Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
| Autor: | Haim D. Rabinowitch, Adi Faigenboim, Dani Eshel, Sarit Rohkin Shalom, Sagie Kimhi, Tomer E. Ben Michael, Itzhak Esquira, Chen Gershberg, Amir Sherman, Rina Kamenetsky, Einat Shemesh Mayer |
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| Jazyk: | angličtina |
| Předmět: |
Assembly
Plant genetics Flowers Breeding Biology Genes Plant Plant Roots Flowering Transcriptome Gene Expression Regulation Plant Gene expression Genetics Cluster Analysis Garlic Gene Gene Library Regulation of gene expression Sulfur metabolism Sequence Analysis RNA Gene Expression Profiling food and beverages Allium sativum Enzymes Plant Leaves Gene expression profiling Inflorescence Garlic virus Seeds Flexiviridae Sulfur Research Article Biotechnology |
| Zdroj: | BMC Genomics |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-015-1212-2 |
| Popis: | Background Garlic 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. Results A 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. Conclusions The 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1212-2) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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