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20 results for “synteny”
Data for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae"
<p>Data and code for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae". Preprint available at bioRxiv: https://doi.org/10.1101/2022.09.07.506897.</p>
Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
<p class="BodyAA">The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.</p>
VCF file created by Synteny and Rearrangement Indicator software
<p>VCF file created by Synteny and Rearrangement Indicator software for the rat reference genome mRatBN7.2 and the SHRSP genome assembly</p>
Angiosperm NLR Synteny Network Databases
<p>PEP and BED Files of 124 Angiosperm Employed in the Study 'Deciphering Plant NLR Genomic Evolution: A Synteny-Informed Classification Reveals Insights into TNL Gene Loss'</p>
Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny
<p class="MsoListParagraph">Superrosids form one of the largest clades of angiosperms, including 18 orders (Vitales, Saxifragales and core rosids) which exhibits remarkable morphological and ecological diversity. However, phylogenetic relationships within superrosids remain unclear.</p> <p class="MsoListParagraph">To resolve the phylogeny of superrosids, we screened 122 single copy nuclear genes from 37 species, representing all 18 orders.</p> <p class="MsoListParagraph">Vitales was revealed as sister to all other superrosids. Within core rosids, the fabids should be restricted only to the nitrogen-fixing clade, while Picramniales, the CM clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales composed an "expanded" malvids. The COM clade (sensu APG IV) did not form a monophyletic group. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either malvids or fabids. The difficult phylogeny of superrosids is likely due to the combined effects of ancient reticulation and incomplete lineage sorting.</p> <p class="MsoListParagraph">To provide broader genomic representation of Saxifragales, we constructed a high-quality chromosome-level genome assembly for <em>Tiarella polyphylla</em> (Saxifragaceae). Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, which also indicated that Saxifragales has a closer relationship with core rosids.</p> <p class="MsoListParagraph">Our findings contribute to a better understanding of the phylogeny and evolution of angiosperms.</p>
Ostrinia population genomics: Custom scripts and synteny mapping results
<p>We sampled seven <em>Ostrinia furnacalis </em>(Guenée) populations across 23 degrees of latitude in China to elucidate the genetic basis of diapause variation and evolutionary mechanisms driving parallel clinal responses. Using pooled whole-genome sequencing (Pool-seq) data, population genomic analyses revealed hundreds of single nucleotide polymorphisms (SNP) whose allele frequencies covaried with mean diapause phenotypes along the cline. Archived on Dryad are the custom R scripts used in the population genomic analyses as well as the mapping of <em>O. furnacalis</em> scaffolds to <em>Bombyx mori</em> reference chromosomes (for visualizing population genetic statistics across chromosomes).</p>
Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution
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Ostrinia population genomics: Custom scripts and synteny mapping results
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Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny
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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
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Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity
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Fig.2 in Contributions to Trachelyopterus (Siluriformes: Auchenipteridae) species diagnosis by cytotaxonomic autapomorphies: from U2 snRNA chromosome polymorphism to rDNA and histone gene synteny
Fig.2 Karyotypes of T. striatulus (a), T. galeatus (b), and Trachelyopterus aff. galeatus (c). m: metacentric; sm: submetacentric; st: subtelocentric; a: acrocentric. Probes: 18S rDNA, 5S rDNA and U2 snRNA (green signal); and H3/H4 histone genes (red signal) µm. Bar=5 µm
Fig. 1 in Contributions to Trachelyopterus (Siluriformes: Auchenipteridae) species diagnosis by cytotaxonomic autapomorphies: from U2 snRNA chromosome polymorphism to rDNA and histone gene synteny
Fig. 1 Karyotypes of Trachelyopterus porosus (a), T. galeatus coriaceus (b), and Trachelyopterus aff. coriaceus (c). m: metacentric; sm: submetacentric; st: subtelocentric; a: acrocentric. Probes: 18S rDNA, 5S rDNA and U2 snRNA (green signal); and H3/H4 histone genes (red signal). Bar= 5 µm
Detection of colinear blocks, and synteny and evolutionary analyses based on utilization of MCScanX
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Data from: Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion
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Supplementary Data for "Unbiased anchors for reliable genome-wide synteny detection" (Kaether,Remmel,Lemke,Stadler;2024)
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Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus
Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from non-model organisms. This manuscript details the application of restriction site associated DNA sequencing (RADseq) to generate a marker dense genetic map for Brook trout (Salvelinus fontinalis). The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic salmon for 38 linkage groups, with Rainbow trout for 37 linkage groups, Arctic char for 36 linkage groups, and with a previously published Brook trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of eight metacentric and 34 acrocentric chromosomes in Brook trout. Six metacentric chromosomes seem to be conserved with Arctic char suggesting there have been at least two species specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome) was mapped to Brook trout BC35, which is homologous with Atlantic salmon Ssa09qa, Rainbow trout Omy25, and Arctic char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.
Biosynthetic Gene Cluster Synteny - Orthologous Polyketide Synthases in Hypogymnia physodes, Hypogymnia tubulosa and Parmelia sulcata
<p>Supplementary Material of Publication</p>
Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus
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Ancient synteny links metabolism with erythroid development
GEO Series GSE273384. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
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