Phylogenic position and low genomic diversity of “<i>Candidatus Rickettsia kotlanii</i>” inferred by complete genome sequences of two Japanese isolates

Gotoh, Yasuhiro; Takano, Ai; Andoh, Masako; Kasama, Kentaro; Nakamura, Keiji; Ando, Shuji; Hayashi, Tetsuya

doi:10.1111/1348-0421.13065

Cited by 2 publications

(1 citation statement)

References 25 publications

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“…Despite these general benefits, however, all current state-of-the-art hybrid assembly approaches that can be applied for metagenomes (31; 32; 33; 34) operate at the species level, as the finest taxonomic resolution. Note that all of them have been widely applied in studies that require metagenomic assembly as an essential step (35; 36; 37; 38; 39).…”

Section: Introductionmentioning

confidence: 99%

HyLight: Strain aware assembly of low coverage metagenomes

Kang,

Zhang,

Luo

et al. 2023

Preprint

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Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of a microbial community at strain level poses major methodical challenges, because relative frequencies of individual strains match the rate of sequencing errors, which hampers the identification of their characteristic genetic variants. While next-generation sequencing (NGS) reads are too short to span complex repetitive regions, the considerably longer third-generation sequencing (TGS) reads are affected by larger sequencing error rates or are just significantly more expensive. Suppressing TGS coverage to limit costs implies losses in terms of the accuracy of the assemblies. Therefore, existing approaches have remained fragmentary: all approaches presented so far agree on losses in strain awareness, accuracy, possibly excessive costs of the assemblies, or combinations thereof.We present HyLight as, to the best of our knowledge, the first metagenome assembly approach that is not affected by any of the aforementioned drawbacks. In experiments, we demonstrate that HyLight assemblies are strain-aware, contiguous, contain little errors, and because operating on low coverage TGS data of the cheap kind, come at drastically reduced costs. HyLight implements hybrid assembly, which exploits the complementarity of TGS and NGS data. For unifying the two types of data, HyLight utilizes strain resolved overlap graphs (OG), which support the accurate reconstruction of the individual members of microbial communities at strain level: HyLight outperforms existing approaches in terms of strain identity preserving sequence by on average 25.53% (across all experiments / data sets: first quartile: 21.53%, median: 26.81%, third quartile: 31.98%), achieving near-complete strain awareness on many data sets. In summary, HyLight appears to implement the first protocol that delivers assemblies that are strain-aware, contiguous and accurate in combination.

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Section: Introductionmentioning

confidence: 99%

HyLight: Strain aware assembly of low coverage metagenomes

Kang,

Zhang,

Luo

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

HyLight: Strain aware assembly of low coverage metagenomes

Kang,

Zhang,

et al. 2024

Nat Commun

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Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.

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Phylogenic position and low genomic diversity of “Candidatus Rickettsia kotlanii” inferred by complete genome sequences of two Japanese isolates

Cited by 2 publications

References 25 publications

HyLight: Strain aware assembly of low coverage metagenomes

HyLight: Strain aware assembly of low coverage metagenomes

HyLight: Strain aware assembly of low coverage metagenomes

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