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opencc-zeroDec 2016View details →

Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

opencc-by-4.0Dec 2014View details →

Figure. PCA analysis based on GH-MspI, GH-AluI, PRL, and DGAT1 loci in Turkish native cattle breeds (Turkish Grey - TG, East Anatolian Red - EAR, Anatolian Black - AB, and South Anatolian Red - SAR). in Growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) gene polymorphisms in Turkish native cattle breeds

Figure. PCA analysis based on GH-MspI, GH-AluI, PRL, and DGAT1 loci in Turkish native cattle breeds (Turkish Grey - TG, East Anatolian Red - EAR, Anatolian Black - AB, and South Anatolian Red - SAR).

opencc-by-4.0Oct 2019View details →

Figure 2 in Investigation of GH and GHR Alu I gene polymorphisms on meat yields in Anatolian water buffalo breed using PCR-RFLP method

Figure 2. Enzyme digestion results of exons 4 and 5 of the GH gene (M: 50-bp DNA ladder; 1–5 and 7: LL genotype, 6: LV genotype).

opencc-by-4.0Oct 2019View details →

Figure 4 in Investigation of GH and GHR Alu I gene polymorphisms on meat yields in Anatolian water buffalo breed using PCR-RFLP method

Figure 4. Enzyme digestion results of the exon 10 region of the GHR gene (M: 50-bp DNA ladder, A: AG genotype, B: AA genotype).

opencc-by-4.0Nov 2018View details →

Fig. 1 in Undescribed color polymorphism of the Asiatic palm weevil, Rhynchophorus vulneratus Panzer (Coleoptera: Curculionidae) in Indonesia: biodiversity study based on COI gene

Fig. 1. Genealogical relationship of 105 sequence haplotypes of palm weevils collected from Indonesia and Rhynchophorus ferrugineus from Saudi Arabia and Pakistan based on the cytochrome oxidase subunit I (COI) gene (657 bp) using the neighbor joining method with 1,000 bootstraps. The colors indicate the palm weevil color morphs or species: - Asiatic palm weevil with rusty red morphs (APW–RR); - Asiatic red palm weevil with red stripe morphs (APW–RS); - Asiatic palm weevil with intermediate color between rusty red and red stripe morphs (APW–I); - black palm weevil (BPW as an outgroup); and - red palm weevil, R. ferrugineus (RPW). The numbers at the branching points indicate the bootstrap values. CA = Lineage A, CB = Lineage B, CC = Lineage C, SCA = Sub-cluster A, SCB = Sub-cluster B.

opencc-by-4.0Jul 2023View details →

Data platform (genotyping data set) related to ERDF postdoctoral project No. 1.1.1.2/VIAA/4/20/718 "The role of vitamin D gene polymorphisms and its receptors in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis".

Data platform (genotyping dataset) related to the ERDF postdoctoral project No. 1.1.1.2/VIAA/4/20/718 “The role of vitamin D and its receptor gene polymorphisms in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis”. About the project and gathered data: The dataset contains  genotyping data on 289 sex-balanced samples (approximately 60% women / 40% men)) were created at the the multiple sclerosis (MS) Clinic of the Latvian Maritime Medical Center (LMMC) in 2011 (disease duration of 1-51 years); the collection was updated within the framework of the ERDF MS project (2017-2020) and replenished during the ERDF postdoctoral project No. 1.1.1.2/VIAA/4/20/718 “The role of vitamin D and its receptor gene polymorphisms in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis” (2021-2023). For the Genotyping dataset relevant information for each patient from the MS disease cohort, referring to proteasomal gene genetic variations (microsatellites and SNPs): (HSMS006 (PSMA6), HSMS602 (FAM177A1), HSMS701 (KIAA0391), HSMS702 (KIAA0391) HSMS801 (KIAA0391), rs11543947(PSMB5), rs2277460 (mi110), rs1048990 (mi8) (PSMA6), rs1048990 (mi8) (PSMA6), rs2295826/rs2295827(PSMC6), rs2348071 (PSMA3), rs2071543, rs9357155 (PSMB8), rs17587(PSMB9), rs74421874 (PSMD9); rs9275596 from HLA region; vitamin D-related genes (VDR and GC) polymorphisms: rs2228570, rs1544410, rs7975232, rs731236 (VDR) and rs7041, rs4588 (GC).

opencc-zeroMay 2024View details →

Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasises how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

publicApr 2023View details →

Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

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publicMay 2024View details →

Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

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opencc-zeroSep 2020View details →

Data from: K-13 Propeller gene polymorphisms isolated between 2014 and 2017 from Cameroonian Plasmodium falciparum malaria patients

The emergence of artemisinin-resistant parasites since the late 2000s at the border of Cambodia and Thailand poses serious threats to malaria control globally, particularly in Africa which bears the highest malaria transmission burden. This study aimed to obtain reliable data on the current state of the kelch13 molecular marker for artemisinin resistance in Plasmodium falciparum in Cameroon. DNA was extracted from the dried blood spots collected from epidemiologically distinct endemic areas in the Center, Littoral and North regions of Cameroon. Nested PCR products from the Kelch13-propeller gene were sequenced and analyzed on an ABI 3730XL automatic sequencer. Of 219 dried blood spots, 175 were sequenced successfully. We identified six K13 mutations in 2.9% (5/175) of samples, including 2 non-synonymous, the V589I allele had been reported in Africa already and one new allele E612K had not been reported yet. These two non-synonymous mutations were uniquely found in parasites from the Littoral region. One sample showed two synonymous mutations within the kelch13 gene. We also observed two infected samples with mixed K13 mutant and K13 wild-type infection. Taken together, our data suggested the circulation of the non-synonymous K13 mutations in Cameroon. Albeit no mutations known to be associated with parasite clearance delays in the study population, there is need for continuous surveillance for earlier detection of resistance as long as ACTs are used and scaled up in the community.

opencc-zeroDec 2020View details →

Influence of polymorphisms in the vascular endothelial growth factor gene on allograft rejection after kidney transplantation: a meta-analysis

Purpose Reported associations of allograft rejection in kidney transplant patients with VEGF single nucleotide polymorphisms (SNPs) have been inconsistent between studies, which prompted a meta-analysis to obtain more precise estimates. Methods Using the PICO elements, kidney transplant patients (P) were compared by genotype data between rejectors (I) and non-rejectors (C) in order to determine the risk of allograft rejection (O) attributed to the VEGF SNPs. Literature search of four databases yielded seven articles. To calculate risks for allograft rejection, four SNPs were examined. Meta-analysis treatments included outlier and subgroup analyses, the latter was based on ethnicity (Indians/Caucasians) and rejection type (acute/chronic). Multiple comparisons were corrected with the Bonferroni test. Results Five highly significant outcomes (Pa < 0.01) survived Bonferroni correction, one of which showed reduced risk for the var allele (OR 0.61, 95% CI 0.45-0.82). The remaining four indicated increased risk for the wt allele where the chronic rejection (OR 2.10, 95% CI 1.36-3.24) and Indian (OR 1.44, 95% CI 1.13-1.84) subgroups were accorded susceptibility status. Conclusions Risk associations for renal allograft rejection were increased and reduced on account of the wt and var alleles, respectively. These findings could render the VEGF polymorphisms useful in the clinical genetics of kidney transplantation.

opencc-zeroApr 2020View details →

Data from: Changes in gene expression during female reproductive development in a colour polymorphic insect

Pleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) have key roles in the development of complex phenotypes, especially in polymorphic taxa. The development of discrete and heritable phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits. We quantified gene expression changes during ontogenetic colour development in a polymorphic insect (damselfly: Ischnura elegans), with three heritable female morphs, one being a male mimic. This female colour polymorphism is maintained by male mating harassment and sexual conflict. Using transcriptome sequencing and de novo assembly, we demonstrate that all three morphs downregulate gene expression during early colour development. The morphs become increasingly differentiated during sexual maturation and when developing adult colouration. These different ontogenetic trajectories arise because the male-mimic shows accelerated (heterochronic) development, compared to the other female morphs. Many loci with regulatory functions in reproductive development are differentially regulated in the male-mimic, including upstream and downstream regulators of ecdysone signalling and transcription factors potentially influencing sexual differentiation. Our results suggest that long-term sexual conflict does not only maintain this polymorphism, but has also modulated the evolution of gene expression profiles during colour development of these sympatric female morphs.

opencc-zeroMay 2020View details →

Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation

The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog Ranitomeya sirensis is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.

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CTRC gene polymorphism (p.G60G, c.180) in acute pancreatitis

The aim of the study was to determine the relationship between the presence of G60G polymorphism (c.180C>T; rs497078) CTRC and the incidence as well as the clinical course of acute pancreatitis (AP). The study included  299 patients with acute pancreatitis, inhabitants of the Kielce Region in Poland, who gave their informed consent for collecting genetic material. The control group consisted of 417 healthy inhabitants.

opencc-zeroMar 2016View details →

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Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm

Trees growing at high altitude or latitude have to be adapted, amongst others, to the lower temperatures, a shorter vegetation period, heavier snow load and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day-night shift and seasonal change. Potentially adaptive "candidate" genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation, phenotypic traits measured in natural populations and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterised by superior resistance to snow breakage in regions with heavy snow fall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony) and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.

opencc-zeroSep 2019View details →

zenodo36/100

Figure 1 in Investigation of GH and GHR Alu I gene polymorphisms on meat yields in Anatolian water buffalo breed using PCR-RFLP method

Figure 1. PCR products of exons 4 and 5 of the GH gene (428-bp band, M: 100-bp DNA ladder).

opencc-by-4.0Oct 2019View details →

opencc-zeroSep 2021View details →

Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity

Carcinus maenas is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing. Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R). Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.