Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants

Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Tao Zhao, Eric Schranz*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

3 Citations (Scopus)


In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.

Original languageEnglish
Title of host publicationPlant Comparative Genomics
EditorsA. Pereira-Santana, S.D. Gamboa-Tuz, L.C. Rodríguez-Zapata
Place of PublicationNew York
PublisherHumana Press
Number of pages17
ISBN (Electronic)9781071624296
ISBN (Print)9781071624289
Publication statusPublished - Jul 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Bax Inhibitor
  • Comparative genomics
  • Gene family
  • Microsynteny
  • Synteny network


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