Dataset Information

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

ABSTRACT:

Background

Reconstructing ancestral gene orders in the presence of duplications is important for a better understanding of genome evolution. Current methods for ancestral reconstruction are limited by either computational constraints or the availability of reliable gene trees, and often ignore duplications altogether. Recently, methods that consider duplications in ancestral reconstructions have been developed, but the quality of reconstruction, counted as the number of contiguous ancestral regions found, decreases rapidly with the number of duplicated genes, complicating the application of such approaches to mammalian genomes. However, such high fragmentation is not encountered when reconstructing mammalian genomes at the synteny-block level, although the relative positions of genes in such reconstruction cannot be recovered.

Results

We propose a new heuristic method, MULTIRES, to reconstruct ancestral gene orders with duplications guided by homologous synteny blocks for a set of related descendant genomes. The method uses a synteny-level reconstruction to break the gene-order problem into several subproblems, which are then combined in order to disambiguate duplicated genes. We applied this method to both simulated and real data. Our results showed that MULTIRES outperforms other methods in terms of gene content, gene adjacency, and common interval recovery.

Conclusions

This work demonstrates that the inclusion of synteny-level information can help us obtain better gene-level reconstructions. Our algorithm provides a basic toolbox for reconstructing ancestral gene orders with duplications. The source code of MULTIRES is available on https://github.com/ma-compbio/MultiRes .

SUBMITTER: Rajaraman A

PROVIDER: S-EPMC5123302 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Publications

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

Rajaraman Ashok A Ma Jian J

BMC bioinformatics 20161111 Suppl 14

<h4>Background</h4>Reconstructing ancestral gene orders in the presence of duplications is important for a better understanding of genome evolution. Current methods for ancestral reconstruction are limited by either computational constraints or the availability of reliable gene trees, and often ignore duplications altogether. Recently, methods that consider duplications in ancestral reconstructions have been developed, but the quality of reconstruction, counted as the number of contiguous ancest ...[more]

PMID: 28185565

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Project description:The neuronal and neuroendocrine peptides oxytocin (OT) and vasotocin (VT), including vasopressins, have six cognate receptors encoded by six receptor subtype genes in jawed vertebrates. The peptides elicit a broad range of responses that are specifically mediated by the receptor subtypes including neuronal functions regulating behavior and hormonal actions on reproduction and water/electrolyte balance. Previously, we have demonstrated that these six receptor subtype genes, which we designated VTR1A, VTR1B, OTR, VTR2A, VTR2B and VTR2C, arose from a syntenic ancestral gene pair, one VTR1/OTR ancestor and one VTR2 ancestor, through the early vertebrate whole-genome duplications (WGD) called 1R and 2R. This was supported by both phylogenetic and chromosomal conserved synteny data. More recently, other studies have focused on confounding factors, such as the OTR/VTR orthologs in cyclostomes, to question this scenario for the origin of the OTR/VTR gene family; proposing instead less parsimonious interpretations involving only one WGD followed by complex series of chromosomal or segmental duplications. Here, we have updated the phylogeny of the OTR/VTR gene family, including a larger number of vertebrate species, and revisited seven representative neighboring gene families from our previous conserved synteny analyses, adding chromosomal information from newer high-coverage genome assemblies from species that occupy key phylogenetic positions: the polypteriform fish reedfish (Erpetoichthys calabaricus), the cartilaginous fish thorny skate (Amblyraja radiata) and a more recent high-quality assembly of the Western clawed frog (Xenopus tropicalis) genome. Our analyses once again add strong support for four-fold symmetry, i.e., chromosome quadruplication in the same time window as the WGD events early in vertebrate evolution, prior to the jawed vertebrate radiation. Thus, the evolution of the OTR/VTR gene family can be most parsimoniously explained by two WGD events giving rise to the six ancestral genes, followed by differential gene losses of VTR2 genes in different lineages. We also argue for more coherence and clarity in the nomenclature of OT/VT receptors, based on the most parsimonious scenario.

Dataset Information

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

Background

Results

Conclusions

Publications

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

Similar Datasets

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