G-Anchor: A novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences

Vasileios Panagiotis Lenis, Martin Swain, Denis Mikhailovich Larkin

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Abstract

Background
Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses.

Results
Here we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species’ reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours, and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources.

Conclusions
G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences, and that are not highly repetitive, polypoid or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons.

G-Anchor is freely available via https://github.com/vasilislenis/G-Anchor
Original languageEnglish
JournalGigaScience
Volume7
Issue number5
DOIs
Publication statusPublished - 03 Apr 2018

Keywords

  • whole-genome alignment
  • sequence mapping
  • sequencing anchoring
  • Highly Conserved Elements (HCE)
  • genome evolution

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