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111 results for “genome duplications”
Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes
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Data from: Gene duplication, population genomics and species-level differentiation within a tropical mountain shrub
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Kinetochore and ionomic adaptation to whole genome duplication
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The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae)
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Data from: Species tree estimation and the impact of gene loss following whole-genome duplication
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Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
<p>In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid <em>Arabidopsis lyrata</em> and <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (<em>ASY1</em>, <em>ASY3</em>, <em>PDS5b</em>, <em>PRD3</em>, <em>REC8</em>, <em>SMC3</em>, <em>ZYP1a/b</em>) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel <em>ASYNAPSIS3</em> (<em>ASY3</em>) allele derived from <em>A</em>. <em>lyrata</em>. The <em>ASY3</em> allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the <em>ASY3 TD</em> haplotype was significantly lower than in plants heterozygous for <em>ASY3 TD/ND</em> (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for <em>ASY3 TD</em> compared to a plant heterozygous for <em>ASY3 ND/TD</em>. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.</p>
Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
<p>Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.</p>
The complex history of genome duplication and hybridization in North American gray treefrogs
<p>Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. While systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid <em>Hyla chrysoscelis</em> and the tetraploid <em>Hyla versicolor</em>, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with Approximate Bayesian Computation (ABC), to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.</p>
Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
<p class="BodyA"><span><b>Background:</b> The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus <i>Hibiscus </i>L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. <i>Hibiscus </i>is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested three alternative scenarios describing different polyploidization events.</span></p> <p class="BodyA"><span><b>Results:</b> Using target sequence capture, we designed a new probe set for <i>Hibiscus </i>and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of <i>Hibiscus</i> sampled shared one genome duplication with <i>H. syriacus</i> and one whole genome duplication occurred along the branch leading to <i>H. syriacus</i>.</span></p> <p class="BodyA"><span><b>Conclusions:</b> Here, we corroborated the independent genome doubling previously found in the lineage leading to <i>H. syriacus </i>and a shared genome doubling of this lineage and the remainder of <i>Hibiscus</i>. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within <i>Hibiscus</i>) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.</span></p>
Data from: Whole-genome duplication and host genotype affect rhizosphere microbial communities
<p>The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. Yet, the ways in which specific genetic architectures of host plants shape microbiomes is unknown. Genome duplication events are common in the evolutionary history of plants, influence many important plant traits, and, thus, they may affect associated microbial communities. Using experimentally induced whole genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in<i> Arabidopsis thaliana</i>. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia <i>vs</i>. Landsberg) and ploidy levels (diploid <i>vs</i>. tetraploid). We modeled relative abundances of bacterial taxa using the Dirichlet and multinomial distributions via a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic architecture and bacterial community assembly with potential ramifications for host fitness. Moreover, we uncovered an intriguing role of ploidy-level for shaping plant microbiomes. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes.</p>
Data from: Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome
A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both nonduplicated and duplicated loci by taking locus-specific copy number into account. We apply this method to RAD sequence data from different ecotypes of a polyploid-origin salmonid (Oncorhynchus nerka) and reveal signatures of divergent selection that would have been missed if duplicated loci were filtered. We also find conserved signatures of elevated divergence at pairs of homeologous chromosomes with residual tetrasomic inheritance, suggesting that joint evolution of some nondiverged gene duplicates may affect the adaptive potential of these genes. These findings illustrate that including duplicated loci in genomic analyses enables novel insights into the evolutionary consequences of WGDs and local segmental gene duplications.
The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications
<div> <div> <p><a href="https://onlinelibrary.wiley.com/doi/10.1111/age.13181">https://onlinelibrary.wiley.com/doi/10.1111/age.13181</a></p> <h1>The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications</h1> <div> </div> <div> <div> <div> <div><a href="https://onlinelibrary.wiley.com/authored-by/Chen/Jianhai">Jianhai Chen</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Zhong/Jie">Jie Zhong</a>, <a href="https://onlinelibrary.wiley.com/authored-by/He/Xuefei">Xuefei He</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Li/Xiaoyu">Xiaoyu Li</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Ni/Pan">Pan Ni</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Safner/Toni">Toni Safner</a>, <a href="https://onlinelibrary.wiley.com/authored-by/%C5%A0prem/Nikica">Nikica Šprem</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Han/Jianlin">Jianlin Han</a></div> </div> </div> </div> <p>The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long-range information provided by 10× Linked-Reads sequencing. We achieved a high-quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference-assistant scaffolding method. Using the ‘assembly-to-assembly’ approach, we identified intra-chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (<em>R</em><sup>2</sup> > 0.64, <em>p</em> < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large-scale inter-chromosomal evolution, by resolving parental-derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (<em>p</em> < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (<em>p</em> < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter-chromosomal interaction between the sex chromosome and autosomes.</p> </div> </div> <div>The work has been pulished here: https://onlinelibrary.wiley.com/doi/full/10.1111/age.13181</div> <div> </div> <div>The current dataset include the genome annotation files.</div> <div> </div> <div>For the whole-genomic assembly, please check NCBI: </div> <div>https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_021656055.1/</div> <div> <table> <tbody> <tr> <th> </th> <th>GenBank</th> </tr> </tbody> <tbody> <tr> <td>Genome size</td> <td>2.5 Gb</td> </tr> <tr> <td>Total ungapped length</td> <td>2.4 Gb</td> </tr> <tr> <td>Number of scaffolds</td> <td>12,642</td> </tr> <tr> <td>Scaffold N50</td> <td>28.3 Mb</td> </tr> <tr> <td>Scaffold L50</td> <td>25</td> </tr> <tr> <td>Number of contigs</td> <td>41,323</td> </tr> <tr> <td>Contig N50</td> <td>157.9 kb</td> </tr> <tr> <td>Contig L50</td> <td>4,562</td> </tr> <tr> <td>GC percent</td> <td>42</td> </tr> <tr> <td>Genome coverage</td> <td>56.0x</td> </tr> <tr> <td>Assembly level</td> <td>Scaffold</td> </tr> </tbody> </table> <p> </p> <h2>Assembly methods</h2> <div>Sequencing technology 10xgenomics Assembly method Supernova v. 2.1.1 <p> </p> <p>part_** are genome fasta for the GCA_021656055.1</p> <p>You could use the following to combine and uncompress.</p> </div> </div> <div> <div> <div><code><span>cat</span> part_* > archive_combined.zip </code></div> </div> <div> <div> </div> <div><code>unzip archive_combined.zip</code></div> </div> </div> <div> </div> <div> </div>
The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
<p><span>The Major Histocompatibility Complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assemble and annotate the MHC genomic region of the great reed warbler (<em>Acrocephalus arundinaceus</em>), using long-read sequencing and optical mapping. The MHC region is large (>5.5Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content</span><span> than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologs among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.</span></p>
Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation
<p><span>In lineages of allopolyploid origin, entire parental subgenomes may coexist, with two or more sets of homoeologous chromosomes that differ in gene content and syntenic structure. Presence or absence of genes, and microsynteny along chromosomal blocks, can be used to differentiate subgenomes and can be coded as phylogenetic data. We assembled chromosome-level genomes of representative species across an ancient allopolyploid lineage, the walnut family (Juglandaceae)</span><span>, with <em>Myrica</em> and other Fagales as outgroups, and used genome-structural data to infer a phylogeny. </span><span>Microsynteny (with various collinear block sizes) and gene content analyses, using the dominant or recessive progenitor subgenomes or both, all yielded identical topologies that place <em>Engelhardia</em> (a SE Asian and Central American clade) with <em>Platycarya</em>, an </span><span>enigmatic monospecific taxon endemic in </span><span>East</span> <span>Asia</span><span>, but well-represented in the Paleocene-Eocene of North America and Europe. </span><span>Morphological studies including fossils also found the <em>Platycarya</em>/<em>Engelhardia</em> clade because of leaf architecture, floral morphology, and nut walls without lacunae, but DNA-alignment-based phylogenetics carried out here and in previous studies never detected this uniformly wind-dispersed clade, instead grouping <em>Platycarya</em> with <em>Carya</em> and <em>Juglans</em>. The novel analyses further reveal </span><span>the family's hybrid origin from extinct or unsampled progenitors nested within Myricaceae and that <em>Rhoiptelea</em> <em>chiliantha</em></span><span>, the Chinese sister species to all other Juglandaceae, </span><span>contains proportionally more genes related to DNA repair and evolved at a rate 2.6- to 3.5-times slower than the remaining species</span><span>. Our results have implications for the molecular clock hypothesis and suggest that genomic structure contains so-far undervalued phylogenetic signal</span><span>.</span></p>
Intercontinental dispersal and whole‐genome duplication contribute to loss of self‐incompatibility in a polyploid complex
Premise of the Study <div class="article-section__content en main"> <p>Angiosperm species often shift from self-incompatibility to self-compatibility following population bottlenecks. Across the range of a species, population bottlenecks may result from multiple factors, each of which may affect the geographic distribution and magnitude of mating-system shifts. We describe how intercontinental dispersal and genome duplication facilitate loss of self-incompatibility.</p> Methods <p>Self and outcross pollinations were performed on plants from 24 populations of the <i>Campanula rotundifolia</i> polyploid complex. Populations spanned the geographic distribution and three dominant cytotypes of the species (diploid, tetraploid, hexaploid).</p> Key Results <p>Loss of self-incompatibility was associated with both intercontinental dispersal and genome duplication. European plants were largely self-incompatible, whereas North American plants were intermediately to fully self-compatible. Within both European and North American populations, loss of self-incompatibility increased as ploidy increased. Ploidy change and intercontinental dispersal both contributed to loss of self-incompatibility in North America, but range expansion did not affect self-incompatibility within Europe or North America.</p> Conclusions <p>When species are subject to population bottlenecks arising through multiple factors, each factor can contribute to self-incompatibility loss. In a widespread polyploid complex, the loss of self-incompatibility can be predicted by the cumulative effects of whole-genome duplication and intercontinental dispersal.</p> </div>
Effects of glaciation and whole genome duplication on the distribution of the Campanula rotundifolia polyploid complex
<div class="article-section__content en main"> Premise Of The Study <p>Both intrinsic and extrinsic factors contribute to a species distribution. Among plants, the extrinsic effects of glaciation and intrinsic effects of whole genome duplication are powerful drivers of biogeographical patterns, but the interplay of these factors is poorly understood. Here, we investigate the roles glaciation and whole-genome duplication have played in the evolution of the widespread polyploid complex <i>Campanula rotundifolia</i>.</p> Methods <p>We assessed the cytotype of 37 populations that spanned the geographic and cytotypic range of the <i>C. rotundifolia</i> complex. We constructed a chloroplast phylogeny for these populations and used RAD-seq to create nuclear phylogenies and networks for a subset of 23 populations; and estimated divergence times of major clades using Bayesian estimation of substitution rates.</p> Key Results <p><i>Campanula rotundifolia</i> originated in south-central Europe and underwent range expansion throughout much of Europe and North America. Multiple genome duplications have occurred in <i>C. rotundifolia</i>—at least two tetraploid and three hexaploid formations.</p> Conclusions <p>Nuclear and chloroplast phylogenies are largely congruent with a history of populations surviving glacial maxima in known Pleistocene refugia in Europe and North America. Divergent European clades are consistent with two disjunct glacial refugia within Europe. North America was colonized by hexaploids derived from Western European lineages. A glacial refugium in Midwestern North America likely facilitated post-glacial recolonization of North America and limited genetic divergence. These results implicate both glaciation and whole-genome duplication as contributing factors to the extant biogeography of <i>C. rotundifolia</i>.</p> </div>
Targeted genome editing in vivo corrects a Dmd duplication restoring wild‐type dystrophin expression
<p class="Paragraph">Tandem duplication mutations are increasingly found to be the direct cause of many rare heritable diseases, accounting for up to 10% of cases. Unfortunately, animal models recapitulating such mutations are scarce, limiting our ability to study them and develop genome editing-based therapies. Here, we describe the generation of the <em>Dup18-30 </em>mouse model, harbouring a multi-exonic tandem duplication in the <i>Dmd</i> gene which recapitulates a human mutation. Duplication correction of this mouse was achieved by implementing a single-guide RNA (sgRNA) CRISPR/Cas9 approach. This strategy precisely removed a duplication mutation <i>in vivo</i>, restored full-length dystrophin expression, and was accompanied by improvements in both histopathological and clinical phenotypes. We conclude that CRISPR/Cas9 represents a powerful tool to accurately model and treat tandem-duplication mutations. </p> <p class="Paragraph">This dataset includes the deep amplicon sequencing analysis performed to detect single-sgRNA/Cas9 off-target and on-target effects in the <em>Dup18-30</em> mice after treatment.</p>
Data for: Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure
<p>Distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle without understanding of genomic architecture for phenotypic traits. This study provides a high-resolution portrait of genomic variation in Chinook salmon (<em>Oncorhynchus</em> <em>tshawytscha</em>) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered dataset of ~13 million SNPs from low coverage whole genome resequencing of 53 populations (3,566 barcoded individuals), we contrasted patterns of genomic variation within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Allele frequency variation in GREB1L/ROCK1 was highly correlated with mean migration timing for early- and late-run populations within each of the lineages (r<sup>2</sup> between 0.58–0.95; P < 0.001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.</p>
The complex history of genome duplication and hybridization in North American gray treefrogs
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Targeted genome editing in vivo corrects a Dmd duplication restoring wild‐type dystrophin expression
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