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41 results for “Genome Skimming”
Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family
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Data from: Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron
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Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
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Data from: Lessons from genome skimming of arthropod-preserving ethanol
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Sequences of Staudtia kamerunensis obtained through low coverage whole genome skimming
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Data from: Plastome of Quercus xanthoclada and comparison of genomic diversity among selected Quercus species using genome skimming
The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described but genetic diversity at a global scale within and among oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada, and compared its sequence those available from other main taxonomic groups in Quercus. We quantify genomic divergence among oaks and performed a sliding window analysis to detect the most variable regions among members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs among oaks species and sections, and stress the need for a large global assessment of the genetic diversity in this economically and ecologically important genus.
Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study, next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina HiSeq 2500 instrument. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Skimming the skaters: genome skimming improves phylogenetic resolution of Halobatinae (Hemiptera: Gerridae)
<p>Datasets, codes, and results.</p>
Data from: Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data
<p><span><i>Oresitrophe</i> and <i>Mukdenia</i> (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. However, the taxonomy of <i>Mukdenia</i>, especially of<i> M. acanthifolia</i>, has been controversial. Genome skimming of <i>M. acanthifolia</i> and <i>M. rossii</i>, including three individuals for each species is reported and complete plastomes, partial mitogenomes and ETS/ITS sequences were assembled using these data. Their plastomes ranged from 156,341 bp to 157,018 bp in length and had similar structural characteristics and gene content of other flowering plants. These genomes were typically quadripartite, comprising 113 unique genes (79 protein coding genes, 30 tRNAs and 4 rRNAs). Comparative analysis showed that the plastomes of <i>Mukdenia</i> and <i>Oresitrophe</i> were relatively conservative, reflecting the genome size and structure, gene contents, RNA editing sites and codon usage. Five plastid regions that were hotspots of change (<i>trn</i>H-<i>psb</i>A, <i>psb</i>C-<i>trn</i>S, <i>trn</i>M-<i>atp</i>E, <i>pet</i>A-<i>psb</i>J and <i>ccs</i>A-<i>ndh</i>D) were identified within <i>Mukdenia</i>, and six regions (<i>trn</i>H-<i>psb</i>A, <i>pet</i>N-<i>psb</i>M, <i>trn</i>M-<i>atp</i>E, <i>rps</i>16-<i>trn</i>Q, <i>ycf</i>1 and <i>ndh</i>F) contained a higher number of species-specific parsimony-informative sites that can serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between <i>Mukdenia</i> and <i>Oresitrophe</i>, we combined our data with published data based on three different datasets. The monophyly of each species (<i>O. rupifraga</i>, <i>M. acanthifolia</i> and <i>M. rossii</i>) and the inferred topology ((<i>M. rossii</i>, <i>M. acanthifolia</i>), <i>O. rupifraga</i>) were well supported in trees reconstructed using the complete plastomes, but <i>M. acanthifolia</i> and <i>M. rossii</i> did not form separate clade in the ETS+ITS data. We found low recovery of genes in the Angiosperms 353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordances between the trees reconstructed from plastid and nuclear data. The results from this study suggest that <i>M. acanthifolia</i> should be treated as a distinct species.</span></p>
Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny
<div class="page"> <div class="layoutArea"> <div class="column"> <p class="MsoNormal">Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.</p> </div> </div> </div>
Figure 4 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 4 mVISTA percent identity plot comparing the four Quercus chloroplast genomes with Q. xanthoclada as a reference. Vertical scale indicates the percentage of identity ranging from 50% to 100%. Coding regions are in blue and non-coding regions are in pink.
Figure 3 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 3 Sliding window analysis of the whole plastomes of five oak species. (window length: 500 bp, step size: 250 bp). X-axis: position of the mid-point of the window, Y-axis: number of SNPs (solid line) and indels (dashed line) positions of each window in bp. Coding regions and directions of transcription are indicated by arrows, inverted repeats by grey areas. Putative barcode loci are highlighted for SNPs and indels. For readability, only a few major genes are indicated.
Figure 2 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 2 ML phylogenetic tree of the nine selected plastomes in GenBank, plus the plastome of Quercus xanthoclada. The tree is rooted with Trigonobalanus doichangensis. Bootstraps (1000 replicates) are shown at the nodes, values below 50% not shown. Scale in substitution per site.
Figure 1 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 1 Circular gene map of the plastid genome of Quercus xanthoclada. Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counter clockwise. Genes are colour-coded according to their functional groups.
Figure 5 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 5 Venn diagram showing the private and shared SNPs amongst the five oak species. Each area is coloured according to the relative number of shared SNPs in this area.
Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny
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Data from: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: a case study in Oreocarya (Boraginaceae)
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Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
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Data from: Plastome of Quercus xanthoclada and comparison of genomic diversity among selected Quercus species using genome skimming
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Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos
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International Brain Laboratory public data
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OpenNeuro
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