Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 1;39(1):btac806.
doi: 10.1093/bioinformatics/btac806.

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

Fabricio Almeida-Silva  1   2 , Tao Zhao  3 , Kristian K Ullrich  4 , M Eric Schranz  5 , Yves Van de Peer  1   2   6   7
Affiliations

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

Fabricio Almeida-Silva et al. Bioinformatics. .

Abstract

Summary: Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.

Availability and implementation: syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Workflow and possible applications of syntenet. (A) Schematic model of the whole pipeline for synteny network inference and analysis. Boxes represent the different steps of the pipeline, with the corresponding function names in italicized fonts on the right and below. (B) Example heatmap of phylogenomic profiles that can be created with the function phylogenomic_profile(). Dashed boxes highlight family-specific synteny clusters. Interestingly, species with recent whole-genome duplications (e.g. Malus domestica and Glycine max) have a greater number of genes in most synteny clusters. Data were obtained from Zhao and Schranz (2019), and code to create the figure is available on Supplementary Data S1. (C) Network representation of some family-specific synteny clusters from Figure 1B produced with the function plot_network(). (D) Microsynteny-based phylogeny of angiosperms. Data were obtained from Zhao et al. (2021), and code to reproduce the figure is available on Supplementary Data S2
See this image and copyright information in PMC

References

    1. Altschul S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed
    1. Buchfink B. et al. (2021) Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods, 18, 366–368. - PMC - PubMed
    1. Eddelbuettel D., François R. (2011) Rcpp: seamless R and C++ integration. J. Stat. Softw., 40, 1–18.
    1. Jayakodi M. et al. (2020) The barley pan-genome reveals the hidden legacy of mutation breeding. Nature, 588, 284–289. - PMC - PubMed
    1. Li M.H. et al. (2022) Genomes of leafy and leafless platanthera orchids illuminate the evolution of mycoheterotrophy. Nat. Plants, 8, 373–388. - PMC - PubMed

Publication types