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Reference genome assembly for Australian Ascochyta rabiei Isolate ArME14

Shah, R.M., Williams, A.H., Hane, J.K., Lawrence, J.A., Farfan-Caceres, L.M., Debler, J.W., Oliver, R.P. and Lee, R.C. (2020) Reference genome assembly for Australian Ascochyta rabiei Isolate ArME14. Genes|Genomes|Genetics, 10 (7). pp. 2131-2140.

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Abstract

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

Item Type: Journal Article
Publisher: Genetics Society of America (GSA)
Copyright: © 2020 by the Genetics Society of America
URI: http://researchrepository.murdoch.edu.au/id/eprint/57060
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