Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host

AbstractTransposable elements (TE) are an important source of genetic variation with a dynamic and content that greatly differ in a wide range of species. The origin of the intraspecific content variation is not always clear and little is known about the precise nature of it. Here, we surveyed the species-wide content of the Ty LTR-retrotransposons in a broad collection of 1,011 Saccharomyces cerevisiae natural isolates to understand what can stand behind the variation of the repertoire, i.e. the type and number of Ty elements. We have compiled an exhaustive catalog of all TE variants present in the S. cerevisiae species by identifying a large set of new variants. The characterization of the TE content in each isolate clearly highlighted that each subpopulation exhibits a unique and specific repertoire, retracing the evolutionary history of the species. Most interestingly, we have shown that ancient interspecific hybridization events had a major impact in the birth of new variants and therefore in the shaping of the TE repertoires. We also investigated the transpositional activity of these elements in a large set of natural isolates, and we found a broad variability related to the level of ploidy as well as the genetic background. Overall, our results pointed out that the evolution of the Ty content is deeply impacted by clade-specific events such as introgressions and therefore follows the population structure. In addition, our study lays the foundation for future investigations to better understand the transpositional regulation and more broadly the TE-host interactions.Authors summaryMobile DNA elements are widely distributed in the genomes of many eukaryotes, but their contents greatly vary between species, populations and even individuals. In fact, little is known about the origin of this variation of transposable element (TE) content across individuals of the same species. Here, we surveyed the Ty LTR-retrotransposon content in a broad collection of 1,011 Saccharomyces cerevisiae yeast natural isolates. We have defined an exhaustive and precise catalog of the TE variants present in the S. cerevisiae species. We found that the TE content follows the evolutionary history of the species because each subpopulation has a unique and specific content. Interestingly, our results highlighted that ancient interspecific hybridization events led to the appearance of new TE variants and therefore had a strong impact on the variation of the TE repertoires in this species. We also investigated the transpositional activity of these elements and found a wide variability related to the genetic background diversity. Altogether, our results have led to a better understanding of the variability of TE content at a species level.

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A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191081 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 142-150

Author(s):

Jessica Worthington Wilmer ◽

Andrew P. Amey ◽

Carmel McDougall ◽

Melanie Venz ◽

Stephen Peck ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

The West ◽

European Settlement ◽

Low Genetic Diversity ◽

Eastern Australia ◽

Wide Range ◽

History Of ◽

Open Forests ◽

Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

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INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720006001709 ◽

2006 ◽

Vol 04 (01) ◽

pp. 59-74 ◽

Cited By ~ 20

Author(s):

YING-JUN HE ◽

TRINH N. D. HUYNH ◽

JESPER JANSSON ◽

WING-KIN SUNG

Keyword(s):

Approximation Algorithms ◽

Phylogenetic Tree ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Phylogenetic Network ◽

Evolutionary Relationships ◽

Large Set ◽

Tree Network ◽

History Of ◽

Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

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Evolutionary History of LTR Retrotransposon Chromodomains in Plants

International Journal of Plant Genomics ◽

10.1155/2012/874743 ◽

2012 ◽

Vol 2012 ◽

pp. 1-17 ◽

Cited By ~ 11

Author(s):

Anton Novikov ◽

Georgiy Smyshlyaev ◽

Olga Novikova

Keyword(s):

Evolutionary History ◽

Higher Plants ◽

Ltr Retrotransposon ◽

Ltr Retrotransposons ◽

Moss Species ◽

Plant Genomes ◽

Group I ◽

Wide Range ◽

History Of ◽

Computer Based

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

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GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

Molecular Biology and Evolution ◽

10.1093/molbev/msz179 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2604-2619 ◽

Cited By ~ 2

Author(s):

Elodie Laine ◽

Yasaman Karami ◽

Alessandra Carbone

Keyword(s):

Evolutionary History ◽

Recent Progress ◽

State Of The Art ◽

Fast Method ◽

Biological Sequences ◽

Epistatic Model ◽

Input Alignment ◽

Wide Range ◽

History Of ◽

Better Than

Abstract The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering, and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling intersite dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present Global Epistatic Model for predicting Mutational Effects (GEMME) (www.lcqb.upmc.fr/GEMME), an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods. It accurately predicts the mutational landscapes of a wide range of protein families, including viral ones and, more generally, of much conserved families. Given an input alignment, it generates the full mutational landscape of a protein in a matter of minutes. It is freely available as a package and a webserver at www.lcqb.upmc.fr/GEMME/.

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MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

GigaScience ◽

10.1093/gigascience/giab036 ◽

2021 ◽

Vol 10 (5) ◽

Cited By ~ 1

Author(s):

Mengni Liu ◽

Jianyu Chen ◽

Xin Wang ◽

Chengwei Wang ◽

Xiaolong Zhang ◽

...

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Cancer Evolution ◽

Evolutionary Patterns ◽

Evolutionary Trajectory ◽

Wide Range ◽

Heterogeneous Features ◽

History Of ◽

Somatic Alterations ◽

Tumor Biopsies

Abstract Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.

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Rearrangements occurring adjacent to a single Ty1 yeast retrotransposon in the presence and absence of full-length Ty1 transcription.

Genetics ◽

10.1093/genetics/131.4.833 ◽

1992 ◽

Vol 131 (4) ◽

pp. 833-850

Author(s):

P R Sutton ◽

S W Liebman

Keyword(s):

Saccharomyces Cerevisiae ◽

Homologous Recombination ◽

Transposable Element ◽

Gene Conversion ◽

Genetic Background ◽

Repetitive Sequences ◽

Full Length ◽

Yeast Genome ◽

Yeast Saccharomyces Cerevisiae ◽

Ty1 Retrotransposon

Abstract The structures of two unusual deletions from the yeast Saccharomyces cerevisiae are described. These deletions extend from a single Ty1 retrotransposon to an endpoint near a repetitive tRNA(Gly) gene. The deletions suggest that unique sequences flanked by two nonidentical repetitive sequences, or bordered on only one side by a transposable element, have the potential to be mobilized in the yeast genome. Models for the formation of these two unusual deletions were tested by isolating and analyzing 32 additional unusual deletions of the CYC1 region that extend from a single Ty1 retrotransposon. Unlike the most common class of deletions recovered in this region, these deletions are not attributable solely to homologous recombination among repetitive Ty1 or delta elements. They arose by two distinct mechanisms. In an SPT8 genetic background, most unusual deletions arose by transposition of a Ty1 element to a position adjacent to a tRNA(Gly) gene followed by Ty1-Ty1 recombination. In an spt8 strain, where full-length Ty1 transcription and, therefore, transposition are reduced, most deletions were due to gene conversion of a 7-kb chromosomal interval flanked by a Ty1 element and a tRNA(Gly) gene.

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Evolutionary analyses of the gasdermin family suggest conserved roles in infection response despite loss of pore-forming functionality

BMC Biology ◽

10.1186/s12915-021-01220-z ◽

2022 ◽

Vol 20 (1) ◽

Author(s):

Diego Angosto-Bazarra ◽

Cristina Alarcón-Vila ◽

Laura Hurtado-Navarro ◽

María C. Baños ◽

Jack Rivers-Auty ◽

...

Keyword(s):

Evolutionary History ◽

Family Members ◽

Cartilaginous Fish ◽

Limited Information ◽

Functional Roles ◽

Ancestral Lineage ◽

Wide Range ◽

History Of ◽

Infection Response ◽

Pore Forming Proteins

Abstract Background Gasdermins are ancient (>500million-years-ago) proteins, constituting a family of pore-forming proteins that allow the release of intracellular content including proinflammatory cytokines. Despite their importance in the immune response, and although gasdermin and gasdermin-like genes have been identified across a wide range of animal and non-animal species, there is limited information about the evolutionary history of the gasdermin family, and their functional roles after infection. In this study, we assess the lytic functions of different gasdermins across Metazoa species, and use a mouse model of sepsis to evaluate the expression of the different gasdermins during infection. Results We show that the majority of gasdermin family members from distantly related animal clades are pore-forming, in line with the function of the ancestral proto-gasdermin and gasdermin-like proteins of Bacteria. We demonstrate the first expansion of this family occurred through a duplication of the ancestral gasdermin gene which formed gasdermin E and pejvakin prior to the divergence of cartilaginous fish and bony fish ~475 mya. We show that pejvakin from cartilaginous fish and mammals lost the pore-forming functionality and thus its role in cell lysis. We describe that the pore-forming gasdermin A formed ~320 mya as a duplication of gasdermin E prior to the divergence of the Sauropsida clade (the ancestral lineage of reptiles, turtles, and birds) and the Synapsid clade (the ancestral lineage of mammals). We then demonstrate that the gasdermin A gene duplicated to form the rest of the gasdermin family including gasdermins B, C, and D: pore-forming proteins that present a high variation of the exons in the linker sequence, which in turn allows for diverse activation pathways. Finally, we describe expression of murine gasdermin family members in different tissues in a mouse sepsis model, indicating function during infection response. Conclusions In this study we explored the evolutionary history of the gasdermin proteins in animals and demonstrated that the pore-formation functionality has been conserved from the ancient proto-gasdermin protein. We also showed that one gasdermin family member, pejvakin, lost its pore-forming functionality, but that all gasdermin family members, including pejvakin, likely retained a role in inflammation and the physiological response to infection.

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Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

Journal of General Virology ◽

10.1099/vir.0.047928-0 ◽

2013 ◽

Vol 94 (4) ◽

pp. 738-748 ◽

Cited By ~ 45

Author(s):

Ying Tao ◽

Mang Shi ◽

Christina Conrardy ◽

Ivan V. Kuzmin ◽

Sergio Recuenco ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary History ◽

Evolutionary Rate ◽

Mammalian Species ◽

Evolutionary Analysis ◽

Viral Pathogens ◽

Genomic Features ◽

Wide Range ◽

History Of ◽

Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

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Triplet-based similarity score for fully multilabeled trees with poly-occurring labels

Bioinformatics ◽

10.1093/bioinformatics/btaa676 ◽

2020 ◽

Author(s):

Simone Ciccolella ◽

Giulia Bernardini ◽

Luca Denti ◽

Paola Bonizzoni ◽

Marco Previtali ◽

...

Keyword(s):

Open Source ◽

Evolutionary History ◽

Similarity Measures ◽

Real Data ◽

Similarity Score ◽

Supplementary Information ◽

Supplementary Data ◽

Wide Range ◽

Golden Standard ◽

History Of

Abstract Motivation The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases. Results To overcome these limitations, in this article, we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data. Availability and implementation An open source implementation of MP3 is publicly available at https://github.com/AlgoLab/mp3treesim. Supplementary information Supplementary data are available at Bioinformatics online.

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