PMC:4502367 / 7269-8725 JSONTXT

{"project":"2_test","denotations":[{"id":"25917918-21695235-43386532","span":{"begin":84,"end":88},"obj":"21695235"},{"id":"25917918-21994252-43386533","span":{"begin":193,"end":197},"obj":"21994252"},{"id":"25917918-21994252-43386534","span":{"begin":861,"end":865},"obj":"21994252"},{"id":"25917918-23587118-43386535","span":{"begin":1281,"end":1285},"obj":"23587118"}],"text":"For the gene annotation, the genomes of Z. tritici (isolate IPO323) (Goodwin et al. 2011), Z. pseudotritici (isolate ST04IR_2.2.1), and Z. ardabiliae (isolate ST04IR_1.1.1) (Stukenbrock et al. 2011) were used. For the annotation of Z. brevis, the genome of the isolate Zb18110 was sequenced. Genomic DNA was isolated using a standard phenol-chloroform protocol (Sambrook and Russell 2001), and sequencing of 100-bp paired-end reads was performed using a HiSeq2000 Illumina platform (AROS Applied Biotechnology, Denmark). A de novo assembly of the Z. brevis Illumina reads was generated using the CLC Genomics Workbench version 5 (CLC, Aarhus, Denmark) with standard settings for paired-end read assembly. This assembly is available under the NCBI BioProject (PRJNA273516) on Genbank. The assembled genomes of Z. pseudotritici, Z. ardabiliae (Stukenbrock et al. 2011), and Z. brevis used for the gene annotation contained a very low number of repetitive DNA. Therefore, new assemblies better representing the repeat content of these species genomes were constructed using Illumina sequences obtained from the isolates Z. pseudotritici ST04IR_5.5, Z. ardabiliae ST11IR_6.1.1, and Z. brevis Zb163. Assemblies of these new Illumina genomes were generated using SOAPdenovo2 (Luo et al. 2012) with optimized k-mer values allowing the inclusion of repeats in the assemblies. These three assemblies are available under the NCBI BioProject (PRJNA274679) on Genbank."}