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18 results for “target-enrichment”
Data from: Bratzel et al. (2022) Target-enrichment sequencing reveals for the first time a well-resolved phylogeny of the core Bromelioideae (Bromeliaceae). Taxon
<p>DNA sequence alignments used for phylogenetic analyses in Bratzel et al. (2022) Target-enrichment sequencing reveals for the first time a well-resolved phylogeny of the core Bromelioideae (Bromeliaceae). Taxon.</p>
Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
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Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)
<p>Bait sets, sequences, trees and scripts</p>
Data from: An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives
<p>Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2,476 loci) on 99 specimens of scleractinian corals spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades.Focused sampling in the staghorn corals (genus <i>Acropora</i>)highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (± 298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the <i>Acropora</i>are incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within <i>Acropora.</i>The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful.</p>
Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.
Figure 4 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 4. Stacked barplots showing the number of reads uniquely matching different reference sequences for the three targeted mitochondrial genes with a similarity threshold of 98%. The Rana pigra type was not included because the number of reads was too low.
Figure 8 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 8. Lateral views of the heads of preserved adult males of Mantidactylus (Mantidactylus) radaka sp. nov. in comparison with M. (M.) guttulatus and M. (M.) grandidieri. Note the more distinct and larger tympanum (indicated by yellow arrows) in the latter two species. Not to scale.
Figure 6 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 6. Photographs of living specimens of Mantidactylus radaka sp. nov. (a, b) Male holotype ZSM 644/2001 (field number FGMV 2001.132) from Manarikoba forest, Tsaratanana Massif. (c–f) Female paratype ZSM 1800/2010 (ZCMV 12345) from Camp 1 (Antevialambazaha), Tsaratanana Massif. (g, h) Female paratype ZSM 97/2016 (MSZC 0080) from Ampotsidy. (i, j) Male paratype MSZC 0120 (uncatalogued in UADBA) from Ampotsidy. (k) Unidentified specimen from Camp 0 (Ankijagna Lagnana), Tsaratanana Massif. (l) Paratype ZSM 582/2014 (DRV 6073) from Camp 0 (Ankijagna Lagnana). (m, n) Unidentified female specimen from Manongarivo (Camp 0), probably preserved in UADBA collection.
Data from: Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems
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Data from: An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives
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Alteration of genome folding via engineered transposon insertion [Target-enriched sequencing]
GEO Series GSE137371. Homo sapiens. 2 samples. Type: Other.
Target-Enrichment Sequencing for Detailed Characterization of Small RNAs
GEO Series GSE102845. Mus musculus. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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