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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1212-2) contains supplementary material, which is available to authorized users.

Mechanisms of vegetative propagation in bulbs : a molecular approach

“…A search for orthology groups that only contained proteins from the bulbous species tulip, lily, and garlic (Kamenetsky et al 2015), revealed a set of 281 unique groups that might represent bulbous plant specific genes.…”

“…The Illumina HiSeq platform was used to sequence a pooled sample for lily and for tulip, each made up of a mixture of equal amounts of poly adenylated mRNA obtained from flowers, stem, leaves, bulb and bulblets. Even though short reads are generated with the Illumina HiSeq platform, a tremendous throughput can be reached, resulting in an improved coverage of rare transcripts in comparison to the other platforms used in some of the previous transcriptome studies of bulbous species (Shahin et al 2012b;Kamenetsky et al 2015). The generated data was used to assemble reference transcriptomes for tulip and lily.…”

Validation of RNA Interference for Improvement in Mustard (Brassica sp.): A Review

“…Kamenetsky et al, (2015) studied the distribution of four Allexiviruses are garlic virus-A, garlic virus-C, garlic virus-E and garlic virus-X in six organs of garlic namely basal plate, leaves, inflorescence, flowers, roots and cloves. They found differential viral transcript expression levels in different tissues using transcriptome analysis in virus-free and virus-infected garlic plants.…”

The hot, the cold and the tulip : the regulation of flowering time and dormancy release

“…A maximum likelihood tree was constructed with MEGA 5.1 (Tamura et al, 2011) AsTFL1-1 and AsTFL1-2) of Allium sativum were identified in the data of Kamenetsky et al, (2015), by an assembly of the raw data with Trinity (Haas et al, 2013). The other Lilium FT-like sequences LiFTL1, LiFTL2…”

“…Even though short reads are generated with the Illumina HiSeq platform, a tremendous throughput can be reached, resulting in an improved coverage of rare transcripts in comparison to the other platforms used in some of the previous transcriptome studies of bulbous species (Shahin et al, 2012;Kamenetsky et al, 2015).…”