DNA transposon expansion is associated with genome size increase in mudminnows

Abstract Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5-5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in Umbra limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.

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DNA transposon expansion is associated with genome size increase in mudminnows

10.1101/2021.06.07.447207 ◽

2021 ◽

Author(s):

Robert Lehmann ◽

Ales Kovarik ◽

Konrad Ocalewicz ◽

Lech Kirtiklis ◽

Andrea Zuccolo ◽

...

Keyword(s):

Genome Size ◽

North American ◽

Size Increase ◽

Dna Transposon ◽

Whole Genome Duplications ◽

Genome Expansion ◽

Genome Duplications ◽

Robertsonian Rearrangements ◽

Eukaryotic Organisms ◽

Genome Assemblies

Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5-5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in Umbra limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by extensive DNA transposon expansion without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.

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Surprising amount of stasis in repetitive genome content across the Brassicales

10.1101/2020.06.15.153296 ◽

2020 ◽

Author(s):

Aleksandra Beric ◽

Makenzie E Mabry ◽

Alex E Harkess ◽

M. Eric Schranz ◽

Gavin C Conant ◽

...

Keyword(s):

Genome Size ◽

Contributing Factors ◽

Plant Genomes ◽

New Methods ◽

Whole Genome Duplications ◽

Genome Size Evolution ◽

Size Evolution ◽

Genome Duplications ◽

Genome Content ◽

Low Coverage

Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana - chosen as the model plant system for this reason - as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we find no correlation between genome size and TE content, and more surprisingly we identify no significant changes to TE landscape following WGD.

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Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab140 ◽

2021 ◽

Author(s):

Aleksandra Beric ◽

Makenzie E Mabry ◽

Alex E Harkess ◽

Julia Brose ◽

M Eric Schranz ◽

...

Keyword(s):

Genome Size ◽

Repetitive Elements ◽

Contributing Factors ◽

New Methods ◽

Whole Genome Duplications ◽

Genome Size Evolution ◽

Size Evolution ◽

Genome Duplications ◽

Comparative Phylogenetics ◽

Low Coverage

Abstract Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

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Size is not everything: rates of genome size evolution, not C -value, correlate with speciation in angiosperms

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.2289 ◽

2015 ◽

Vol 282 (1820) ◽

pp. 20152289 ◽

Cited By ~ 37

Author(s):

Mark N. Puttick ◽

James Clark ◽

Philip C. J. Donoghue

Keyword(s):

Genome Size ◽

Sister Group ◽

Land Plants ◽

Whole Genome ◽

Whole Genome Duplications ◽

Rates Of Evolution ◽

Genome Size Evolution ◽

Size Evolution ◽

Genome Duplications ◽

Duplication Events

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.

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Faculty Opinions recommendation of Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1007665.123659 ◽

2002 ◽

Author(s):

Marie-Angele Grandbastien

Keyword(s):

Genome Size ◽

Size Reduction ◽

Illegitimate Recombination ◽

Genome Expansion

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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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