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Described in 2009, the Patch-nosed Salamander (Urspelerpes brucei) is a miniature species of lungless salamander with a geographic range of only ~ 45 km2. This species is endemic to the foothills of the Appalachian Mountains in extreme northeastern Georgia and northwestern South Carolina. The Tugaloo River—a waterway of some 50 m in width that forms the political boundary between the two states—bisects the tiny range of U. brucei and likely acts as a barrier to gene flow. Using RADcap data and a suite of complementary population genomic analyses, we evaluated the role that this river and its tributaries may play in enabling and/or interrupting gene flow among populations of U. brucei, and we investigated patterns of within-population and between-population genetic variation. Our results revealed a general pattern of isolation-by-stream distance and indicated that a population separated by the Tugaloo River is moderately more differentiated than what is explainable by stream distance alone. Unique in both its physiography and geologic history, this region in which U. brucei lives also harbors more than a dozen other species of lungless salamanders. Therefore, the genetic patterns that we have elucidated may have larger implications for differentiation among populations of other species with similar dispersal abilities. [ABSTRACT FROM AUTHOR]

Recent phylogenomic analyses within the insect superfamily Coreoidea (Hemiptera: Heteroptera) have begun to challenge previous phylogenetic hypotheses of the Coreidae and Alydidae based on more traditional cladistic and non-cladistic studies. Phylogenomic studies have found the coreid subfamilies Hydarinae and Pseudophloeinae to be more closely related to a potentially paraphyletic Alydidae (an "AHP" clade) in contrast with traditional cladistic studies. However, taxon sampling within these higher-level groups has remained sparse in current phylogenetic analyses, and the taxonomic positions and monophyly of some of these taxa continue to be unclear. Here, we expand upon previous phylogenomic studies using ultraconserved element loci by increasing taxon sampling within the AHP clade. Using concatenation and summary coalescent approaches, we specifically tested previous support for an AHP clade, the paraphyly of Alydidae, the phylogenetic position of Hydarinae, and the monophyly of the two tribes of Pseudophloeinae. Our results robustly support an AHP clade and resolved the position of Hydarinae as the sister group to a clade consisting of a paraphyletic Alydidae and Pseudophloeinae, regardless of analytical method and locus/gene tree filtering strategies we employed. We also found support for the monophyly of the pseudophloeine tribes Clavigrallini and Pseudophloeini, but generic relationships within each of these tribes varied across analyses. We discuss past non-cladistic morphological studies that have suggested the potential for an AHP clade in light of our results, and we highlight further systematic work needed to discern the AHP clade as a morphologically diagnosable group for future re-classification of the Alydidae and Coreidae. [ABSTRACT FROM AUTHOR]

Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network. Sequences from one of these clades clearly diverged from all others, having on average the lower isoelectric points and hydropathy indices, the highest number of N-glycosylation sites, and N-terminal sequence peptides for secretion. Putative proteins from this clade are absent from brown-rot and ectomycorrhizal species that have lost the capability of degrading lignin enzymatically. They are almost exclusively present in white-rot and other saprotrophic Basidiomycota that digest lignin enzymatically, thus lending support for a specific role of DyPs from this clade in biochemical lignin modification. Additional nearly full-length fungal DyP genes were isolated from the environment by sequence capture by hybridization; they all belonged to the clade of the presumably secreted DyPs and to another related clade. We suggest focusing our attention on the presumably intracellular DyPs from the other clades, which have not been characterized thus far and could represent enzyme proteins with novel catalytic properties. Key points: • A fungal DyP phylogeny delineates seven main sequence clades. • Putative extracellular DyPs form a single clade of Basidiomycota sequences. • Extracellular DyPs are associated to white-rot fungi. [ABSTRACT FROM AUTHOR]

Background: Madin–Darby canine kidney (MDCK) cells are widely used for vaccine production, however, the safety of MDCK cells needs to be considered seriously because of high tumorigenicity. Micro RNAs (miRNAs) that are involved in the tumorigenicity of MDCK cells have been never been reported. Objective: To reveal the role of miRNA in the tumorigenic phenotype of MDCK cell line. Methods: The miRNA expression profiles of two monoclonal MDCK cells (M09CL and M35CL) with low tumorigenicity and one MDCK cell line (M73P) with high tumorigenicity were characterized and investigated by using small RNA-seq technology. Results: A total of 5 known miRNAs and 5 novel miRNAs were highly expressed in M73P. In addition, 4 known miRNAs and 4 novel miRNAs were highly expressed in M09CL and M35CL. The target genes of the differentially expressed miRNAs were significantly enriched in several biological processes, and the majority of these genes were involved in pathways in cancer and the MAPK signaling pathway. Through interaction analysis, 4 up-regulated miRNAs (cfa-miR-452, cfa-miR-8826, cfa-miR-224, and cfa-miR-2387) and their crucial target genes related to the tumor regulation network were identified. Results indicated these 4 miRNAs might play crucial roles in the tumorigenesis of MDCK cells. Conclusion: Our findings, which were based on the functional prediction of miRNAs and target genes, suggested that miRNAs might influence the tumorigenicity of MDCK cells by regulating target genes. Moreover, the results provided important data for understanding the miRNA-mediated regulatory networks that control the tumorigenicities of MDCK cells. [ABSTRACT FROM AUTHOR]

Genomic resources are under-developed for rodents, including well-studied species such as prairie dogs (Cynomys spp.). We conducted whole-genome resequencing on 10 Gunnison's prairie dogs (C. gunnisoni, GUPD) and identified 12,842,055 high-quality SNPs, from which four sets of bait sequences were created. We designed two sets each (containing either 20k or 60k baits) for projects using contemporary (120 bp baits) or historical (100 bp baits) DNA. These bait sets can be used to study a variety of ecological and evolutionary questions in prairie dogs and other ground squirrel taxa. [ABSTRACT FROM AUTHOR]

Cis-regulatory sequences play a crucial role in regulating gene expression and are evolutionary hot spots that drive phenotypic divergence among organisms. Sequencing some cis-regulatory regions of interest in many different species is common in comparative genetic studies. For nonmodel organisms lacking genomic data, genome walking is often the preferred method for this type of application. However, applying genome walking will be laborious and time-consuming when the number of cis-regulatory regions and species to be analyzed is large. In this study, we propose a novel method called amplicon genome fishing (AGF), which can isolate and sequence cis-regulatory regions of interest for any organism. The main idea of the AGF method is to use fragments amplified from the target cis-regulatory regions as enrichment baits to capture and sequence the whole target cis-regulatory regions from genomic library pools. Unlike genome walking, the AGF method is based on hybridization capture and high-throughput sequencing, which makes this method rapid and efficient for projects where some cis-regulatory regions have to be sequenced for many species. We used human amplicons as capture baits and successfully sequenced five target enhancer regions of Homo sapiens, Mus musculus, Gallus gallus, and Xenopus tropicalis, proving the feasibility and repeatability of AGF. To show the utility of the AGF method in real studies, we used it to sequence the ZRS enhancer, a cis-regulatory region associated with the limb loss of snakes, for twenty-three vertebrate species (includes many limbless species never sequenced before). The newly obtained ZRS sequences provide new perspectives into the relationship between the ZRS enhancer's evolution and limb loss in major tetrapod lineages. [ABSTRACT FROM AUTHOR]

Known for its remarkable biodiversity and high levels of endemism, the Brazilian Atlantic Rainforest has been characterized as one of the most threatened biomes on the planet. Despite strong interest in recent years, we still lack a comprehensive scenario to explain the origin and maintenance of diversity in this region, partially given the relatively low power of analyses involving few independent genetic loci. In this study, we examine a phylogenomic dataset of five ant species to investigate phylogeographical patterns across the Brazilian Atlantic Forest. We sequenced ultraconserved elements to generate hundreds of loci using a bait set developed specifically for hymenopterans. We analyzed the data using Bayesian and maximum likelihood approaches of phylogenetic inference. Results were then integrated with environmental niche modeling of current and past climates, including the Last Glacial Maximum and the last interglacial period. The studied species showed differentiation patterns that were consistent with the north/south division of the Atlantic Rainforest indicated in previous studies for other taxa. However, there were differences among species, both in the location of phylogeographic breaks and in the pattern of genetic variation within these areas. Samples from southern localities tended to show recent genetic structure, although a site in Tapiraí (state of São Paulo) repeatedly showed an intriguing older history of differentiation. All species experienced shifts in areas of suitability through the time. Our study suggests that distinct groups may have responded idiosyncratically to the climatic changes that took place in the Brazilian Atlantic Forest. The amount of intraspecific genetic structure was related to the inferred geographical distribution of habitat suitability according to current and past times. Also, a parallel between the amount of Quaternary climatic suitability and the level of interspecific differentiation was detected for four species. Finally, despite strong contractions at the northeastern region of the forest, the remaining areas appear to have been able to act as refugia. [ABSTRACT FROM AUTHOR]

Although new sequencing technology has enabled biologists to examine genome-wide variation in their taxa of interest, new experimental design, analysis, and cost hurdles impede many researchers from using the benefits of next-generation sequencing. Here we present a workflow to help researchers identify genomic intervals associated with a desired gene function by using gene ontology terms to filter an annotated genome. Resulting intervals comprise a target region that can then be used to design complementary sequences or baits for capturing desired targets in a target enrichment experiment. We show that target regions produced by our workflow and Ensembl Genebuild share intervals but nonetheless differ, and then demonstrate our workflow's utility for target enrichment experiments involving non-model organisms. Using available turtle genomes and bait sequences designed to capture a workflow-generated target region, in silico analysis predicts between 48 and 86 % of baits will bind to complementary sequences in genomes across the Order Testudines (turtles and tortoises). We then use these bait sequences in an actual target enrichment experiment and show that bait performance falls within the range predicted by in silico analysis. We show that by selecting a reference genome related as closely as possible to taxa of interest and focusing on important and likely conserved gene functions, users can acquire valuable genomic data from non-model organisms. [ABSTRACT FROM AUTHOR]

The identification of the causative genetic variants in quantitative trait loci (QTL) influencing phenotypic traits is challenging, especially in crosses between outbred strains. We have previously identified several QTL influencing tameness and aggression in a cross between two lines of wild-derived, outbred rats (Rattus norvegicus) selected for their behavior towards humans. Here, we use targeted sequence capture and massively parallel sequencing of all genes in the strongest QTL in the founder animals of the cross. We identify many novel sequence variants, several of which are potentially functionally relevant. The QTL contains several regions where either the tame or the aggressive founders contain no sequence variation, and two regions where alternative haplotypes are fixed between the founders. A re-analysis of the QTL signal showed that the causative site is likely to be fixed among the tame founder animals, but that several causative alleles may segregate among the aggressive founder animals. Using a formal test for the detection of positive selection, we find 10 putative positively selected regions, some of which are close to genes known to influence behavior. Together, these results show that the QTL is probably not caused by a single selected site, but may instead represent the joint effects of several sites that were targets of polygenic selection. [ABSTRACT FROM AUTHOR]