Skip to content
DraconiticResearch
Search Sources API
197,788 studies31 sourcesUpdated 34 min ago
Peer-reviewedCC BYJournal of Evolutionary Biology

ntSynt-viz: visualizing synteny patterns across multiple genomes

  • Lauren Coombe1,2
  • René L. Warren1,2
  • İnanç Birol1,3,2
  1. 1Department of Basic and Translational Research, BC Cancer Research Institute , 675 W 10th Ave, BC, V5Z 1L3, Vancouver, BC ,
  2. 2BC Cancer Genome Sciences Centre
  3. 3Department of Medical Genetics, University of British Columbia , 6200 University Blvd, V6T 1Z4, Vancouver, BC ,
Open at sourceDOICite

Abstract

With the explosion of chromosome-scale genome assemblies being generated in recent years, there is vast potential for comparative genomics analyses through detecting multi-genome synteny. While existing tools can detect synteny blocks between multiple genomes, their text-based outputs make it challenging to intuitively explore large-scale synteny patterns. Interpretable, information-rich and easy-to-use synteny visualization tools are imperative to enable important biological insights from the synteny block data output by the aforementioned utilities. Here, we present ntSynt-viz, a command-line tool for automated sorting, normalization, and plotting of multi-genome synteny blocks. We show how ntSynt-viz provides clearer and more easily interpretable chromosome painting ribbon plots compared to the state-of-the-art tools NGenomeSyn and plotsr when evaluating synteny between 14 human genomes, and compared to NGenomeSyn when comparing 9 hoverfly genomes. As plotsr is limited to comparing genomes with equal chromosome numbers, it was not applicable to the hoverfly dataset. Furthermore, we demonstrate how ntSynt-viz can also be applied to visualize syntenic patterns encoded in pangenome graphs, using a Minigraph-Cactus graph built from 16 Drosophila genomes. We expect that ntSynt-viz will provide crucial insights into large-scale synteny patterns between divergent genomes, thereby advancing research into key evolutionary questions.

Related

  1. END nucleases are antiphage defence systems targeting multiple phages with modified genomes
    Wearn‐Xin Yee, Yan‐Jiun Lee, Kira S. Makarova +8
    Nature MicrobiologyPeer-reviewedLicence not stated12 citedEcologyMicrobiologyOpenAlex
  2. Statistical analysis provides new insights into patterns and mechanisms of the WANCY hotspot on vertebrate mitochondrial genomes
    C. Xu, M. Wilkinson
    bioRxivPreprintCC BYFull textGenetics & genomicsbioRxiv
  3. Microhomology-Driven Genomic Alterations in Cancer Genomes: Patterns, Prevalence, and Clinical Implications.
    D. Kostka, P. Sztromwasser, M. Kimmel +1
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  4. XtractPAV: an automated pipeline for identifying presence-absence variations across multiple genomes
    Rana Sheraz Ahmad, Muhammad Sadaqat, Muhammad Tahir Ul Qamar +2
    BMC GenomicsPeer-reviewedCC BY-NC-ND 4.0Full textEcologyEnvironmental science & pollutionHAL
  5. Visualization and Characterization of Gene Group Distribution Patterns Across Genomes
    Yanying Wu
    arXivPreprintCC BY 4.0Full textBioinformatics & computational biologyGenetics & genomicsarXiv

Cite

BibTeXRIS
BibTeX
@article{coombe2026ntsyntviz,
  title = {{ntSynt-viz: visualizing synteny patterns across multiple genomes}},
  author = {Lauren Coombe and René L. Warren and İnanç Birol},
  journal = {Journal of Evolutionary Biology},
  year = {2026},
  month = sep,
  doi = {10.1093/jeb/voag079},
  url = {https://doi.org/10.1093/jeb/voag079},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - ntSynt-viz: visualizing synteny patterns across multiple genomes
AU  - Lauren Coombe
AU  - René L. Warren
AU  - İnanç Birol
PY  - 2026
DA  - 2026/09/03
JO  - Journal of Evolutionary Biology
DO  - 10.1093/jeb/voag079
UR  - https://doi.org/10.1093/jeb/voag079
AB  - With the explosion of chromosome-scale genome assemblies being generated in recent years, there is vast potential for comparative genomics analyses through detecting multi-genome synteny. While existing tools can detect synteny blocks between multiple genomes, their text-based outputs make it challenging to intuitively explore large-scale synteny patterns. Interpretable, information-rich and easy-to-use synteny visualization tools are imperative to enable important biological insights from the synteny block data output by the aforementioned utilities. Here, we present ntSynt-viz, a command-line tool for automated sorting, normalization, and plotting of multi-genome synteny blocks. We show how ntSynt-viz provides clearer and more easily interpretable chromosome painting ribbon plots compared to the state-of-the-art tools NGenomeSyn and plotsr when evaluating synteny between 14 human genomes, and compared to NGenomeSyn when comparing 9 hoverfly genomes. As plotsr is limited to comparing genomes with equal chromosome numbers, it was not applicable to the hoverfly dataset. Furthermore, we demonstrate how ntSynt-viz can also be applied to visualize syntenic patterns encoded in pangenome graphs, using a Minigraph-Cactus graph built from 16 Drosophila genomes. We expect that ntSynt-viz will provide crucial insights into large-scale synteny patterns between divergent genomes, thereby advancing research into key evolutionary questions.
SN  - 1010-061X
SN  - 1420-9101
ER  -