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78 results for “chromosome rearrangement”
Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
<h2>The Id locus, with a potential polygenic nature, is inverted alongside ZARU1 at the distal end of the q-arm of chromosome Z, indicating a shared ancestry among BBC breeds.</h2>
Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome
<p><strong><em>Myzus persicae </em>clone O v2 frozen release</strong></p> <p>Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae de novo</em> repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae</em> <em>de novo r</em>epeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Acyrthosiphon pisum</em> clone JIC1 v1 frozen release</strong></p> <p>Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum</em> <em>de novo</em> repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum de novo</em> repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Rhodnius prolixus</em> DNA zoo chromosome-scale genome assembly annotation</strong></p> <p><em>R. prolixus </em>chromosome-scale genome assembly was obtained here: <a href="https://www.dnazoo.org/assemblies/Rhodnius_prolixus">https://www.dnazoo.org/assemblies/Rhodnius_prolixus</a>.</p> <p>Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta</p> <p>BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff</p> <p>BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa</p> <p><strong><em>Triatoma rubrofasciata</em> chromosome-scale genome assembly annotation</strong></p> <p><em>T. rubrofasciata </em>chromosome-scale genome assembly was obtained here: <a href="http://dx.doi.org/10.5524/100614">http://dx.doi.org/10.5524/100614</a></p> <p>Genome assembly: zhuichun_assembly.fasta</p> <p>BRAKER2 gene models: zhuichun_assembly.braker2.gff</p> <p>BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa</p> <p><strong>Hemiptera orthogroups and species tree</strong></p> <p>OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details:</p> <p>Species included, taxon IDs and data source:</p> <p>Mcer = Myzus cerasi v1.1 (<a href="https://bipaa.genouest.org/sp/myzus_cerasi/">https://bipaa.genouest.org/sp/myzus_cerasi/</a>)</p> <p>MperO = Myzus persicae clone O v2 (This study)</p> <p>Dnox = Diuraphis noxia Thorpe et. al. gene predictions (<a href="https://bipaa.genouest.org/sp/diuraphis_noxia/">https://bipaa.genouest.org/sp/diuraphis_noxia/</a>)</p> <p>Apis = Acyrthosiphon pisum JIC1 v1 (This study)</p> <p>Pnig = Pentalonia nigronervosa (This study)</p> <p>Rmai = Rhopalosiphum maidis v0.1 (<a href="http://gigadb.org/dataset/100572">http://gigadb.org/dataset/100572</a>)</p> <p>Rpad = Rhopalosiphum padi v1.0 (<a href="https://bipaa.genouest.org/sp/rhopalosiphum_padi/">https://bipaa.genouest.org/sp/rhopalosiphum_padi/</a>)</p> <p>Agly = Aphis glycines biotype 4 v2.1 (<a href="https://zenodo.org/record/3453468#.XnpL5JOgLRY">https://zenodo.org/record/3453468#.XnpL5JOgLRY</a>)</p> <p>BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (<a href="http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi">http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi</a>)</p> <p>Trub = Triatoma rubrofasciata (This study)</p> <p>Rpro = Rhodnius prolixus (This study)</p> <p>Ofas = Oncopeltus fasciatus OGS v1.0 (<a href="https://i5k.nal.usda.gov/Oncopeltus_fasciatus">https://i5k.nal.usda.gov/Oncopeltus_fasciatus</a>)</p> <p>Sfuc = Sogatella furcifera v1 (<a href="http://dx.doi.org/10.5524/100255">http://dx.doi.org/10.5524/100255</a>)</p> <p>Nlug = Nilaparvata lugens (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42</a>)</p> <p>Files:</p> <p>Proteomes included in the analysis: proteomes.tar.gz</p> <p>Orthogroups: Orthogroups.txt</p> <p>Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv</p> <p>Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt</p> <p>Species tree alignment: SpeciesTreeAlignment.fa</p> <p>r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex</p> <p>r8s time calibrated species tree: r8s_tree.nwk</p>
A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae
<p>European flat oyster (<em>Ostrea edulis</em>) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite <em>Bonamia ostreae</em>. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with <em>B. ostreae</em> exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long-term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs hatchery) when using neutral markers, and to bonamiosis status (NV vs LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier datasets showed high genetic divergence (FST > 0.25) unlike neutral loci (FST not ≠ 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE-C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE-C8. A range of relevant immune functions were specifically enriched among genes annotated on OE-C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker-assisted selection could be applied to breed resilient strains of <em>O. edulis</em> to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following <em>B. ostreae</em> infection is demonstrated.</p>
Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
<p>Orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, including phylogenetic reconstruction and orthologous gene mapping, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. Our findings demonstrate that the canonical bilaterian genome structure has been lost across an entire phylum, reveal that linkage group fission can occur very frequently in specific lineages, and provide a powerful source of phylogenetic information.</p>
Fixed allele differences associated with the centromere reveal chromosome morphology and rearrangements in a reptile (Varanus acanthurus Boulenger)
<p>Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multi-platform next generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa, however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (<em>Varanus</em> <em>acanthurus</em> BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout Northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the <em>V. acanthurus</em> complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support <em>de novo</em> chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterised by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken and the platypus. We demonstrated that the synteny of genes in chordates remains conserved despite centromere repositioning across these taxa.</p>
Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation : simulated data
<p>Data simulated with Aevol (<a href="http://www.aevol.fr">www.aevol.fr</a>), a software available on gitlab ( <a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a> ), for our paper submitted to Molecular Ecology entitled "Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation".</p>
Data from: Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies
<p>Large-scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution of populations, yet it remains unclear exactly how rearrangements become established and eventually fix. Rearrangements could fix by genetic drift if they are weakly deleterious or neutral, or they may instead be favoured by positive natural selection. Here we compare genome assemblies of three closely related <em>Brenthis</em> butterfly species and characterise a complex history of fission and fusion rearrangements. An inferred demographic history of these species suggests that rearrangements became fixed in populations with large long-term effective size (<em>N<sub>e</sub></em>). However, we also find large runs of homozygosity within individual genomes and show that a model of population structure with smaller local <em>N<sub>e</sub></em> can reconcile these observations. Using a recently developed analytic framework for characterising hard selective sweeps, we find that chromosome fusions are not enriched for evidence of past sweeps compared to other regions of the genome. Nonetheless, one chromosome fusion in the <em>B. daphne</em> genome is associated with a valley of diversity where genealogical branch lengths are distorted, consistent with a selective sweep. Our results suggest that drift is a stronger force in these populations than suggested by overall genetic diversity, but that the fixation of strongly underdominant rearrangements remains unlikely. Additionally, although chromosome fusions do not typically exhibit signatures of selective sweeps, a single example raises the possibility that natural selection may sometimes play a role in their fixation.</p>
Data from: The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus
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Fixed allele differences associated with the centromere reveal chromosome morphology and rearrangements in a reptile (Varanus acanthurus Boulenger)
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Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
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Data from: Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies
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A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae
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Shared, modular chromosome rearrangements enable parallel adaptation in a marine fish
Genomic architecture and standing variation can play a key role in ecological adaptation, and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behaviour in regional analyses. However, the degree of parallelism , the extent of independent inheritance, and functional distinctiveness of these rearrangements remains poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangement with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures have likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
Data from: Chromosomal rearrangements do not seem to affect the gene flow in hybrid zones between karyotypic races of the common shrew (Sorex araneus)
Chromosomal rearrangements are proposed to promote genetic differentiation between chromosomally differentiated taxa and therefore promote speciation. Due to their remarkable karyotypic polymorphism, the shrews of the Sorex araneus group were used to investigate the impact of chromosomal rearrangements on gene flow. Five intraspecific chromosomal hybrid zones characterized by different levels of karyotypic complexity were studied using 16 microsatellites markers. We observed low levels of genetic differentiation even in the hybrid zones with the highest karyotypic complexity. No evidence of restricted gene flow between differently rearranged chromosomes was observed. Contrary to what was observed at the interspecific level, the effect of chromosomal rearrangements on gene flow was undetectable within the S. araneus species.
Data from: The role of chromosomal rearrangements and geographical barriers in the divergence of lineages in a South American subterranean rodent (Rodentia: Ctenomyidae: Ctenomys minutus)
Identifying factors and the extent of their roles in the differentiation of populations is of great importance for understanding the evolutionary process in which a species is involved. Ctenomys minutus is a highly karyotype- polymorphic subterranean rodent, with diploid numbers ranging from 42 to 50 and autosomal arm numbers ranging from 68 to 80, comprising a total of 45 karyotypes described so far. This species inhabits the southern Brazilian coastal plain, which has a complex geological history, with several potential geographical barriers acting on different time scales. We assessed the geographical genetic structure of C. minutus, examining 340 individuals over the entire distributional range and using information from chromosomal rearrangements, mitochondrial DNA (mtDNA) sequences, and 14 microsatellite loci. The mtDNA results revealed 7 main haplogroups, with the most recent common ancestors dating from the Pleistocene, whereas clustering methods defined 12 populations. Some boundaries of mtDNA haplogroups and population clusters can be associated with potential geographical barriers to gene flow. The isolation by distance pattern also plays an important role in fine-scale genetic differentiation, which is strengthened by the narrowness of the coastal plain and by common features of subterranean rodents (i.e., small fragmented populations and low dispersal rates), which limit gene flow among populations. A step-by-step mechanism of chromosomal evolution can be suggested for this species, mainly associated with the metapopulation structure, genetic drift, and the geographical features of the southern Brazilian coastal plain. However, chromosomal variation plays no or very little role in the diversification of C. minutus populations.
Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes
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Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
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Data from: Chromosomal rearrangements do not seem to affect the gene flow in hybrid zones between karyotypic races of the common shrew (Sorex araneus)
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Data from: The role of chromosomal rearrangements and geographical barriers in the divergence of lineages in a South American subterranean rodent (Rodentia: Ctenomyidae: Ctenomys minutus)
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