Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis

Research advancements in the maintenance mechanism of Sporidiobolus pararoseus enhancing the quality of soy sauce during fermentation

Soy sauce is a traditional condiment that undergoes microbial fermentation of various ingredients to achieve its desired color, scent, and flavor. Sporidiobolus pararoseus, which is a type of Rhodocerevisiae, shows promising potential as a source of lipids, carotenoids, and enzymes that can enrich the taste and color of soy sauce. However, there is currently a lack of systematic and comprehensive studies on the functions and mechanisms of action of S. pararoseus during soy sauce fermentation. In this review, it is well established that S. pararoseus produces lipids that are abundant in unsaturated fatty acids, particularly oleic acid, as well as various carotenoids, such as β-carotene, torulene, and torularhodin. These pigments are synthesized through the mevalonic acid pathway and possess remarkable antioxidant properties, acting as natural colorants. The synthesis of carotenoids is stimulated by high salt concentrations, which induces oxidative stress caused by NaCl. This stress further activates crucial enzymes involved in carotenoid production, ultimately leading to pigment formation. Moreover, S. pararoseus can produce high-quality enzymes that aid in the efficient utilization of soy sauce substrates during fermentation. Furthermore, this review focused on the impact of S. pararoseus on the color and quality of soy sauce and comprehensively analyzed its characteristics and ingredients. Thus, this review serves as a basis for screening high-quality oleaginous red yeast strains and improving the quality of industrial soy sauce production through the wide application of S. pararoseus.

Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep

Tibetan sheep have lived on the Qinghai-Tibetan Plateau for thousands of years and have good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism by which Tibetan sheep adapt to this extreme environment, especially the role of genetic regulation, is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in the adaptation to high-altitude hypoxia of Tibetan sheep, we analysed the expression profile of lncRNAs and mRNAs in the liver and lung tissues of sheep using comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and one Hu sheep population (low altitude). The results showed a total of 7848 differentially expressed (DE) lncRNA transcripts, and 22,971 DE mRNA transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR, and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA–mRNA and lncRNA–mRNA interaction networks further revealed transcripts potentially involved in adaptation to high-altitude hypoxia, and the hub genes DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, and TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1, were also identified as candidate genes associated with high-altitude hypoxia adaptation. In conclusion, a collection of novel expressed lncRNAs, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results are the first to identify the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provide insights into the genetic regulation mechanisms by which Tibetan sheep adapt to high-altitude hypoxic environments.

RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars

BACKGROUND

Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel.

RESULTS

Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with a N50 of 3603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways.

CONCLUSIONS

Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.

Transcriptomic and metabolomic analysis reveals the role of CoA in the salt tolerance of Zygophyllum spp

BACKGROUND

Zygophyllum is an important medicinal plant, with notable properties such as resistance to salt, alkali, and drought, as well as tolerance of poor soils and shifting sand. However, the response mechanism of Zygophyllum spp. to abiotic stess were rarely studied.

RESULTS

Here, we aimed to explore the salt-tolerance genes of Zygophyllum plants by transcriptomic and metabolic approaches. We chose Z. brachypterum, Z. obliquum and Z. fabago to screen for salt tolerant and sensitive species. Cytological observation showed that both the stem and leaf of Z. brachypterum were significantly thicker than those of Z. fabago. Then, we treated these three species with different concentrations of NaCl, and found that Z. brachypterum exhibited the highest salt tolerance (ST), while Z. fabago was the most sensitive to salt (SS). With the increase of salt concentration, the CAT, SOD and POD activity, as well as proline and chlorophyll content in SS decreased significantly more than in ST. After salt treatment, the proportion of open stomata in ST decreased significantly more than in SS, although there was no significant difference in stomatal number between the two species. Transcriptomic analysis identified a total of 11 overlapping differentially expressed genes (DEGs) in the leaves and roots of the ST and SS species after salt stress. Two branched-chain-amino-acid aminotransferase (BCAT) genes among the 11 DEGs, which were significantly enriched in pantothenate and CoA biosynthesis, as well as the valine, leucine and isoleucine biosynthesis pathways, were confirmed to be significantly induced by salt stress through qRT-PCR. Furthermore, overlapping differentially abundant metabolites showed that the pantothenate and CoA biosynthesis pathways were significantly enriched after salt stress, which was consistent with the KEGG pathways enriched according to transcriptomics.

CONCLUSIONS

In our study, transcriptomic and metabolomic analysis revealed that BCAT genes may affect the pantothenate and CoA biosynthesis pathway to regulate the salt tolerance of Zygophyllum species, which may constitute a newly identified signaling pathway through which plants respond to salt stress.

Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea (Pisum sativum L.)

Pea (Pisum sativum L.), as a major source of plant protein, is becoming one of the major cultivated crop species worldwide. In pea, the pericarp is an important determinant of the morphological characteristics and seed yield. To investigate the molecular mechanism of pericarp elongation as well as sucrose and starch accumulation in the pods of different pea cultivars, we performed transcriptomic analysis of the pericarp of two types of pea cultivar (vegetable pea and grain pea) using RNA-seq. A total of 239.44 Gb of clean sequence data were generated, and were aligned to the reference genome of Pisum sativum L. In the two samples, 1935 differentially expressed genes (DEGs) were identified. Among these DEGs, three antioxidant enzyme superoxide dismutase (SOD) were detected to have higher expression levels in the grain pea pericarps at the pod-elongating stages. Otherwise, five peroxidase (POD)-encoding genes were detected to have lower expression levels in the vegetative pericarps at the development stage of pea pod growth. Furthermore, genes related to starch and sucrose metabolism in the pea pod, such as SUS, INV, FBA, TPI, ADPase, SBE, SSS, and GBSS, were found to be differentially expressed. The RNA-seq data were validated through real-time quantitative RT-PCR of 13 randomly selected genes. Our findings provide the gene expression profile of, as well as differential expression information on, the two pea cultivars, which will lay the foundation for further studies on pod development and nutrition accumulation in the pea and provide valuable information for pea cultivar improvement.

Identification of the Genes Involved in Anthocyanin Biosynthesis and Accumulation in Taxus chinensis

Taxus chinensis is a precious woody species with significant economic value. Anthocyanin as flavonoid derivatives plays a crucial role in plant biology and human health. However, the genes involved in anthocyanin biosynthesis have not been identified in T. chinensis. In this study, twenty-five genes involved in anthocyanin biosynthesis were identified, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, anthocyanidin synthase, flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, dihydroflavonol 4-reductase, anthocyanidin reductase, and leucoanthocyanidin reductase. The conserved domains and phylogenetic relationships of these genes were characterized. The expression levels of these genes in different tissues and different ages of xylem were investigated. Additionally, the anthocyanin accumulation in xylem of different ages of T. chinensis was measured. The results showed the anthocyanin accumulation was correlated with the expression levels of dihydroflavonol 4-reductase, anthocyanidin synthase, flavonoid 3'-hydroxylase, and flavonoid 3',5'-hydroxylase. Our results provide a basis for studying the regulation of the biosynthetic pathway for anthocyanins and wood color formation in T. chinensis.

Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Background

Colored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed coat color is an important agronomic trait for the breeding and study of hulless barley.

Results

Genotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) analysis of a doubled haploid (DH) mapping population (Nierumuzha × Kunlun10) was conducted to map the purple seed coat color genes (Psc). A high-density genetic map of hulless barley was constructed, which contains 3662 efficient SNP markers with 1129 bin markers. Seven linkage groups were resolved, which had a total length of 645.56 cM. Chromosome length ranged from 60.21 cM to 127.21 cM, with average marker density of 0.57 cM. A total of five loci accounting for 3.79% to 23.86% of the observed phenotypic variation for Psc were detected using this high-density map. Five structural candidate genes (F3’M, HID, UF3GT, UFGT and 5MAT) and one regulatory factor (Ant1) related to flavonoid or anthocyanin biosynthesis were identified..

Conclusions

Five structural candidate genes and one regulatory factor related to flavonoid or anthocyanin biosynthesis have been identified using a high-density genetic map of hulless barley. This study lays the foundation for map-based cloning of Psc but provides a valuable tool for studying marker-trait associations and its application to marker-assisted breeding of hulless barley.

Electronic supplementary material

The online version of this article (10.1186/s41065-018-0072-6) contains supplementary material, which is available to authorized users.

Multi-omics metabolism analysis on irradiation-induced oxidative stress to Rhodotorula glutinis

Oxidative stress is induced in many organisms by various natural abiotic factors including irradiation. It has been demonstrated that it significantly improves growth rate and lipid production of Rhodotorula glutinis. However, the specific mechanism of how irradiation influences the metabolism of R. glutinis remains still unavailable. To investigate and better understand the mechanisms involved in irradiation-induced stress resistance in R. glutinis, a multi-omics metabolism analysis was implemented. The results confirmed that irradiation indeed not only improved cell biomass but also accelerated the production of carotenoids and lipids, especially neutral lipid. Compared with the control, metabolome profiling in the group exposed to irradiation exhibited an obvious difference in the activation of the tricarboxylic acid cycle and triglyceride (TAG) production. The results of proteome analysis (data are available via ProteomeXchange with identifier PXD009678) showed that 423 proteins were changed significantly, and proteins associated with protein folding and transport, the Hsp40 and Sec12, were obviously upregulated, indicating that cells responded to irradiation by accelerating the protein folding and transport of correctly folded proteins as well as enhanced the degradation of misfolded proteins. A significant upregulation of the carotenoid biosynthetic pathway was observed which revealed that increased carotenoid content is a cellular defense mechanism against oxidative stress generated by irradiation. Therefore, the results of comprehensive omics analysis provide intensive insights on the response mechanism of R. glutinis to irradiation-induced oxidative stress which could be helpful for using irradiation as an effective strategy to enhance the joint production of the neutral lipid and carotene.