Comparison of transcriptome and metabolome analysis revealed differences in cold resistant metabolic pathways in different apple cultivars under low temperature stress

Horticultural Plant Journal, Год журнала: 2022, Номер 9(2), С. 183 - 198

Опубликована: Сен. 13, 2022

Freezing injury in winter is an important abiotic stress that seriously affects plant growth and development. Deciduous fruit trees resist freezing by inducing dormancy. However, different cultivars of the same species have cold resistance strategies. Little known about molecular mechanism apple response to during Therefore, this study, 1-year-old branches cold-resistant cultivar 'Hanfu' (HF) cold-sensitive 'Changfuji No. 2' (CF) were used explore their through physiological, biochemical, transcriptomics, metabolomics analyses. Combining physiological biochemical data, we found HF had a stronger osmotic regulation ability antioxidant enzyme activity than CF, as well resistance. The functional enrichment analysis showed both significantly enriched pathways related signal transduction, hormone regulation, sugar metabolism under stress. In addition, differentially expressed genes (DEGs) encoding galactinol synthase, raffinose stachyose synthetase family oligosaccharides (RFOs) metabolic upregulated HF, accumulated, while contents CF lower. accumulated 4-aminobutyric acid, spermidine, ascorbic acid scavenge reactive oxygen (ROS). While oxidized glutathione, vitamin C, spermidine decreased stress, consequently, ROS was low. Furthermore, transcription factors apetala 2/ethylene responsive factor (AP2/ERF) WRKY strongly induced summary, difference key components major affecting obtained results deepen our understanding

Язык: Английский

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A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

DNA Research, Год журнала: 2022, Номер 30(1)

Опубликована: Окт. 5, 2022

A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 540 Mb, which 96.2% contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 31 contigs a median size 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data curated sequences via MAKER pipeline generated 24,255 gene models. Results indicated is highly congruent published reference genome. Gross duplicate analyses revealed little large-scale intra-genome duplication. Reduced copy number for well-annotated families relative other core eudicots observed, especially transcription factors. Variation B. investigated by flow cytometry among 50 individuals producing estimates 633 875 Mb/1C. Read-depth mapping whole-genome germplasm suggested relatively few regions appeared associated high-copy variation.

Язык: Английский

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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites’ Biosynthesis

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(24), С. 15932 - 15932

Опубликована: Дек. 14, 2022

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used traditional medicine industrial additives. Plants have relatively little in way of secondary metabolites via biosynthesis. Recently, whole-genome sequencing medicinal identification metabolite production were revolutionized by rapid development cheap cost technology. Advances functional genomics, such as transcriptomics, proteomics, metabolomics, pave discoveries related key genes. The multi-omics approaches can offer tremendous insight into variety, distribution, biosynthetic gene clusters (BGCs). Although many reviews reported on plant genome, chemistry, pharmacology, there is no review giving a comprehensive report about genome to study biosynthesis pathway metabolites. Here, we introduce application tools identifying genes Moreover, explore comparative genomics polyploidy family analysis plants. This promotes which contributes screening plant-based drugs prompts research efficiency medicine.

Язык: Английский

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Advances in understanding cold tolerance in grapevine

PLANT PHYSIOLOGY, Год журнала: 2023, Номер 192(3), С. 1733 - 1746

Опубликована: Фев. 15, 2023

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes buds of grapevine should withstand low temperatures (LTs) annually during winter. However, widely cultivated Vitis vinifera cold-sensitive cannot survive severe winter in regions with extremely LTs, such as viticulture northern China. By contrast, few wild species like V. amurensis riparia exhibit excellent freezing tolerance. mechanisms underlying cold tolerance remain largely unknown. In recent years, much progress has been made elucidating mechanisms, owing to advances sequencing molecular biotechnology. Assembly genomes together resequencing transcriptome data enable researchers conduct genomic transcriptomic analyses various genotypes populations explore genetic variations involved addition, number pivotal genes have identified functionally characterized. this review, we summarize major physiological put forward questions field. We also discuss strategies for improving stress. Understanding will facilitate development grapevines adaption global climate change.

Язык: Английский

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Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Сен. 3, 2021

Abstract Background Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute introgression, we investigate six wild Vitis species are native the Southwestern United States useful for breeding grapevine ( V. vinifera ) rootstocks. Results By creating a reference genome assembly from one species, arizonica , by resequencing 130 accessions, focus on identifying putatively introgressed regions (pIRs) between species. We find pairs with signals of introgression them, comprising up ~ 8% extant some pairs. The pIRs tend be gene poor, located in high recombination enriched genes implicated disease resistance functions. assess potential pIR function, explore SNP associations bioclimatic variables bacterial levels after infection causative agent Pierce’s Xylella fastidiosa ). SNPs associated both climate levels, suggesting is driven biotic abiotic stressors. Conclusions Altogether, this study yields insights genomic extent pressures shape adaptive history economically important relatives critical crop.

Язык: Английский

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Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Horticulture Research, Год журнала: 2023, Номер 10(3)

Опубликована: Фев. 1, 2023

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra), a diploid, horticultural important woody is native to much of eastern North America. Although it highly valued for its wood and nut, there few resources understanding EBW genetics. Here, we present high-quality genome assembly J. nigra based on Illumina, Pacbio, Hi-C technologies. The size was 540.8 Mb, with scaffold N50 35.1 99.0% the anchored 16 chromosomes. Using this reference, resequencing 74 accessions revealed effective population declined during glacial maximum. A single whole-genome duplication event identified in genome. Large syntenic blocks among nigra, regia, microcarpa predominated, but inversions more than 600 kb were identified. By comparing those regia microcarpa, detected InDel sizes 34.9 Mb 18.3 respectively. Transcriptomic analysis differentially expressed genes five presumed NBS-LRR (NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT) upregulated development husks shells compared developing embryos. We also candidate essential roles seed oil synthesis, including FAD (FATTY ACID DESATURASE) OLE (OLEOSIN). Our work advances fatty acid bioaccumulation disease resistance crops, provides an resource conducting genomics-enabled breeding walnut.

Язык: Английский

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Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

Frontiers in Plant Science, Год журнала: 2021, Номер 12

Опубликована: Июнь 1, 2021

Cold stress poses a serious treat to cultivated kiwifruit since this plant generally has weak ability tolerate freezing tolerance temperatures. Surprisingly, however, the underlying mechanism of kiwifruit’s remains largely unexplored and unknown, especially regarding key pathways involved in conferring trait. Here, we studied metabolome transcriptome profiles freezing-tolerant genotype KL ( Actinidia arguta ) freezing-sensitive RB A. ), identify main important metabolites related their tolerance. A total 565 were detected by wide-targeting metabolomics method. Under (−25°C) cold stress, KEGG (Kyoto Encyclopedia Genes Genomes) pathway annotations showed that flavonoid metabolic specifically upregulated KL, which increased its scavenge for reactive oxygen species (ROS). The changes identified accompanied specific upregulation codeinone reductase gene, chalcone isomerase an anthocyanin 5-aromatic acyltransferase gene. Nucleotides metabolism phenolic acids RB, indicated had higher energy weaker dormancy ability. Since LPCs (LysoPC), LPEs (LysoPE) free fatty accumulated simultaneously both genotypes, these could serve as biomarkers cold-induced frost damages. These components evidently participated regulation genotypes. In conclusion, results study demonstrated inherent differences composition activity between under conditions.

Язык: Английский

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Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances

BMC Plant Biology, Год журнала: 2021, Номер 21(1)

Опубликована: Авг. 11, 2021

Abstract Background Kiwifruit ( Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this highly vulnerable freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying tolerance, we carried out a hybrid transcriptome analysis two A. arguta Actinidi ) genotypes, KL and RB, whose tolerance high low, respectively. Both genotypes were subjected − 25 °C for 0 h, 1 4 h. Results SMRT (single-molecule real-time) RNA-seq data assembled using de novo method, producing 24,306 unigenes with N50 value 1834 bp. Kyoto Encyclopedia Genes Genomes (KEGG) enrichment DEGs showed that they involved in ‘starch sucrose metabolism’, ‘mitogen-activated protein kinase (MAPK) signaling pathway’, ‘phosphatidylinositol system’, ‘inositol phosphate ‘plant hormone signal transduction’. In particular, identified 3 key genes cellulose degradation, trehalose synthesis, starch degradation processes. Moreover, activities beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), BAM (beta-amylase), encoded by abovementioned genes, enhanced cold Three transcription factors (TFs) belonging AP2/ERF, bHLH (basic helix-loop-helix), MYB families response. Furthermore, weighted gene coexpression network (WGCNA) indicated , TPS5 BAM3.1 response coexpressed together CBF3 MYC2 MYB44 genes. Conclusions Cold stress led various changes kiwifruit, ‘MAPK transduction’, metabolism’ processes significantly affected low temperature. metabolism may be pathway tolerant kiwifruit resist temperature damages. These results increase our understanding complex mechanisms reveal series candidate use breeding new cultivars tolerance.

Язык: Английский

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VabHLH137 promotes proanthocyanidin and anthocyanin biosynthesis and enhances resistance to Colletotrichum gloeosporioides in grapevine

Horticulture Research, Год журнала: 2022, Номер 10(2)

Опубликована: Дек. 2, 2022

Abstract Proanthocyanidins (PAs) and anthocyanins are involved in the response of plants to various environmental stresses. However, mechanism behind defense-induced PA biosynthetic regulation is still not completely elucidated, also grapevine. This study performed a transcriptome sequencing analysis grape berries infected with Colletotrichum gloeosporioides highlight induction VabHLH137 factor from basic helix–loop–helix (bHLH) XII subfamily by fungus, which appeared be significantly co-expressed PA-related genes. The functional overexpression knockdown transgenic calli showed that it positively regulated anthocyanin biosynthesis. Moreover, increased resistance C. gloeosporioides. A yeast one-hybrid electrophoretic mobility shift assay revealed directly bound VaLAR2 promoter, enhancing its activity interacting VaMYBPAR, transcriptional activator Furthermore, transient experiments although + VaMYBPAR complex activated expression, failed further enhance expression compared alone. findings indicated enhanced biosynthesis activating providing new insight into

Язык: Английский

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Genomic insights into domestication and genetic improvement of fruit crops

PLANT PHYSIOLOGY, Год журнала: 2023, Номер 192(4), С. 2604 - 2627

Опубликована: Май 10, 2023

Abstract Fruit crops cultivated in almost all countries and regions around the world serve as important agricultural commodities of significant economic value because they contribute to overall food security by providing a diverse nutrient supply sustain human life health. Recent advances high-throughput sequencing technologies offer unprecedented opportunities for pursuing genomic genetic studies fruit crops. Here, we will review major crop genome efforts undertaken over past 15 years that have contributed accumulation publicly available resources. We highlight expanding pool data better unravel origin domestication trees, well deciphering genetics horticultural traits these trees. Furthermore, explore how utilization features trees along with new genomic-assisted tools, including selection gene editing, are informing guiding plant geneticists breeders moving forward their breeding efforts. Finally, outline future prospects unresolved questions remain both research improvement

Язык: Английский

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