title: Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef).
abstract: BACKGROUND
  Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource.
  
  
  RESULTS
  The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten.
  
  
  CONCLUSIONS
  It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.
authors.forename: Gina
authors.initials: G
authors.lastname: Cannarozzi
authors.forename: Sonia
authors.initials: S
authors.lastname: Plaza-Wüthrich
authors.forename: Korinna
authors.initials: K
authors.lastname: Esfeld
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Larti
authors.forename: Yi Song
authors.initials: YS
authors.lastname: Wilson
authors.forename: Dejene
authors.initials: D
authors.lastname: Girma
authors.forename: Edouard
authors.initials: E
authors.lastname: de Castro
authors.forename: Solomon
authors.initials: S
authors.lastname: Chanyalew
authors.forename: Regula
authors.initials: R
authors.lastname: Blösch
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.forename: Michel
authors.initials: M
authors.lastname: Schneider
authors.forename: Laurent
authors.initials: L
authors.lastname: Falquet
authors.forename: Cris
authors.initials: C
authors.lastname: Kuhlemeier
authors.forename: Kebebew
authors.initials: K
authors.lastname: Assefa
authors.affiliation: University of Bern, Institute of Plant Sciences, Altenbergrain 21, Bern CH-3013, Switzerland. zerihun.tadele@ips.unibe.ch.
authors.forename: Zerihun
authors.initials: Z
authors.lastname: Tadele
mesh_terms: D002874:Chromosome Mapping; D031750:Eragrostis / Q000145:classification / Q000235:genetics*; D015723:Gene Library; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010744:Phosphoric Monoester Hydrolases / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D055315:Prolamins / Q000145:classification / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D055315:Prolamins; D022661:RNA, Untranslated; D010744:Phosphoric Monoester Hydrolases