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669 results for “comparative genomics”
Figure 8 in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 8. RSCU of 14 newly sequenced litostomatean genomes/transcriptomes. Each codon is ploưed.
Data from: comparative genomic analysis of Salmonella enterica subsp. enterica serovar Abortusequi
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Data from: Comparative genomics of the mimicry switch in Papilio dardanus
The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and contains 24 genes, including the transcription factor genes engrailed (en) and invected (inv). H is located in a region of conserved gene order, which argues against any role for genomic translocations in the evolution of a hypothesized multi-gene mimicry locus. Natural populations of P. dardanus show significant associations of specific morphs with single nucleotide polymorphisms (SNPs), centred on en. In addition, SNP variation in the H region reveals evidence of non-neutral molecular evolution in the en gene alone. We find evidence for a duplication potentially driving physical constraints on recombination in the lamborni morph. Absence of perfect linkage disequilibrium between different genes in the other morphs suggests that H is limited to nucleotide positions in the regulatory and coding regions of en. Our results therefore support the hypothesis that a single gene underlies wing pattern variation in P. dardanus.
Data from: "Comparative genomic resources for spiny lizards (genus Sceloporus)" in Genomic Resources Notes accepted 1 August 2014-30 September 2014
To advance comparative genomic studies of the spiny fence lizards (genus Sceloprous), we provide the genomic annotations for 35 Sceloporus species.
Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong
Background: The ST239 lineage is a globally disseminated, multiply drug-resistant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). We performed whole-genome sequencing of representative HA-MRSA isolates of the ST239 lineage from bacteremic patients in hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three published complete genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster strains were also undertaken. Results: Homology analysis, based on highest-percentage nucleotide identity, indicated that HK isolates were closely related to TW20, whereas BJ isolates were more closely related to T0131 from Tianjin. Phylogenetic analysis, incorporating a total of 30 isolates from different continents, revealed that strains from HK clustered with TW20 into the 'Asian clade', whereas BJ isolates and T0131 clustered closely with strains of the 'Turkish clade' from Eastern Europe. HK isolates contained the typical φSPβ-like prophage with the SasX gene similar to TW20. In contrast, BJ isolates contained a unique 15 kb PT1028-like prophage but lacked φSPβ-like and φSA1 prophages. Besides distinct mobile genetic elements (MGE) in the two clusters, OGG analyses and whole-genome alignment of these clusters highlighted differences in genes located in the core genome, including the identification of single nucleotide deletions in several genes, resulting in frameshift mutations and the subsequent predicted truncation of encoded proteins involved in metabolism and antimicrobial resistance. Conclusions: Comparative genomics, based on de novo assembly and deep sequencing of HK and BJ strains, revealed different origins of the ST239 lineage in northern and southern China and identified differences between the two clades at single nucleotide polymorphism (SNP), core gene and MGE levels. The results suggest that ST239 strains isolated in Hong Kong since the 1990s belong to the Asian clade, present mainly in southern Asia, whereas those that emerged in northern China were of a distinct origin, reflecting the complexity of dissemination and the dynamic evolution of this ST239 lineage.
Data from: Understanding the genomic basis of adaptive response to variable osmotic niches in freshwater prawns: a comparative intraspecific RNA-Seq analysis of Macrobrachium australiense
Understanding the molecular basis of adaptive response to variable environmental conditions is a central goal of evolutionary biology. Here we sought to identify potential outlier SNPs (single nucleotide polymorphisms) in three wild populations of a freshwater prawn (Macrobrachium australiense) that are exposed to differing osmotic niches by using a comparative transcriptomics approach. De novo assembly of approximately 542 million (75 nt) pair end reads collected from 10 individuals revealed 123,396 longer contigs/transcripts of variable length, that showed 97.38% transcriptome assembly completeness. Differential gene expression (DGE) analysis of major osmoregulatory genes revealed that Calreticulin, Na+/H+ exchanger and V-type (H+) ATPase showed the highest expression levels in the Blunder Creek (low ionic) population, while Crustacean cardiovascular peptide (CCP), Na+/K+-ATPase, Na+/K+/2Cl- Co-transporter (NKCC) and Na+/HCO3 exchanger showed the highest expression levels in the Bulimba Creek (higher ionic) population. In total, 16 gene ontology (GO) term categories were functionally enriched among the three studied populations. We identified 4144 raw and 835 high quality filtered SNPs in the three M. australiense populations, of which 84 SNPs were identified as outliers. Outliers were detected in 4 important osmoregulatory genes that include: Calreticulin, Na+/H+ exchanger, Na+/K+-ATPase and V-type-(H+)-ATPase. All outliers in the osmoregulatory genes were located in non-coding regulatory regions (untranslated regions, UTRs) of the gene. We hypothesize that the outlier SNPs identified here in M. australiense populations exposed naturally to different osmotic conditions influence specific gene expression patterns that allow individuals to respond to local environmental conditions.
Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization
The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of 2D vs 3D distance measurements in the analysis of various features of spatial genome organization. We find in general good agreement between 2D and 3D analysis with higher convergence of measurements as the interrogated distance increases, especially in flat cells. Overall, 3D distance measurements are more accurate than 2D distances, but are also more susceptible to noise. In particular, z-stacks are prone to error due to imaging properties such as limited resolution along the z-axis and optical aberrations, and we also find significant deviations from unimodal distance distributions caused by low sampling frequency in z. These deviations are ameliorated by significantly higher sampling frequency in the z-direction. We conclude that 2D distances are preferred for comparative analyses between cells, but 3D distances are preferred when comparing to theoretical models in large samples of cells. In general and for practical purposes, 2D distance measurements are preferable for many applications of analysis of spatial genome organization.
Genomes and annotation files for comparative circularome analysis
<p>Part of a manuscript on eccDNAs in Magnaporthe oryzae</p>
Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments
<p>Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.</p>
Supplementary material 1 from: Li Z, Huang Z, Wan X, Yu J, Dong H, Zhang J, Zhang C, Wang S (2023) Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae. Comparative Cytogenetics 17: 163-180. https://doi.org/10.3897/compcytogen.17.101427
Taxonomic and accession information on cp genomes downloaded from NCBI database
Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong
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Data from: Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics.
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Data from: Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis
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Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization
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Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. Zeae
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Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales
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Data from: Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins
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Data from: Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces
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Data from: Pinpointing genes underlying annual/perennial transitions with comparative genomics
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Comparative genomics reveals divergent thermal selection in warm- and cold-tolerant marine mussels
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.