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Volume 10, Issue 3

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic strains by hybrid genome assembly Open Access

Abstract

Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus . By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from fruit bodies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biotrophic fungal genome , heterokaryotic fungal genome , hybrid genome assembly , intraspecific genome variability and NGS comparison
Funding
This study was supported by the:
  • PAPIIT-UNAM (Award IT-200719)
    • Principle Award Recipient: MauricioA. Trujillo-Roldán
  • PAPIIT-UNAM (Award IN-212521)
    • Principle Award Recipient: RobertoGaribay-Orijel
  • PAPIIT-UNAM (Award IN-210217)
    • Principle Award Recipient: RobertoGaribay-Orijel
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly
M Gen 10, 001218 (2024); https://doi.org/10.1099/mgen.0.001218
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