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Inferring synteny between genome assemblies: a systematic evaluation.

Dang Liu1,2, Martin Hunt3,4, Isheng J Tsai5,6

  • 1Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.

BMC Bioinformatics
|February 1, 2018
PubMed
Summary
This summary is machine-generated.

Synteny analysis using fragmented genome assemblies can underestimate gene conservation by up to 40%. A minimum N50 of 1 Mb is crucial for reliable comparative genomics and accurate synteny identification.

Keywords:
Assembly qualityComparative genomicsGenome syntenyNematode genomes

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Area of Science:

  • Genomics
  • Comparative Genomics
  • Bioinformatics

Background:

  • Genome assemblies are routinely generated across all life domains.
  • Comparative genomics, including synteny analysis, is a standard step in genome analysis.
  • Synteny analysis methods were primarily developed using complete genomes, with limited understanding of their performance on fragmented draft assemblies.

Purpose of the Study:

  • To investigate the impact of genome assembly fragmentation on synteny identification and downstream analyses.
  • To assess the robustness of current synteny inference tools and methods when applied to draft genome assemblies.
  • To determine the minimum assembly contiguity required for reliable synteny analysis.

Main Methods:

  • Fragmenting genome assemblies of model nematodes to varying degrees.
  • Performing synteny identification and downstream analyses on fragmented assemblies.
  • Evaluating the performance of popular synteny inference tools and gene ontology enrichment tests.

Main Results:

  • Synteny between species can be underestimated by up to 40% with fragmented assemblies.
  • Disagreements were observed between different tools for inferring synteny blocks.
  • Erroneous gene ontology enrichment tests were demonstrated, questioning the reliability of previous analyses.
  • Reference-guided assembly scaffolding can lead to chimeric scaffolds and inflated metrics.
  • Annotation quality has minimal impact on synteny if the assembly is highly contiguous.

Conclusions:

  • A minimum N50 contiguity of 1 Mb is essential for robust downstream synteny analysis.
  • The findings highlight the critical need for high-quality, gold-standard genome assemblies.
  • Current sequencing technology advancements should enable the routine achievement of such assembly standards.