Version 1
: Received: 6 September 2023 / Approved: 7 September 2023 / Online: 7 September 2023 (07:21:52 CEST)
Version 2
: Received: 8 February 2024 / Approved: 8 February 2024 / Online: 8 February 2024 (10:45:41 CET)
Version 3
: Received: 8 February 2024 / Approved: 9 February 2024 / Online: 9 February 2024 (09:15:51 CET)
How to cite:
Steenwyk, J.; King, N. From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics. Preprints2023, 2023090495. https://doi.org/10.20944/preprints202309.0495.v3
Steenwyk, J.; King, N. From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics. Preprints 2023, 2023090495. https://doi.org/10.20944/preprints202309.0495.v3
Steenwyk, J.; King, N. From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics. Preprints2023, 2023090495. https://doi.org/10.20944/preprints202309.0495.v3
APA Style
Steenwyk, J., & King, N. (2024). From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics. Preprints. https://doi.org/10.20944/preprints202309.0495.v3
Chicago/Turabian Style
Steenwyk, J. and Nicole King. 2024 "From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics" Preprints. https://doi.org/10.20944/preprints202309.0495.v3
Abstract
Reconstructing the Tree of Life remains a central goal in biology. Early methods, relying on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which use hundreds to thousands of loci for phylogenetic inquiry, have provided a clearer picture of life's history, but certain branches remain problematic. To resolve difficult nodes on the Tree of Life, two recent studies tested the utility of synteny, the conserved collinearity of orthologous genetic loci in two or more organisms, for phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. We identify and discuss specific opportunities and challenges that bear on the value of synteny data and other rare genomic changes for phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the Tree of Life.
Keywords
phylogenomics; synteny; chromosomes; long-read sequencing; tree of life; orthology; phylogenetic trees; incongruence
Subject
Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
