ArticlePloS one2014
SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
- Pervasive weak incompatibilities shape phenotypic variation and genome evolution in yeast hybrids.Nature communications · 2026Article
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- Weak pervasive incompatibilities and compensatory adaptation drive hybrid genome evolution in yeast.bioRxiv : the preprint server for biology · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila.BMC genomics · 2025Article
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- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Targeted genetic manipulation and yeast-like evolutionary genomics in the green algabioRxiv : the preprint server for biology · 2025Article
- The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.PLoS biology · 2025Article
- Tracing the evolution and genomic dynamics of mating-type loci inbioRxiv : the preprint server for biology · 2025Article
- Strong Signatures of Selection on Candidate Genes Underlying Core Speciation Mechanisms in Desert Tortoises.Molecular ecology resources · 2025Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
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- A metric and its derived protein network for evaluation of ortholog database inconsistency.BMC bioinformatics · 2025Article
- Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course "Evolutionary and Comparative Genomics".Bioinformatics advances · 2025Article
- Microsynteny is a powerful front for microbial strain tracking.Cell reports methods · 2024Article
- Complete genome of the Medicago anthracnose fungus,Microbial genomics · 2024Article
- Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.Nature protocols · 2024Review
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.PLoS biology · 2024Article
11 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Reconstructing synteny blocks is an essential step in comparative genomics studies. Different methods were already developed to answer various needs such as genome (re-)annotation, identification of duplicated regions and whole genome duplication events or estimation of rearrangement rates. We present SynChro, a tool that reconstructs synteny blocks between pairwise comparisons of multiple genomes. SynChro is based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks and then automatically completes these blocks with non-RBH syntenic homologs. This approach has two main advantages: (i) synteny block reconstruction is fast (feasible on a desk computer for large eukaryotic genomes such as human) and (ii) synteny block reconstruction is straightforward as all steps are integrated (no need to run Blast or TribeMCL prior to reconstruction) and there is only one parameter to set up, the synteny block stringency [Formula: see text]. Benchmarks on three pairwise comparisons of genomes, representing three different levels of synteny conservation (Human/Mouse, Human/Zebra Finch and Human/Zebrafish) show that Synchro runs faster and performs at least as well as two other commonly used and more sophisticated tools (MCScanX and i-ADHoRe). In addition, SynChro provides the user with a rich set of graphical outputs including dotplots, chromosome paintings and detailed synteny maps to visualize synteny blocks with all homology relationships and synteny breakpoints with all included genetic features. SynChro is freely available under the BSD license at http://www.lcqb.upmc.fr/CHROnicle/SynChro.html.
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