title: Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.).
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.
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. vhrkamen@volcani.agri.gov.il.
authors.forename: Rina
authors.initials: R
authors.lastname: Kamenetsky
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. adif@volcani.agri.gov.il.
authors.forename: Adi
authors.initials: A
authors.lastname: Faigenboim
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. einat.shemesh@mail.huji.ac.il.|Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. einat.shemesh@mail.huji.ac.il.
authors.forename: Einat
authors.initials: E
authors.lastname: Shemesh Mayer
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. tomerbetmem@gmail.com.|Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. tomerbetmem@gmail.com.
authors.forename: Tomer
authors.initials: T
authors.lastname: Ben Michael
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. chen.bernath@gmail.com.
authors.forename: Chen
authors.initials: C
authors.lastname: Gershberg
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. sagiekimhi@gmail.com.
authors.forename: Sagie
authors.initials: S
authors.lastname: Kimhi
authors.affiliation: Classeed Ltd., Gibraltar, British. esquirai@gmail.com.
authors.forename: Itzhak
authors.initials: I
authors.lastname: Esquira
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. saritr@volcani.agri.gov.il.|Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel. saritr@volcani.agri.gov.il.
authors.forename: Sarit
authors.initials: S
authors.lastname: Rohkin Shalom
authors.affiliation: Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel. dani@agri.gov.il.
authors.forename: Dani
authors.initials: D
authors.lastname: Eshel
authors.affiliation: Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. Haim.Rabinowitch@mail.huji.ac.il.
authors.forename: Haim D
authors.initials: HD
authors.lastname: Rabinowitch
authors.affiliation: Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel. asherman@volcani.agri.gov.il.
authors.forename: Amir
authors.initials: A
authors.lastname: Sherman
mesh_terms: D016000:Cluster Analysis; D004798:Enzymes / Q000378:metabolism; D052677:Flexiviridae / Q000472:pathogenicity; D035264:Flowers / Q000235:genetics / Q000378:metabolism / Q000821:virology; D005737:Garlic / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000821:virology; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism / Q000821:virology; D012639:Seeds / Q000235:genetics / Q000378:metabolism / Q000821:virology; D017423:Sequence Analysis, RNA; D013455:Sulfur / Q000378:metabolism; D059467:Transcriptome
chemical_list: D004798:Enzymes; D013455:Sulfur