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Microbial Genomics logo Microbial Genomics

Volume 10, Issue 1

An imputed ancestral reference genome for the complex better captures structural genomic diversity for reference-based alignment workflows Open Access

Abstract

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC mapped more short sequencing reads and called more pairwise SNPs relative to the Comas sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.

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Keyword(s): Mycobacterium tuberculosis , reference genome and reference-based alignment
Funding
This study was supported by the:
  • Canada Research Chairs (Award Tier 1 Canada Research Chair)
    • Principle Award Recipient: MarcelA Behr
  • Huck Institutes of the Life Sciences (Award Chair in Global Health)
    • Principle Award Recipient: VivekKapur
  • Bill and Melinda Gates Foundation (Award OPP1176950)
    • Principle Award Recipient: VivekKapur
  • Canadian Institutes for Health Research (Award FDN-148362)
    • Principle Award Recipient: MarcelA Behr
  • Fonds de Recherche du Québec - Santé (Award Clinician Scientist Training Program for Residents in Medical Specialties)
    • Principle Award Recipient: LukeB Harrison
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-04
2025-01-16
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/content/journal/mgen/10.1099/mgen.0.001165
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An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows
M Gen 10, 001165 (2024); https://doi.org/10.1099/mgen.0.001165
/content/journal/mgen/10.1099/mgen.0.001165
/content/journal/mgen/10.1099/mgen.0.001165
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