Limits...
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.

Show MeSH

Related in: MedlinePlus

Hierarchical cluster analysis of gene-expression patterns of 26 annotated variants and isoforms of O-acetylserine(thiol)-lyase (OASS) in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each variant (rows) in each organ (columns). Expression values (FPKM) are log2-transformed and then median-centered by variant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Hierarchical cluster analysis of gene-expression patterns of 26 annotated variants and isoforms of O-acetylserine(thiol)-lyase (OASS) in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each variant (rows) in each organ (columns). Expression values (FPKM) are log2-transformed and then median-centered by variant.

Mentions: Using de novo assembly of the garlic transcriptome, we distinguished about 100 variants and isoforms of nine enzymes involved in sulfur metabolism in different organs of the garlic plant (Table 4). Isoforms of OASS varied significantly in their distribution in the garlic organs (Figure 5). Over-representation was notable in the cloves, roots, basal plate and leaves, whereas in the reproductive tissues, most of the annotated isoforms were less abundant. The isoforms were clustered into six groups, with clear expression patterns in the different organs. For instance, within cluster #3 (highlighted in light blue in Figure 5), the three variants were enriched exclusively in cloves. The 10 variants and isoforms of SAT were also differentially expressed in the six garlic organs (data not shown), but organ clustering differed from that of OASS.Table 4


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 of 26 annotated variants and isoforms of O-acetylserine(thiol)-lyase (OASS) in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each variant (rows) in each organ (columns). Expression values (FPKM) are log2-transformed and then median-centered by variant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Hierarchical cluster analysis of gene-expression patterns of 26 annotated variants and isoforms of O-acetylserine(thiol)-lyase (OASS) in six vegetative and reproductive organs of garlic. The heat map shows the relative expression levels of each variant (rows) in each organ (columns). Expression values (FPKM) are log2-transformed and then median-centered by variant.
Mentions: Using de novo assembly of the garlic transcriptome, we distinguished about 100 variants and isoforms of nine enzymes involved in sulfur metabolism in different organs of the garlic plant (Table 4). Isoforms of OASS varied significantly in their distribution in the garlic organs (Figure 5). Over-representation was notable in the cloves, roots, basal plate and leaves, whereas in the reproductive tissues, most of the annotated isoforms were less abundant. The isoforms were clustered into six groups, with clear expression patterns in the different organs. For instance, within cluster #3 (highlighted in light blue in Figure 5), the three variants were enriched exclusively in cloves. The 10 variants and isoforms of SAT were also differentially expressed in the six garlic organs (data not shown), but organ clustering differed from that of OASS.Table 4

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