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One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence in Haemonchus contortus

Jeff A. Wintersinger, Grace M. Mariene, James D. Wasmuth
doi: https://doi.org/10.1101/384008
Jeff A. Wintersinger
Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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Grace M. Mariene
Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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James D. Wasmuth
Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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  • For correspondence: jwasmuth@ucalgary.ca
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Abstract

Background Numerous quality issues may compromise genomic data’s representation of its underlying organism. In this study, we compared two genomes published by different research groups for the parasitic nematode Haemonchus contortus, corresponding to divergent isolates. We analyzed differences between the genomes, attempting to ascertain which were attributable to legitimate biological differences, and which to technical error in one or both genomes.

Results We found discrepancies between the H. contortus genomes in both assembly and annotation. The genomes differed in representation of genes that are highly conserved across eukaryotes, with clear evidence of misassembly underlying conserved genes missing from one genome or the other. Only 45% of genes in one genome were orthologous to genes in the other genome, with one genome exhibiting almost as much orthology to C. elegans as its counterpart H. contortus strain. The two genomes differed substantially in probable causes underlying this unexpectedly low orthology. One genome included many more inparalogues than the other, and more frequently assembled inparalogues together on the same portions of contiguous sequence. It also exhibited cases of better-conserved gene position relative to C. elegans.

Conclusion The discrepancies between the two genomes far exceeded those expected as a consequence of biological differences between the two H. contortus isolates. This implies substantial quality issues in one or both genomes, suggesting that researchers must exercise caution when using genomic data for newly sequenced species.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 07, 2018.
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One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence in Haemonchus contortus
Jeff A. Wintersinger, Grace M. Mariene, James D. Wasmuth
bioRxiv 384008; doi: https://doi.org/10.1101/384008
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One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence in Haemonchus contortus
Jeff A. Wintersinger, Grace M. Mariene, James D. Wasmuth
bioRxiv 384008; doi: https://doi.org/10.1101/384008

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