Model Adequacy Tests for Likelihood Models of Chromosome-Number Evolution

Mapping Intimacies ◽

10.1101/2020.10.05.326231 ◽

2020 ◽

Author(s):

Anna Rice ◽

Itay Mayrose

Keyword(s):

Chromosome Number ◽

Real Data ◽

Central Feature ◽

List Type ◽

Evolutionary Patterns ◽

Model Adequacy ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Chromosome Number Evolution ◽

Modelling Assumptions

SummaryChromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data.Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows to determine whether the model can generate data with similar characteristics as those found in the observed ones.We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitted model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present.The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods developments.

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Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

Genes ◽

10.3390/genes9110563 ◽

2018 ◽

Vol 9 (11) ◽

pp. 563 ◽

Cited By ~ 6

Author(s):

Anna Szczepaniak ◽

Michał Książkiewicz ◽

Jan Podkowiński ◽

Katarzyna Czyż ◽

Marek Figlerowicz ◽

...

Keyword(s):

Selection Pressure ◽

Coenzyme A ◽

Phylogenetic Inference ◽

Whole Genome ◽

Evolutionary Patterns ◽

Acetyl Coenzyme A ◽

Acetyl Coenzyme ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Acetyl Coenzyme A Carboxylase

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

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Model Adequacy Tests for Probabilistic Models of Chromosome‐Number Evolution

New Phytologist ◽

10.1111/nph.17106 ◽

2020 ◽

Author(s):

Anna Rice ◽

Itay Mayrose

Keyword(s):

Chromosome Number ◽

Probabilistic Models ◽

Model Adequacy ◽

Chromosome Number Evolution

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Molecular evolution of GDP-L-galactose phosphorylase, a key regulatory gene in plant ascorbate biosynthesis

AoB Plants ◽

10.1093/aobpla/plaa055 ◽

2020 ◽

Vol 12 (6) ◽

Author(s):

Junjie Tao ◽

Zhuan Hao ◽

Chunhui Huang

Keyword(s):

Molecular Evolution ◽

Abiotic Stress Tolerance ◽

Regulatory Gene ◽

Purifying Selection ◽

Plant Evolution ◽

Rapid Expansion ◽

Whole Genome ◽

Evolutionary Patterns ◽

Whole Genome Duplications ◽

Genome Duplications

Abstract Ascorbic acid (AsA) is a widespread antioxidant in living organisms, and plays essential roles in the growth and development of animals and plants as well as in the response to abiotic stress tolerance. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood; however, the molecular evolutionary patterns of the gene remain unclear. In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, and the phylogenetic relationships, gene duplication and molecular evolution analyses of the genes were systematically investigated. Results showed that GGP genes are present throughout the plant kingdom and five shared whole-genome duplications and several lineage-specific whole-genome duplications were found, which led to the rapid expansion of GGPs in seed plants, especially in angiosperms. The structure of GGP genes was more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins had a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that GGP genes were predominated by purifying selection, indicating that the gene is functionally conserved due to its vital importance in AsA biosynthesis. Most of the branches under positive selection identified by the branch-site model were mainly in the chlorophytes lineage, indicating episodic diversifying selection may contribute to the evolution of GGPs, especially in the chlorophyte lineage. The conserved function of GGP and its rapid expansion in angiosperms maybe one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

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Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽

10.3390/genes12081190 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1190

Author(s):

Yuqi Huang ◽

Minghao Sun ◽

Lenan Zhuang ◽

Jin He

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Functional Characterization ◽

Vertebrate Evolution ◽

Molecular Phylogenetic Analysis ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Molecular Phylogenetic ◽

Duplication Events ◽

Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

Nature Communications ◽

10.1038/s41467-021-25177-3 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Hua Sun ◽

Song Cao ◽

R. Jay Mashl ◽

Chia-Kuei Mo ◽

Simone Zaccaria ◽

...

Keyword(s):

Human Tumors ◽

Multiple Time ◽

Cancer Treatments ◽

Whole Genome Duplications ◽

Patient Derived Xenograft ◽

Genome Duplications ◽

Genomic Characterization ◽

Cancer Types ◽

Multiple Time Points ◽

Pdx Models

AbstractDevelopment of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs’ recapitulation of human tumors.

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Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)

Genes ◽

10.3390/genes11111375 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1375

Author(s):

Larisa S. Biltueva ◽

Dmitry Yu. Prokopov ◽

Svetlana A. Romanenko ◽

Elena A. Interesova ◽

Manfred Schartl ◽

...

Keyword(s):

Duplication Event ◽

Siberian Sturgeon ◽

Genome Duplication Event ◽

Acipenser Baerii ◽

Whole Genome Duplications ◽

Sturgeon Species ◽

Genome Duplications ◽

Size Groups ◽

Genomic Studies ◽

Syntenic Regions

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

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