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Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

ABSTRACT: Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.

SUBMITTER: Wu J

PROVIDER: S-EPMC8591526 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundGarlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic.ResultsA transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1-4% of the reads were found in the foliage leaves.ConclusionsThe de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics.

Project description:BackgroundGarlic (Allium sativum L.) is the second most widely cultivated Allium which is mainly grown in temperate regions and used as a flavoring agent in a wide variety of foods. Garlic contains various bioactive compounds whose metabolic pathways, plant-pathogen interactions, defensive genes, identify interaction networks, and functional genomics were not previously predicted in the garlic at the genomic level. To address this issue, we constructed two garlic Illumina 2000 libraries from tissues of garlic clove and leaf.ResultsApproximately 43 million 125 bp paired-end reads were obtained in the two libraries. A total of 239,973 contigs were generated by de novo assembly of both samples and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 42% of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 138 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, a number of regulatory genes including the CCHC (Zn) family, followed by WD40, bromodomain, bZIP, AP2-EREBP, BED-type (Zn) proteins, and defense response proteins related to different conserved domains, such as RGA3, NBS-LRR, TIR-NBS-LRR, LRR, NBS-ARC, and CC-NBS-LRR were discovered based on the transcriptome dataset. We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana, O. sativa, and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanisms, their protein-protein interaction network, and plant-pathogen interaction pathways.ConclusionsOur study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L.

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Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

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