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Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.).

Kamenetsky R, Faigenboim A, Shemesh Mayer E, Ben Michael T, Gershberg C, Kimhi S, Esquira I, Rohkin Shalom S, Eshel D, Rabinowitch HD, Sherman A - BMC Genomics (2015)

Bottom Line: Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. vhrkamen@volcani.agri.gov.il.

ABSTRACT

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.

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Related in: MedlinePlus

Hierarchical cluster analysis of gene-expression patterns in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each contig (rows) in each sample (columns). Four identified gene clusters (shown in the left tree) are differentially expressed in one or more organs. Organs are clustered to reproductive and vegetative, with closer proximity between the roots and basal plates (upper tree). Expression values (FPKM) are log2-transformed and then median-centered by transcript.
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Fig3: Hierarchical cluster analysis of gene-expression patterns in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each contig (rows) in each sample (columns). Four identified gene clusters (shown in the left tree) are differentially expressed in one or more organs. Organs are clustered to reproductive and vegetative, with closer proximity between the roots and basal plates (upper tree). Expression values (FPKM) are log2-transformed and then median-centered by transcript.

Mentions: Global gene-expression profiling of the abundant transcriptome revealed differential patterns between the vegetative and reproductive organs (Figure 3). The vegetative organs could be clustered into two defined groups, with the underground organs—roots and basal plate—sharing both close proximity and many expressed sequences. In bulbous geophytes, the basal plate (the compressed actual stem) is morphologically associated with the roots, leaves and renewal buds [38]. When the reproductive stage begins, an apical meristem forms the floral scape and inflorescence. Flower differentiation in garlic is affected by endogenous and environmental signals. However, it is not clear whether florogenesis is regulated by direct signal transduction from the vegetative organs, or is only supported by photosynthetic products and storage materials from foliage leaves and the underground bulb [9,13].Figure 3


Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.).

Kamenetsky R, Faigenboim A, Shemesh Mayer E, Ben Michael T, Gershberg C, Kimhi S, Esquira I, Rohkin Shalom S, Eshel D, Rabinowitch HD, Sherman A - BMC Genomics (2015)

Hierarchical cluster analysis of gene-expression patterns in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each contig (rows) in each sample (columns). Four identified gene clusters (shown in the left tree) are differentially expressed in one or more organs. Organs are clustered to reproductive and vegetative, with closer proximity between the roots and basal plates (upper tree). Expression values (FPKM) are log2-transformed and then median-centered by transcript.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307630&req=5

Fig3: Hierarchical cluster analysis of gene-expression patterns in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each contig (rows) in each sample (columns). Four identified gene clusters (shown in the left tree) are differentially expressed in one or more organs. Organs are clustered to reproductive and vegetative, with closer proximity between the roots and basal plates (upper tree). Expression values (FPKM) are log2-transformed and then median-centered by transcript.
Mentions: Global gene-expression profiling of the abundant transcriptome revealed differential patterns between the vegetative and reproductive organs (Figure 3). The vegetative organs could be clustered into two defined groups, with the underground organs—roots and basal plate—sharing both close proximity and many expressed sequences. In bulbous geophytes, the basal plate (the compressed actual stem) is morphologically associated with the roots, leaves and renewal buds [38]. When the reproductive stage begins, an apical meristem forms the floral scape and inflorescence. Flower differentiation in garlic is affected by endogenous and environmental signals. However, it is not clear whether florogenesis is regulated by direct signal transduction from the vegetative organs, or is only supported by photosynthetic products and storage materials from foliage leaves and the underground bulb [9,13].Figure 3

Bottom Line: Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. vhrkamen@volcani.agri.gov.il.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus