2× genomes - depth does matter

Milinkovitch, Michel C.; Helaers, Raphaël; Depiereux, Eric; Tzika, Athanasia C.; Gabaldón, Toni

doi:10.1186/gb-2010-11-2-r16

Cited by 51 publications

(67 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, keeping the orthogroup topology fixed by requiring one ortholog to be present for every species listed in Supplemental Table S1 also proved problematic because this resulted in a drastic drop of the total number of recovered orthogroups, since most homeologs had to be discarded because orthologs could not be found in every other plant species. This is probably due to both species-specific ortholog loss and problems with orthology-detection performance, since the latter decreases together with genome annotation quality, especially over large evolutionary distances (Trachana et al 2011), and many plant genomes have only been sequenced at relatively low coverage (Milinkovitch et al 2010).…”

Section: Orthogroup Constructionmentioning

confidence: 99%

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

et al. 2014

View full text Add to dashboard Cite

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.

show abstract

Section: Orthogroup Constructionmentioning

confidence: 99%

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

et al. 2014

View full text Add to dashboard Cite

show abstract

“…It communicates with clients (in boxes), each one in charge of one or more gene families, for which they search the gene tree maximizing mammalian species with widely different sequence coverages (Supplemental Table S1). Genomes with low coverage share by chance a number of unsequenced or unannotated genes, making this data set challenging for studying genomic evolution (Milinkovitch et al 2010). We introduced a correction to account for genome coverage to prevent PHYLDOG from interpreting these artifactual ''shared losses'' as a signal for clustering low-coverage genomes together in the species tree.…”

Section: Reconstructing the Evolutionary History Of Mammalian Genomesmentioning

confidence: 99%

Genome-scale coestimation of species and gene trees

et al. 2012

View full text Add to dashboard Cite

Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current methods to reconstruct phylogenies fail to model the two-way dependency between gene trees and the species tree, they often misrepresent gene and species histories. We present a new probabilistic model to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families. We use simulations to show that this method accurately infers the species tree and gene trees, is robust to misspecification of the models of sequence and gene family evolution, and provides a precise historic record of gene duplications and losses throughout genome evolution. We simultaneously reconstruct the history of mammalian species and their genes based on 36 completely sequenced genomes, and use the reconstructed gene trees to infer the gene content and organization of ancestral mammalian genomes. We show that our method yields a more accurate picture of ancestral genomes than the trees available in the authoritative database Ensembl.[Supplemental material is available for this article.]The reconstruction of gene phylogenies based on sequences alone is difficult. First, homologous sequences are often hard to align unambiguously (Wong et al. 2008), which leads to incorrect gene trees and erroneous predictions of events of duplications and losses. Second, sequence alignments generally contain insufficient information to accurately model gene evolution and thus understand their history, as suggested by the positive correlation found between sequence length and congruence to the species tree (Galtier 2007). However, knowing the relationships among the species in which these sequences have evolved can improve gene tree inference. Several methods have successfully implemented this idea by combining sequence evolution models with a model of gene evolution that accounts for duplication and loss (DL) (Vilella et al. 2008;Akerborg et al. 2009;Flicek et al. 2010; Kellis 2010, 2012). Provided the species tree is known, these methods yield significantly better gene trees than other molecular phylogenetic methods. However, because reference species trees themselves generally rely on molecular data, they can be also affected by phylogenetic reconstruction uncertainties and unidentified events of gene duplication and loss. This reveals a circular problem: the reconstruction of a species tree requires identifying events of gene family evolution such as DLs, and both the reconstruction of gene trees and the identification of duplications and losses requires a known species tree. The solution to the conundrum is to explicitly consider this two-way dependence and jointly reconstruct the species phylogeny and the histories of all gene families present in their genomes.The coestimation of gene and species trees requires that several gene families be analyzed simultaneously. This represents a significant departure from existing methods (Vilella et al. 2008;Akerborg et al. 200...

show abstract

“…We also calculated for each relevant clade of vertebrates the number of RAREs that are conserved in all the members of these clades. Although these data can be influenced by the coverage of the studied genome (34), this analysis raised three interesting conclusions. (i) Overall, human RAREs are less conserved in rodents than in other mammals.…”

Section: Resultsmentioning

confidence: 89%

Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

Lalevée

Anno

Chatagnon

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Retinoic acid (RA) receptors regulate gene expression through binding-specific response elements (RAREs). Results: A collection of new DR5 RAREs located Ϯ10 kb from TSSs and conserved among 6 vertebrates species or more has been amassed. Conclusion:We provide a wider knowledge base for analyzing RA target genes. Significance: The RA response of the conserved target genes differs between species and tissues.

show abstract

2× genomes - depth does matter

Abstract: The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.

Cited by 51 publications

References 35 publications

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Genome-scale coestimation of species and gene trees

Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

Contact Info

Product

Resources

About