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10 results for “target gene capture”
Phylogenomics of Gesneriaceae using targeted capture of nuclear genes
<p>Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperm-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group. </p>
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves
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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>
Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
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Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
<p>Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. We showed that incomplete lineage sorting was present at all nodes that exhibited high levels of discordance, which was caused by extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology, and hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that species tree inference can be improved using a total-evidence and multi-faceted approach that utilizes the most amount of data and considers results from different analytical methods and datasets.</p>
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
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A 3’-end capture sequencing method for high-throughput targeted gene expression profiling
GEO Series GSE190096. Homo sapiens. 720 samples. Type: Expression profiling by high throughput sequencing.
Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse Neotropical palm tribe Geonomateae.
<p>The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus <em>Geonoma</em>, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genes for 85% of the species of the tribe, including 84% of the species of the largest genus, <em>Geonoma</em>.<em> </em>Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.</p>
An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq
GEO Series GSE303901. Homo sapiens. 29 samples. Type: Expression profiling by high throughput sequencing.
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene [Region-capture Micro-C (RCMC)]
GEO Series GSE297277. Mus musculus. 12 samples. Type: Other.
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