49 research outputs found

    Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

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    Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype assembly. Figure S7. Orm genes duplicated in house mouse but not in Nile rat. Figure S8. Top20 GO terms overrepresented in Nile rat genes that do not overlap TOGA projections from house mouse. Figure S9. Hmga1b mouse gene absent in the Nile rat genome. Figure S10. G6pd2 mouse gene absent in the Nile rat genome. Figure S11. Schematic diagram of trimming alignment

    MUSCLE alignment of insect cytochrome P450 genes

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    MUSCLE alignment of all sequenced ant CYPs and representative dipteran, hymenopteran and lepidopteran CYPs. All genes were manually checked for presence of conserved motifs (Nelson, D. Methods Mol. Biol. (2006) 320, 1-10). The alignment was further edited to remove the hypervariable non-conserved N-terminal up to (but not including) the N-terminal anchor sequence, as well as the region between the C-helix and I-helix. Further details can be found in Supplemental Data: Cytochrome P450 Genes of Oxley et al

    Structural features of the Hh proteins.

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    <p>The hedgehog proteins are composed by two main domains: the Hedge (N-terminal) and Hog (C-terminal) domains. The Hedge domain forms the HhN portion of the Hh proteins (together with the signaling sequence, SS) that is separated from the rest of protein by an auto-cleavage reaction preformed by the Hog domain <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Lee1" target="_blank">[4]</a>. The Hog domain forms the HhC portion of the Hh proteins and shares similarity with self-splicing Inteins on the Hint module <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Burglin2" target="_blank">[22]</a>. The auto-cleavage reaction occurs on a GCF (glycine-cysteine-phenylalanine) motif that forms the boundary between the two main parts of the Hh proteins, with the cysteine residue initiating a nucleophilic attack on the carbonyl carbon of the preceding residue, the glycine <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Beachy1" target="_blank">[5]</a>. The sterol-recognition region (SRR) forms the C-terminal region of the Hog domain and binds a cholesterol moiety that acts as an electron donor on a second nucleophilic attack that results in the cleavage of the bound between the glycine and cystein residues and in the attachment of the cholesterol moiety to the glycine residue <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Beachy1" target="_blank">[5]</a>. After auto-cleavage, the sterified HhN fragment is further palmitoylated on the cystein residue immediately after the SS region <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Chamoun1" target="_blank">[13]</a> and leaves the endoplasmic reticulum (ER) for later export <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Chen3" target="_blank">[11]</a>.</p

    NEXUS file of maximum likelihood tree for insect CYPs

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    Maximum likelihood phylogeny was constructed using Garli 2.0 (Poisson+G+I evolutionary model; best tree of two runs chosen) using protein alignment provided in this repository. For further details see Supplemental Data: Cytochrome p450 Genes in Oxley et al

    Gene details for Cerapachys biroi chemosensory genes, UGTs and CYPs

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    Tab 1 contains details of all manually annotated chemosensory genes from Cerapachys biroi. Tab 2 contains all sequenced ant UDP glycosyltransferases, organised by clade (as described in supplemental data of Oxley et al.). Tab 3 contains all sequenced ant cytochrome P450 genes, organised by clade (as described in supplemental data of Oxley et al.)

    Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (<i>Shh, Ihh and Dhh</i>) in Vertebrates

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    <div><p>The Hedgehog (<i>Hh</i>) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one <i>Hh</i> gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – <i>Shh</i>; Indian hedgehog – <i>Ihh</i>; and Desert hedgehog – <i>Dhh</i>), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the <i>Hh</i> genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of <i>Hh</i>-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three <i>Hh</i> paralogs. We find suggestions that following the WGD events, vertebrate <i>Hh</i> paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the <i>Hh</i> orthologs. Our results provide new insights on the evolutionary history of the <i>Hh</i> gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.</p></div

    NEXUS file of maximum likelihood tree for insect UGTs

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    Maximum likelihood tree was constructed using Garli 2.0 (Poisson+G+I evolutionary model; best tree of five runs chosen), using the alignments provided in this repository

    In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns

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    <div><p>Gene discovery in the Malaysian giant freshwater prawn (<i>Macrobrachium rosenbergii</i>) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for <i>M. rosenbergii</i> at a massive scale. <i>De novo</i> assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and <i>in silico</i> prediction have identified known and novel protein coding candidate genes (∼24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in <i>M. rosenbergii</i> and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.</p></div

    An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes

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    <div><p>Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%–77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.</p> </div
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