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Cited by 12Genomics and Phylogenetic StudiesFractal and DNA sequence analysisMicrobial Community Ecology and Physiology

A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes

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Zhou, Yizhuang, Zheng, Jifang, Wu, Yepeng, Zhang, Wenting, Jin, Junfei·2020·BMC Genomics
DOI 10.1186/s12864-020-6597-xPMC PMC7045542
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Abstract

Background: Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed. Results: Here, we initially test a published approach called “genome-wide tetranucleotide frequency correlation coefficient” (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called “fragment tetranucleotide frequency correlation coefficient” (FRAGTE), which uses fragments rather than whole genomes for sieving. Our results show that FRAGTE achieves ~ 100% sensitivity and high specificity on simulated genomes, real genomes and metagenome-assembled genomes, demonstrating that FRAGTE is completeness-independent. Additionally, FRAGTE sieved a reduced number of total genomes for subsequent alignment and calculation to greatly improve computational efficiency for the process after sieving. Aside from this computational improvement, FRAGTE also reduces the computational cost for the sieving process. Consequently, FRAGTE extremely improves run efficiency for both the processes of sieving and after sieving (subsequent alignment and calculation) to together accelerate genome-wide species delineation. Conclusions: FRAGTE is a completeness-independent algorithm for sieving. Due to its high sensitivity, high specificity, highly reduced number of sieved genomes and highly improved runtime, FRAGTE will be helpful for whole-genome approaches to facilitate taxonomic studies in prokaryotes.

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  • Studies focusing on closely related species may benefit from algorithms that excel at aligning highly similar sequences, while studies on divergent species may require algorithms that can handle high levels of sequence divergence.

    “For instance, studies focusing on closely related species may benefit from algorithms that excel at aligning highly similar sequences, while studies on divergent species may require algorithms that can handle high levels of sequence divergence [63,64].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [63]

    The Background discusses pre-selecting closely related genomes before alignment, and the Discussion compares that approach with alignment-based methods. Neither passage addresses choosing alignment algorithms according to whether species are closely related or highly divergent; searches for sequence divergence and algorithm selection found no such discussion. No page numbers were available in our copy. (LLM, conf=0.73)

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Cited by

Sorted by citations

Authors
Zhou, Y., Zheng, J., Wu, Y., Zhang, W., & Jin, J.
Affiliations
Guilin Medical University (CN)
Corresponding author
  • Zhou, Yizhuang
  • Jin, Junfei
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2020-02-26
Volume
21
Issue
1
Pages
183-183
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/s12864-020-6597-x
PMC
PMC7045542
OpenAlex
W3012899399
Cited by
12
References
1
Citations by year
2026: 1 · 2025: 5 · 2024: 2 · 2022: 3 · 2019: 1
FWCI
0.24
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Natural Science Foundation of Guangxi Province (2015GXNSFEA139003)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
genome completeness, metagenome-assembled genomes, computational efficiency, whole-genome alignment, prokaryotic taxonomy
MeSH terms
Whole Genome Sequencing, Algorithms, Archaea, Bacteria, Species Specificity, Genome, Bacterial, Computational Biology, Genome, Archaeal, Metagenomics

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