the effects of storage temperatures on maturity indexes, weight losses, colour parameters, anthocyanin profiles, volatile and taste components of blood oranges at six different maturity levels were investigated. Total anthocyanin contents of cold-treated fruits increased to or exceed that of ripe fruits (0.24 ± 0.12 mg/100 g), and fruits harvested from 260 d and 280 d after anthesis shared similar individual anthocyanin profiles to ripe fruits during storage at 8 °C for 30 d and 20 d (III-30 d and IV-20 d groups), respectively. Moreover, comparative analyses of e-nose and e-tongue demonstrated the distances of volatile components and scores of taste attributes including sourness, saltiness, bitterness, sweetness, and umami in III-30 d and IV-20 d groups were close to that of ripe fruits, indicating that the fruits could be sold about 20 to 30 d ahead of the season.

A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including CsDnaJ, CsHSP17.4B, and CsCEBPZ. Their upregulation is inferred to keep phloem protein homeostasis under the stress from HLB and enable subsequent stress responses observed in T19. DVS will advance allelic level studies in citrus.

An up-to-date review: differential biosynthesis mechanisms and enrichment methods for health-promoting anthocyanins of citrus fruits during processing and storage

Anthocyanins, naturally found in citrus, play key roles in improving the qualities of citrus fruits and products. Dietary consumption of fruit-derived anthocyanins is concerned increasingly owing to health-promoting properties. However, anthocyanins are vulnerable to many physical and chemical factors during processing and storage, affecting fruit qualities and consumer acceptance. Thus, the aim of this review is to focus on main advances in chemical structures, differential biosynthesis mechanisms, enrichment methods, and bioactivities of anthocyanins in pigmented and unpigmented citrus fruits. In this review, anthocyanin species and concentrations display tissue specificity in citrus, and the chemical structures and contents of main anthocyanins are summarized. For differential biosynthesis mechanisms, the reasons why most citrus fruits lose the ability of anthocyanin biosynthesis compared with pigmented fruits, and the molecular differences of biosynthesis mechanisms in pigmented citrus fruits are both discussed in detail. Furthermore, anthocyanins' enrichment methods (low-temperature stimulus, light irradiation, xenobiotics inductions, and ripeness influence) during processing and storage have been summarized, which achieve quality improvement by promoting structural gene expression, reducing anthocyanin-degrading enzyme activities, or altering DNA methylation status. Meantime, the health benefits of extract from pigmented citrus and their waste are mentioned, which provides a new approach for citrus waste recycling. HIGHLIGHTSChemical structures of individual anthocyanins in citrus are reviewed.Differential anthocyanin biosynthesis in citrus depends on mutations of Ruby genes.Anthocyanins are enriched in response to exogenous stimulus during storage.Health benefits of extract in blood oranges and their waste are summarized.

Quantitative Transcriptomic and Proteomic Analysis of Fruit Development and Ripening in Watermelon (Citrullus lanatus)

Fruit ripening is a highly complicated process, which is modulated by phytohormones, signal regulators and environmental factors playing in an intricate network that regulates ripening-related genes expression. Although transcriptomics is an effective tool to predict protein levels, protein abundances are also extensively affected by post-transcriptional and post-translational regulations. Here, we used RNA sequencing (RNA-seq) and tandem mass tag (TMT)-based quantitative proteomics to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon, a non-climacteric fruit. A total of 6,226 proteins were quantified, and the large number of quantitative proteins is comparable to proteomic studies in model organisms such as Oryza sativa L. and Arabidopsis. Base on our proteome methodology, integrative analysis of the transcriptome and proteome showed that the mRNA and protein levels were poorly correlated, and the correlation coefficients decreased during fruit ripening. Proteomic results showed that proteins involved in alternative splicing and the ubiquitin proteasome pathway were dynamically expressed during ripening. Furthermore, the spliceosome and proteasome were significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, suggesting that post-transcriptional and post-translational mechanisms might play important roles in regulation of fruit ripening-associated genes expression, which might account for the poor correlation between mRNAs and proteins during fruit ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of fruit ripening.

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

BACKGROUND

Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break.

RESULTS

Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions.

CONCLUSION

In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.

Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms

The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny "mutants" (T). The results showed W, TL, and T varied in gene expression, allelic expression, and alternative splicing. Most genes/pathways with significantly altered expression in TL compared to W remained similarly altered in T. Pathway and gene ontology enrichment analysis revealed that the expression of multiple pathways, including photosynthesis and cell wall biosynthesis, was altered among the three genotypes. Remarkably, two polar auxin transporter genes, PIN7 and LAX3, were expressed at a significantly lower level in TL than in both W and T, implying alternation of polar auxin transport in TL may be responsible for the vigorous growth and thornless phenotype. Furthermore, 131 and 68 plant defense-related genes were significantly upregulated and downregulated, respectively, in TL and T compared with W. These genes may be involved in enhanced salicylic acid (SA) dependent defense and repression of defense inducing callose deposition and programmed cell death. Overall, these results indicated that the phenotype changes of the TL bud-sport were associated with tremendous transcriptome alterations, providing new clues and targets for breeding and gene editing for citrus improvement.

MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo (Citrus grandis Osbeck)

'Liuyuezaoyou' is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck 'Guanximiyou'. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis.

Integrative analysis of metabolome and transcriptome profiles provides insight into the fruit pericarp pigmentation disorder caused by 'Candidatus Liberibacter asiaticus' infection

BACKGROUND

Mandarin 'Shatangju' is susceptible to Huanglongbing (HLB) and the HLB-infected fruits are small, off-flavor, and stay-green at the maturity period. To understand the relationship between pericarp color and HLB pathogen and the effect mechanism of HLB on fruit pericarp coloration, quantitative analyses of HLB bacterial pathogens and carotenoids and also the integrative analysis of metabolome and transcriptome profiles were performed in the mandarin 'Shatangju' variety with four different color fruits, whole green fruits (WGF), top-yellow and base-green fruits (TYBGF), whole light-yellow fruits (WLYF), and whole dark-yellow fruits (WDYF) that were infected with HLB.

RESULTS

the HLB bacterial population followed the order WGF > TYBGF > WLYF > WDYF. And there were significant differences between each group of samples. Regarding the accumulation of chlorophyll and carotenoid, the chlorophyll-a content in WGF was the highest and in WDYF was the lowest. The content of chlorophyll-b in WGF was significantly higher than that in other three pericarps. There were significant differences in the total content of carotenoid between each group. WGF and TYBGF pericarps were low in phytoene, γ-carotene, β-cryptoxanthin and apocarotenal, while other kinds of carotenoids were significantly higher than those in WDYF. And WLYF was only short of apocarotenal. We comprehensively compared the transcriptome and metabolite profiles of abnormal (WGF, TYBGF and WLYF) and normal (WDYF, control) pericarps. In total, 2,880, 2,782 and 1,053 differentially expressed genes (DEGs), including 121, 117 and 43 transcription factors were identified in the three comparisons, respectively. The qRT-PCR confirmed the expression levels of genes selected from transcriptome. Additionally, a total of 77 flavonoids and other phenylpropanoid-derived metabolites were identified in the three comparisons. Most (76.65 %) showed markedly lower abundances in the three comparisons. The phenylpropanoid biosynthesis pathway was the major enrichment pathway in the integrative analysis of metabolome and transcriptome profiles.

CONCLUSIONS

Synthesizing the above analytical results, this study indicated that different color pericarps were associated with the reduced levels of some carotenoids and phenylpropanoids derivatives products and the down-regulation of proteins in flavonoids, phenylpropanoids derivatives biosynthesis pathway and the photosynthesis-antenna proteins.

Comparative transcriptome analysis of unripe and ripe banana (cv. Nendran) unraveling genes involved in ripening and other related processes

Banana is one of the most important fruit crops consumed globally owing to its high nutritional value. Previously, we demonstrated that the ripe pulp of the banana cultivar (cv.) Nendran (AAB) contained a high amount of pro-vitamin A carotenoids. However, the molecular factors involved in the ripening process in Nendran fruit are unexplored. Hence, we commenced a transcriptome study by using the Illumina HiSeq 2500 at two stages i.e. unripe and ripe fruit-pulp of Nendran. Overall, 3474 up and 4727 down-regulated genes were obtained. A large number of identified transcripts were related to genes involved in ripening, cell wall degradation and aroma formation. Gene ontology analysis highlighted differentially expressed genes that play a key role in various pathways. These pathways were mainly linked to cellular, molecular and biological processes. The present transcriptome study also reveals a crucial role of up-regulated carotenoid biosynthesis pathway genes namely, lycopene beta cyclase and geranylgeranyl pyrophosphate synthase at the ripening stage. Genes related to the ripening and other processes like aroma and flavor were highly expressed in the ripe pulp. Expression of numerous transcription factor family genes was also identified. This study lays a path towards understanding the ripening, carotenoid accumulation and other related processes in banana.

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

Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.

Emerging approaches to determine maturity of citrus fruit

Owing to their health-boosting properties and other appreciable properties, citrus fruit is widely consumed and commercialized worldwide. Destination markets around the world vary in their fruit quality requirements and are also highly influenced by climatic conditions, agronomical and postharvest practices. Hence, harvesting decisions are arduous. Maturity indices in citrus fruit are highly variable and dependent on the species and varieties, growing regions, and destination markets. For decades, determination of the maturity of citrus fruit and predicting the near time of harvesting was a challenge for producers, researchers, and food safety agencies. Thus, the current review provides a correlation between maturity and internal components and an overview of techniques of maturity determination for citrus fruits. Also, stress has been given to the destructive and nondestructive methods to determine the maturity level of different citrus species. The techniques presented in this review portray continuous productiveness as an excellent quality assessment, particularly as ripening and maturity analysis tools for citrus fruits. Traditional techniques are time-consuming, laborious, costly, destructive, and tedious. Thus, these nondestructive techniques hold great potential to replace conventional procedures.

Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo

Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.

Transcriptome-wide identification and characterization of the Rab GTPase family in mango

The Rab GTPase family plays a vital role in several plant physiological processes including fruit ripening. Fruit softening during ripening involves trafficking of cell wall polymers and enzymes between cellular compartments. Mango, an economically important fruit crop, is known for its delicious taste, exotic flavour and nutritional value. So far, there is a paucity of information on the mango Rab GTPase family. In this study, 23 genes encoding Rab proteins were identified in mango by a comprehensive in silico approach. Sequence alignment and similarity tree analysis with the model plant Arabidopsis as a reference enabled the bona fide assignment of the deduced mango proteins to classify into eight subfamilies. Expression analysis by RNA-Sequencing (RNA-Seq) showed that the Rab genes were differentially expressed in ripe and unripe mangoes suggesting the involvement of vesicle trafficking during ripening. Interaction analysis showed that the proteins involved in vesicle trafficking and cell wall softening were interconnected providing further evidence of the involvement of the Rab GTPases in fruit softening. Correlation analyses showed a significant relationship between the expression level of the RabA3 and RabA4 genes and fruit firmness at the unripe stage of the mango varieties suggesting that the differences in gene expression level might be associated with the contrasting firmness of these varieties. This study will not only provide new insights into the complexity of the ripening-regulated molecular mechanism but also facilitate the identification of potential Rab GTPases to address excessive fruit softening.

Proteomic Analysis of Heart and Kidney Tissues in Healthy and Metabolic Syndrome Rats after Hesperidin Supplementation

SCOPE

Proteomics has provided new strategies to elucidate the mechanistic action of hesperidin, a flavonoid present in citrus fruits. Thus, the aim of the present study is to determine the effects of hesperidin supplementation (HS) on the proteomic profiles of heart and kidney tissue samples from healthy and metabolic syndrome (MS) rats.

METHODS AND RESULTS

24 Sprague Dawley rats are randomized into four groups: healthy rats fed with a standard diet without HS, healthy rats administered with HS (100 mg kg^-1 day^-1 ), MS rats without HS, and MS rats administered with HS (100 mg kg^-1 day^-1 ) for eight weeks. Heart and kidney samples are obtained, and proteomic analysis is performed by mass spectrometry. Multivariate, univariate, and ingenuity pathways analyses are performed. Comparative and semiquantitative proteomic analyses of heart and kidney tissues reveal differential protein expression between MS rats with and without HS. The top diseases and functions implicated are related to the cardiovascular system, free radical scavenging, lipid metabolism, glucose metabolism, and renal and urological diseases.

CONCLUSION

This study is the first to demonstrate the protective capacity of hesperidin to change to the proteomic profiles in relation to different cardiovascular risk biomarkers in the heart and kidney tissues of MS rats.

Assessment of sugar and sugar accumulation-related gene expression profiles reveal new insight into the formation of low sugar accumulation trait in a sweet orange (Citrus sinensis) bud mutant

The accumulation of soluble sugars in fleshy fruits largely determines their sweetness or taste. A spontaneous sweet orange mutant 'Hong Anliu' (HAL, Citrus sinensis) accumulates low soluble sugar content in fruit juice sacs than its wild type, 'Anliu' (AL) orange; however, the cause of reduced sugar content in 'HAL' fruit remains unclear. In this study, sugar content and expression profiles of genes involved in sugar metabolism and transport were compared between 'HAL' and 'AL' fruit juice sacs. In both cultivars, fructose and glucose displayed the increasing trends with significantly lower contents in 'HAL' than 'AL' after 160 DAF; moreover, sucrose had a declining trend in 'HAL' and increasing trend in 'AL' with fruit development. On the other hand, transcript levels of VINV, CWINV1, CWINV2, SUS4, SUS5, SPS1, SPS2, VPP-1, VPP-2, and some sugar transporter genes were significantly decreased in 'HAL' compared with 'AL' after 100 DAF or 160 DAF. Interestingly, the transcript levels of SPS2 and SUT2 exhibited a similar trend as it was found for sucrose content in both cultivars. These results suggested that the low sugar accumulation in 'HAL' fruit JS is accompanied by the reduced sink strength, sucrose-synthesis ability, and vacuolar storage ability compared with 'AL'; reduction of CWINVs, VINV, SPS2, SUT2, VPP-1, and VPP-2 transcript levels possibly plays a key role in the low storage of soluble sugars in the vacuoles of mutant juice sacs.

Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion

Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening process at the proteomic level have been executed so far. To get a better understanding regarding the sweet cherry abscission mechanism, proteomic analysis between the abscising carpopodium and non-abscising carpopodium of sweet cherry was accomplished using a newly developed Liquid chromatography-mass spectrometry/mass spectrometry with Tandem Mass Tag (TMT-LC-MS/MS) methodology. The embryo viability experiments showed that the vigor of the abscission embryos was significantly lower than that of retention embryo. The activity of cell wall degrading enzymes in abscising carpopodium was significantly higher than that in non-abscising carpopodium. The anatomy results suggested that cells in the abscission zone were small and separated. In total, 6280 proteins were identified, among which 5681 were quantified. It has been observed that differentially accumulated proteins (DAPs) influenced several biological functions and various subcellular localizations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that plenty of metabolic pathways were notably enriched, particularly those involved in phytohormone biosynthesis, cell wall metabolism, and cytoskeletal metabolism, including 1-aminocyclopropane-1-carboxylate oxidase proteins which promote ethylene synthesis, and proteins promoting cell wall degradation, such as endoglucanases, pectinase, and polygalacturonase. Differential expression of proteins concerning phytohormone biosynthesis might activate the shedding regulation signals. Up-regulation of several cell wall degradation-related proteins possibly regulated the shedding of plant organs. Variations of the phytohormone biosynthesis and cell wall degradation-related proteins were explored during the abscission process. Furthermore, changes in cytoskeleton-associated proteins might contribute to the abscission of carpopodium. The current work represented the first study using comparative proteomics between abscising carpopodium and non-abscising carpopodium. These results indicated that embryo abortion might lead to phytohormone synthesis disorder, which effected signal transduction pathways, and hereby controlled genes involved in cell wall degradation and then caused the abscission of fruitlet. Overall, our data may give an intrinsic explanation of the variations in metabolism during the abscission of carpopodium.

Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

BACKGROUND

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

RESULTS

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

CONCLUSIONS

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

Background

Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.

Results

Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage).

Conclusions

The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

Citrus Taste Modification Potentials by Genetic Engineering

Citrus fruits are mainly consumed as fresh fruit and processed juice products. They serve as nutritional and a tasty diet in our daily life. However, the formidable bitterness and delayed bitterness significantly impact the citrus industry attributable to the two major bitter compounds naringin and limonin. The extremely sour and acidic also negatively affects the sensory quality of citrus products. Citrus breeding programs have developed different strategies to improve citrus quality and a wealth of studies have aimed to uncover the genetic and biochemical basis of citrus flavor. In this minireview, we outline the major genes characterized to be involved in pathways shaping the sweet, bitter, or sour taste in citrus, and discuss briefly about the possible approaches to modify citrus taste by genetic engineering.

Targeted transcriptional and proteomic studies explicate specific roles of Bacillus subtilis iturin A, fengycin, and surfactin on elicitation of defensive systems in mandarin fruit during stress

Application of Bacillus cyclic lipopeptides (CLPs); fengycin, iturin A and surfactin has shown a great potential in controlling the spread of green mold pathogen invasion (Penicillium digitatum) in wounded mandarin fruit during postharvest period. The limited defensive protein profiles followed specific expression of pivotal genes relating to plant hormone mediating signaling pathways of the CLPs’ action on stimulating host plant resistance have been exhibited. The present study aimed to elucidate the specific effect of individual CLP obtained from Bacillus subtilis ABS-S14 as elicitor role on activation of plant defensive system at transcriptional and proteomic levels with and without P. digitatum co-application in mandarin fruit. Fengycin and iturin A elevated the gene expression of PAL, ACS1, ACO, CHI, and GLU while significantly stimulating plant POD transcription was only detected in the treatments of surfactin both with and without following P. digitatum. An increase of LOX and PR1 gene transcripts was determined in the treatments of individual CLP with fungal pathogen co-application. Fengycin activated production of unique defensive proteins such as protein involved in ubiquinone biosynthetic process in treated flavedo without P. digitatum infection. Proteins involved in the auxin modulating pathway were present in the iturin A and surfactin treatments. CLP-protein binding assay following proteome analysis reveals that iturin A attached to 12-oxophytodienoate reductase 2 involved in the oxylipin biosynthetic process required for jasmonic acid production which is implicated in induced systemic resistance (ISR). This study suggests specific elicitor action of individual CLP, particularly iturin A showed the most powerful in stimulating the ISR system in response to stresses in postharvest mandarins.

Quantitative proteomic analyses identified multiple sugar metabolic proteins in soybean under shade stress

Soybean-based intercropping is important for sustainable agricultural practice on a regional and global scale. However, most soybean varieties use shade avoidance strategy to acquire more light absorption when suffered in canopy shade in intercropping systems, thus reduced the yield of the whole population on a farmland. The mechanisms underlying early response of soybean in shade avoidance is still largely unknown. Here we report our identification of differentially accumulated proteins in shade-sensitive soybean seedlings by global quantitative proteome analysis under white light (WL) and shade conditions. By using Tandem Mass Tag (TMT) labelling and HPLC fractionation followed by high-resolution LC-MS/MS analysis, 29 proteins were found up-regulated and 412 proteins were found down-regulated in soybean seedlings by 2-h shade stress than that by 2-h WL treatment. Multiple differentially expressed proteins are enriched in carbohydrate metabolic process especially in the biosynthetic pathways of cell wall polysaccharides in soybean seedlings by shade stress comparing to those in WL growth conditions. Physiological assays showed that saccharides were rapidly declined in shoot apex of soybean seedlings under a short-term shading. Our results would provide new insights into the mechanisms of shade avoidance responses in soybean seedlings.

Modifications in Organic Acid Profiles During Fruit Development and Ripening: Correlation or Causation?

The pivotal role of phytohormones during fruit development and ripening is considered established knowledge in plant biology. Perhaps less well-known is the growing body of evidence suggesting that organic acids play a key function in plant development and, in particular, in fruit development, maturation and ripening. Here, we critically review the connection between organic acids and the development of both climacteric and non-climacteric fruits. By analyzing the metabolic content of different fruits during their ontogenetic trajectory, we noticed that the content of organic acids in the early stages of fruit development is directly related to the supply of substrates for respiratory processes. Although different organic acid species can be found during fruit development in general, it appears that citrate and malate play major roles in this process, as they accumulate on a broad range of climacteric and non-climacteric fruits. We further highlight the functional significance of changes in organic acid profile in fruits due to either the manipulation of fruit-specific genes or the use of fruit-specific promoters. Despite the complexity behind the fluctuation in organic acid content during fruit development and ripening, we extend our understanding on the importance of organic acids on fruit metabolism and the need to further boost future research. We suggest that engineering organic acid metabolism could improve both qualitative and quantitative traits of crop fruits.

Protein analysis of moro blood orange pulp during storage at low temperatures

A protein analysis in the pulp of Moro blood oranges (Citrus sinensis L. Osbeck) at the onset and after 30 days of storage at either 4 or 9 °C was performed. All differential proteins belonged to different functional classes (sugar, amino acid and secondary metabolism, defense, stress response, oxidative process, transport and cellular component biogenesis), displaying a differential accumulation in those Moro oranges kept at 9 versus 4 °C, and in those stored at 4 °C versus onset. Anthocyanin biosynthesis structural proteins chalcone synthases and flavonone 3-hydroxylase and different glutathione S-transferases related with their vacuolar transport were up-accumulated in fruits kept at 9 versus 4 °C and versus the onset. Proteins related with defense and oxidative stress displayed a similar pattern, concomitant with a higher anthocyanin content, denoting a possible role of defense and other stress response pathways in anthocyanin production/accumulation.