Generating a Reference Sequence for Aegilops tauschii: First-Pass Annotation of Chromosomes 1D, 2D and 3D

The aim of NSF Project IOS-1238231 is to develop a high-quality reference genome sequence for Aegilops tauschii, the D-genome progenitor to hexaploid wheat. To achieve this aim, pools of eight overlapping BAC clones selected from the Ae. tauschii minimum tiling path are being sequenced using an Illumina Mi-Seq platform. Chromosomes 1D, 2D and 3D haven been sequenced so far, and assemblies within pools have been completed. A first-pass annotation of the assemblies consists of homology-based annotation of DNA elements and LTR retrotransposons, de novo identification of LTR transposons using LTR_FINDER, and homology-based and de novo structural and functional annotations of genes.  Annotation of chromosome arm 3DS, which is estimated to represent ~6.5% of the 4.1 Gb Ae. tauschii genome, uncovered 76% of repetitive DNA, 66% of which were LTR retrotransposons and 10% were DNA transposons. Annotation of the non-masked 3DS sequence identified 2016 high confidence (HC) genes. Seventy-two percent of the HC genes were annotated as full-length (i.e. covering at least 70% of a reference protein). An additional 4235 low confidence genes were identified, mostly by RNA-Seq analysis, suggesting they are expressed repeats, non-coding RNAs and/or pseudogenes. In addition to the annotation of chromosomes 1D, 2D and 3D, we will also discuss the use of different annotation pipelines.