From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

Steenwyk, Jacob; King, Nicole

doi:10.20944/preprints202309.0495.v3

“…These high-quality genomic resources are already available for many species, but their quantity is set to explode in the coming years, thanks in particular to many large-scale biodiversity sequencing projects (African BioGenome Project, AT-LASea, Darwin Tree of Life, Earth Biogenome Project, European Reference Genome Atlas). In this context, a more systematic use of synteny to reconstruct phylogenies is becoming a feasible and promising next step, although this still presents many methodological challenges [30]. In particular, deep nodes remain intrinsically difficult to resolve due to the substantial amount of elapsed evolutionary time, which erodes phylogenetic signal both in DNA sequences and genome structures.…”

Section: Towards a More Systematic Use Of Synteny To Solve The Tree O...mentioning

confidence: 99%

Solving an enigma in the tree of life, at the origins of teleost fishes

Parey,

Berthelot,

Roest Crollius

et al. 2024

Comptes Rendus. Biologies

0

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Tracing the phylogenetic relationships between species is one of the fundamental objectives of evolutionary biology. Since Charles Darwin's seminal work in the 19th century, considerable progress has been made towards establishing a tree of life that summarises the evolutionary history of species. Nevertheless, substantial uncertainties still remain. Specifically, the relationships at the origins of teleost fishes have been the subject of extensive debate over the last 50 years. This question has major implications for various research fields: there are almost 30,000 species in the teleost group, which includes invaluable model organisms for biomedical, evolutionary and ecological studies. Here, we present the work in which we solved this enigma. We demonstrated that eels are more closely related to bony-tongued fishes than to the rest of teleost fishes. We achieved this by taking advantage of new genomic data and leveraging innovative phylogenetic markers. Notably, in addition to traditional molecular phylogeny methods based on the evolution of gene sequences, we also considered the evolution of gene order along the DNA molecule. We discuss the challenges and opportunities that these new markers represent for the field of molecular phylogeny, and in particular the possibilities they offer for re-examining other controversial branches in the tree of life.

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Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

Lewin,

Liao,

Luo

2024

Preprint

4

0

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The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while most annelids have maintained the conserved bilaterian genome structure, a group containing leeches and earthworms possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show leeches and earthworms to have the most highly rearranged genomes of any currently sampled bilaterian. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion or as rapid, all-encompassing changes over short evolutionary timescales.

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Résolution d’une énigme dans l’arbre du vivant, aux origines des poissons téléostéens

2024

Comptes Rendus. Biologies

0

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Tracing the phylogenetic relationships between species is one of the fundamental objectives of evolutionary biology. Since Charles Darwin's seminal work in the 19th century, considerable progress has been made towards establishing a tree of life that summarises the evolutionary history of species. Nevertheless, substantial uncertainties still remain. Specifically, the relationships at the origins of teleost fishes have been the subject of extensive debate over the last 50 years. This question has major implications for various research fields: there are almost 30,000 species in the teleost group, which includes invaluable model organisms for biomedical, evolutionary and ecological studies. Here, we present the work in which we solved this enigma. We demonstrated that eels are more closely related to bony-tongued fishes than to the rest of teleost fishes. We achieved this by taking advantage of new genomic data and leveraging innovative phylogenetic markers. Notably, in addition to traditional molecular phylogeny methods based on the evolution of gene sequences, we also considered the evolution of gene order along the DNA molecule. We discuss the challenges and opportunities that these new markers represent for the field of molecular phylogeny, and in particular the possibilities they offer for re-examining other controversial branches in the tree of life.

show abstract

From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

Cited by 3 publications

References 136 publications

Solving an enigma in the tree of life, at the origins of teleost fishes

Solving an enigma in the tree of life, at the origins of teleost fishes

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

Résolution d’une énigme dans l’arbre du vivant, aux origines des poissons téléostéens

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