Gene sketch of Ae. tauschii, the D genome donor of common wheat
Jizeng Jia
Gene sketch of Ae. tauschii, the D genome donor of common wheat - Beijing (China) Chinese Academy of Agricultural Sciences : 2010 - p. 24
Abstract only
Wheat is one of the most important food crops as well as the model plant with complex genome.Here we present the gene centric genome of Aegilops tauschii, the D genome donor of common wheat using next-generation Illumina GA sequencing technology. We obtained more than 60x genome coverage, with the library insert size ranging from 170bp to 20kb. The short reads were assembled using SOAPdenovo, a successful genome assembler developed specifically for next-generation sequencing reads. The assembly contigs and scaffolds with an N50 length of 1.3kb and 35.6kb, reach about 1.34G and 2.66G, respectively, and the remaining gaps consist of intractable repeats as it appears. To evaluate the assembling result, we mapped 6 BACs independently to the draft genome, and each BAC could be covered with continuous scaffolds without obvious assembly errors. Besides, we sequenced 8 different tissues to achieve a highly reliable transcriptome to supplement the limits of draft genome assembly. Each tissue contributes more than 8Gb data in average to their independent assembly, which was clustered together with TGICL. We depicted 49689 protein-coding loci in our transcriptome, after a careful evaluation using a combination of full-length complementary DNAs and expressed sequence tags. More than 90% of all the ESTs could be well aligned to our contigs with coverage of over 50%. We also evaluated our transcriptome with BACs carried annotated genes. The case study for some important genes, mainly transcription factor, will be reported.
English
Gene sketch of Ae. tauschii, the D genome donor of common wheat - Beijing (China) Chinese Academy of Agricultural Sciences : 2010 - p. 24
Abstract only
Wheat is one of the most important food crops as well as the model plant with complex genome.Here we present the gene centric genome of Aegilops tauschii, the D genome donor of common wheat using next-generation Illumina GA sequencing technology. We obtained more than 60x genome coverage, with the library insert size ranging from 170bp to 20kb. The short reads were assembled using SOAPdenovo, a successful genome assembler developed specifically for next-generation sequencing reads. The assembly contigs and scaffolds with an N50 length of 1.3kb and 35.6kb, reach about 1.34G and 2.66G, respectively, and the remaining gaps consist of intractable repeats as it appears. To evaluate the assembling result, we mapped 6 BACs independently to the draft genome, and each BAC could be covered with continuous scaffolds without obvious assembly errors. Besides, we sequenced 8 different tissues to achieve a highly reliable transcriptome to supplement the limits of draft genome assembly. Each tissue contributes more than 8Gb data in average to their independent assembly, which was clustered together with TGICL. We depicted 49689 protein-coding loci in our transcriptome, after a careful evaluation using a combination of full-length complementary DNAs and expressed sequence tags. More than 90% of all the ESTs could be well aligned to our contigs with coverage of over 50%. We also evaluated our transcriptome with BACs carried annotated genes. The case study for some important genes, mainly transcription factor, will be reported.
English