Re-sequencing shows biased SNP distribution along 8 A. fumigatus chromosomes

Ref ID: 18390

Author:

Suman Pakala, Jessica Hostetler, Suchitra Pakala, Vinita
Joardar, Paul Bowyer, David Denning, William C. Nierman, Natalie D. Fedorova. J. Craig

Author address:

Venter Institute, Rockville MD, USA. Email: natalief@jcvi.org

Full conference title:

Asperfest 8

Abstract:

Aspergillus fumigatus is the most common causative agent of invasive aspergillosis (IA), an invasive and deadly infection that affects mostly
immunocompromised individuals. To enhance genomic resources available the A. fumigatus community, this study aims to provide (i) 2 additional
reference genome sequences; (ii) RNA-Seq based genome annotation upgrades; and (iii) mutational profiling of drug resistant strains. Here we report
the successful completion of the pilot phase of the project. To estimate the feasibility of the NGS approach, we first calculated the Illumina sequencing
error rate at the 10X cut-off, which turns out to be extremely low (2.4E-06). Sequencing two more azole-susceptible isolates, A1163 and AF210,
demonstrated high genetic variability of the A. fumigatus nuclear genome. Our preliminary analysis identified 57,000 and 77,000 SNPs in A1163 and
AF210, respectively, relative to AF293. With a fewexceptions, SNPs were stronglyenriched in the arms of the chromosomes relative to the center. Further
analysis identified over 50 highly variable genes (over 15 SNPs per 1 Kb) including the FluG-like protein and general amidase GmdB, which may be
useful for MLST typing. Notably, the cyp51A gene, associated with azole resistance has 10 SNPs in AF210, some previously described as not related
to drug resistance. The funding for the project has been provided by NIAIAD/NIH.

Abstract Number: 70)

Conference Year: 2011

Link to conference website: NULL

New link: NULL

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