Nucleotide Sequence Variation Research Articles

A 7-nt nucleotide sequence variant within the sheep KDM3B gene affects female reproduction traits

Lysine demethylase 3B (KDM3B) gene is a histone demethylase, demonstrating specific demethylation of the histone H3 lysine 9. It was detected as a sheep reproductive candidate gene by genome-wide scans, and related studies also showed its significance in female reproductive process. However, rare study researched its polymorphism. Herein, we hypothesized that the polymorphisms of KDM3B gene were associated with sheep reproduction traits. A 7-nt nucleotide sequence variant (rs1088697156) within KDM3B gene was identified in a total of 888 individuals, including the Australian White (AUW) sheep and Lanzhou Fat-tailed (LFT) sheep. II (insertion/insertion) and ID (insertion/deletion) genotypes of 7-nt variant were detected, which were at Hardy-Weinberg equilibrium (HWE) in detected breeds. Association analysis illustrated the 7-nt variant was significantly associated with the litter size, duration of pregnancy, live lamb number, live lamb rate, stillbirth number, stillbirth rate of average and different parity (P < 0.05) in AUW sheep. Moreover, ‘ID’ was the dominant genotype with excellent consistency in reproductive traits. It is instrumental to select individuals with ID genotype for improving the sheep reproduction traits. These findings suggest that the 7-nt variant within KDM3B gene can be used as a candidate marker of reproduction traits for sheep breeding improvement by marker-assisted selection.

DNA Methylation, Deamination, and Translesion Synthesis Combine to Generate Footprint Mutations in Cancer Driver Genes in B-Cell Derived Lymphomas and Other Cancers.

Cancer genomes harbor numerous genomic alterations and many cancers accumulate thousands of nucleotide sequence variations. A prominent fraction of these mutations arises as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases followed by the replication/repair of edited sites by DNA polymerases (pol), as deduced from the analysis of the DNA sequence context of mutations in different tumor tissues. We have used the weight matrix (sequence profile) approach to analyze mutagenesis due to Activation Induced Deaminase (AID) and two error-prone DNA polymerases. Control experiments using shuffled weight matrices and somatic mutations in immunoglobulin genes confirmed the power of this method. Analysis of somatic mutations in various cancers suggested that AID and DNA polymerases η and θ contribute to mutagenesis in contexts that almost universally correlate with the context of mutations in A:T and G:C sites during the affinity maturation of immunoglobulin genes. Previously, we demonstrated that AID contributes to mutagenesis in (de)methylated genomic DNA in various cancers. Our current analysis of methylation data from malignant lymphomas suggests that driver genes are subject to different (de)methylation processes than non-driver genes and, in addition to AID, the activity of pols η and θ contributes to the establishment of methylation-dependent mutation profiles. This may reflect the functional importance of interplay between mutagenesis in cancer and (de)methylation processes in different groups of genes. The resulting changes in CpG methylation levels and chromatin modifications are likely to cause changes in the expression levels of driver genes that may affect cancer initiation and/or progression.

Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns

The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution.The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses.A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.

Differential β‐arrestin2 binding of the human β 1 ‐adrenoceptor Arg389Gly polymorphic variants in cardiac myocytes

Rationale The β1-adrenergic receptor (AR) is the primary receptor in cardiomyocytes through which catecholamines increase cardiac function, i.e. contractility and heart rate (positive inotropy and chronotropy). The human β1AR gene (Adrb1), which encodes a G protein-coupled receptor (GPCR), displays high nucleotide sequence variability. One of its several non-synonymous polymorphisms identified to date is the Gly/Arg variation at aminoacid position 389 (C1165G in the open reading frame's nucleotide sequence), with the Arg389 variant being much less frequent in African-Americans than in Caucasians (58% vs. 73%, respectively). Since amino acid 389 is located in the intracellular C-terminus of the encoded receptor, this polymorphism is expected, and has been shown to affect both signaling/function and desensitization of the β1AR. Indeed, Arg389 β1AR has been found to be hyperfunctional, compared to its Gly389 counterpart, in transfected cell lines and in cardiomyocytes in vitro. It is also known to affect the response of individuals to the cardiac stimulant (β1AR-agonist) dobutamine, as well as the responses of heart failure patients to several β-blockers (β1AR-antagonists), including carvedilol, to which the Arg allele confers greater responses. Consistent with this, homozygous Arg389 heart failure patients seem to fare much better than their homozygous Gly389 or heterozygous Arg389Gly counterparts when treated with the same β-blocker drug, a finding that has led to the idea of utilizing genotyping for the β1AR Arg389Gly polymorphism for the purposes of stratification of heart failure patients and of tailoring their b-blocker therapy. Objective To examine the interaction of the two β1AR variants with the signal transducers β-arrestins in neonatal rat ventricular myocytes (NRVMs), in order to identify molecular mechanisms underlying their functional differences. Methods We tested the interaction of the polymorphic β1ARs with β-arrestins via β1AR immunoprecipitation followed by β-arrestin immunoblotting in NRVM protein extracts. Results The β-arrestin1 isoform binds both variants equally well in NRVMs. Conversely, the potentially beneficial in the heart β-arrestin2 isoform interacts only with the Arg389 receptor (not with the Gly389 allele) in NRVMs. Conclusion Arg389 confers unique β-arrestin2-interacting properties to the β1AR in cardiac myocytes, potentially underlying this variant's gain-of-function phenotype.

Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from the Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found a great overlap of neutral variation within the P. mugo complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best-fitting model revealed P. mugo and P. uncinata as sister species with basal P. uliginosa and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of P. mugo complex to P. sylvestris than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide a genetic framework to study species integrity maintained by selection and local adaptation.

МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКАЯ ХАРАКТЕРИСТИКА КОМПОНЕНТОВ СИСТЕМЫ КОМПЛЕМЕНТА ПРИ ТЯЖЕЛОЙ ФОРМЕ АКНЕ

It has been shown that the inflammatory response in acne develops at the early subclinical stages of the disease, sometimes before the formation of comedones. It is known that an important component of the innate immune system is the complement system, which includes more than 60 components, including 9 basic proteins (C1-C9), a variety of activation products (C3a, C3b, iC3b, C3d and C3dg), regulatory and inhibitory molecules [factor H, fH-like protein 1 (FHL1), CR1 (CD35), C4b-binding protein (C4BP), C1inh and vitronectin], proteases and secreted enzymes (factor B, factor D, C3bBb and C4bC2b), as well as receptors for effector molecules [C3aR, C5aR, C5L2 and C1q receptor (C1qR)]. The compliment is the central part of innate immunity, which is the first line of protection against alien and altered host cells. The objectives of this study were to determine and analyze the variants of the nucleotide sequence of the genes of the complement system C1QA, C1S, C2, C3, C5, C6, C7, C8A, C8B, C8G, C9 in patients with severe acne. Materials and methods of research: To achieve the target a prospective open non-randomized one-center study was carried out in 2017–2020. Under our supervision in the clinical setting at the Department of Skin Diseases and Cosmetology of the Pirogov Russian National Research Medical University, there were 50 patients in the main group and 20 participants in the comparison group (70 people in total) (42/60% men and 28/40% women) aged 15 to 46 years (median – 22,1 years). Molecular genetic diagnostics was performed in all 70 patients of the main and control groups by the method of high-throughput DNA sequencing – next-generation sequencing (NGS). Results: when analyzing the nucleotide sequence variants of the complement system genes identified in our study, it is shown that the severe form of acne probably has an association (4 SNPs of the C8A gene, 1 SNPs of the C8B gene, 2 SNPs of the C1S gene, 3 SNPs of the C3 gene, 2 SNPs of the C9 gene, 1 SNPs of the C7 gene, 1 SNPs of the C6 gene, 1 SNPs of the C2 gene, 2 SNPs of the C5 gene, 2 SNPs of the C8G gene), 13 SNPs of the complement system genes in introns (1 SNPs of the C8A gene, 1 SNPs of the C8B gene, 2 SNPs of the C1S gene, 1 SNPs of the C3 gene, 1 SNPs of the C7 gene, 2 SNPs of the C6 gene, 4 SNPs of the C5 gene, 1 SNPs of C8G gene), 6 SNPs of the complement system genes (2 SNPs of the C8B gene: one SNPs each in the 3'UTR and 5'UTR zones; 3 SNPs of the C3 gene in the 5'UTR zone, 1 SNPs of the C7 gene in the 3'UTR zone). Two mutations of the frame shift of the C2 gene (frameshift deletion) and the C9 gene (rs748464075, frameshift insertion) seem to have a protective effect in the development of acne. Conclusion: the obtained variants of the nucleotide sequence of the genes of the complement system C1QA, C1S, C2, C3, C5, C6, C7, C8A, C8B, C8G, C9, apparently, are associated with the formation of severe acne and cause an imbalance of the components of the complement system. It can cause a defect in chemotactic and phagocytic reactions, and as a result a disturbance of the regulation of the inflammatory reaction with chronization of the skin process occures. Thus, results of studies carried out, revealed – for the first time – polymorphic loci of genes of components of the complement system, the imbalance of which is the pathophysiological mechanism of acne.

A new D-Loop mitochondrial nucleotide variation from individual at Naga and Kuta traditional village

The D-Loop region of human mitochondrial DNA (mtDNA) has a higher level of polymorphism compared to nuclear DNA. Therefore, the mtDNA D-Loop area can determine a particular individual or ethnic identity. This study aims to determine the variation of the D-Loop region nucleotide sequence, namely the Hipervariable I (HV1) region in normal tribal individuals in Kampung Naga and Kampung Kuta. The sample used is the hair root. In determining the variation of nucleotides has been carried out a series of stages of research, namely the isolation of mitochondrial DNA from hair root samples using buffer lysis, mtDNA sample amplification using PCR techniques with M1 primers and HV2R primers, detection of D-Loop region mtDNA fragments by agarose gel electrophoresis, and sequencing of PCR products by the Sanger Dideoxy method and nucleotide sequence analysis of the sequencing results. The results of DNA amplification by PCR showed a band in the area of 1.0 kb. Homology analysis was carried out by comparing the nucleotide sequences of samples with the Cambridge nucleotide sequence, which shows that there are 10 variations. The new variation (morph) is determined by comparing the results of the variations of the two samples with variations from Homo Sapiens Indonesia including Baduy, Sundanese, Javanese (Sangiran), and Madura. Homology results showed 4 new variations, namely c(16184)A, t(16209)C, a(16272)G, t(16519)C. Sapiens Kuta village and Sundanese (general) have a close genetic relationship. The ancestors of the two Homo Sapiens were closely related to Homo Sapiens Naga, Homo Sapiens Naga are closely related to the Homo Sapiens of the Baduy. The ancestors of Homo sapiens, Kuta, Sundanese, Naga and Baduy, are closely related to Homo sapiens Sangiran (Java). Homo Sapiens Madura is most likely the oldest Homo sapiens seen from phylogenetic trees. The results of this study are expected to be able to add Indonesia’s normal human database.

The Frequency of Heterozygous Carriage of the PAH Gene Nucleotide Sequence Variants Associated with the Development of Phenylketonuria in the ESSE-Vologda Population-Based Cohort Study

The Frequency of Heterozygous Carriage of the PAH Gene Nucleotide Sequence Variants Associated with the Development of Phenylketonuria in the ESSE-Vologda Population-Based Cohort Study

Chimaera compacta, a new species from southern Indian Ocean, and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae)

Chimaera compacta sp. nov., a new species of shortnose chimaera (Holocephali: Chimaeriformes: Chimaeridae), is described from a single specimen collected at 595–655 m depth, off Amsterdam Island, in the southern Indian Ocean. The species is easily distinguished from its congeners by the combination of the following characters: massive head with short snout; stocky and relatively long trunk 44% BDL, short tail with second dorsal fin base 72% BDL; long pelvic fin anterior margin 26% BDL. Caudal fin dorsal origin slightly posterior to caudal fin ventral origin. Firm, non-deciduous skin; brown color with yellow blotches. Chimaera compacta sp. nov. is morphologically close to Chimaera lignaria Didier 2002 from New Zealand and Chimaera willwatchi Clerkin, Ebert and Kemper 2017 from south western Indian Ocean. The new species can be distinguished from other Chimaera species based on DNA sequences divergence of the COI and NADH2 genes. This species has a nucleotide sequence divergence (uncorrected p distances) for the studied genes of 4.2 and 4.1%, respectively, with its closest relatives. Phylogenetically, Chimaera compacta sp. nov. is nested within a well-supported group including Chimaera carophila Kemper, Ebert, Naylor and Didier 2014, Chimaera didierae Clerkin, Ebert and Kemper 2017, C. lignaria, Chimaera macrospina Didier, Last and White 2008, Chimaera notafricana Kemper, Ebert, Compagno and Didier 2010, Chimaera opalescens Luchetti, Iglesias and Sellos 2011, and C. willwatchi. It is the first Chimaeridae described for the Territory of the French Southern and Antarctic Lands.

Ecology of avian influenza viruses in migratory birds wintering within the Yangtze River wetlands

Migratory birds are considered natural reservoirs of avian influenza A viruses (AIVs). To further our viral ecology knowledge and understand the subsequent risk posed by wild birds, we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River, China. We collected over 8000 samples and isolated 122 AIV strains. Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases. The results showed that the Yangtze River wintering wetlands functioned as a mixing ground, where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences; moreover, a portion of AIV gene segments were persistent inter-seasonally. Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes. In addition, we observed that viral gene segments in wintering wetlands were closely related to known North American isolates, indicating that intercontinental gene flow occurred. Notably, highly pathogenic H5 and low pathogenic H9 viruses, which usually circulate in poultry, were found to have crossed the poultry/wild bird interface, with the viruses introduced to wintering birds. Overall, this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands. Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.

Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species.

The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secondary structure elements designated P1-P10 helics and loops. We found a 12 nt nucleotide sequences TACCACAGGGAT at site 2 in the 3'-end of 28S rDNA, site 2 introns just insert the upstream or the downstream of the12 nt nucleotide sequences. Afters sequence analysis of all 18S and 28S rDNA introns from tested isolates, three high conserved regions around 30 nt nucleotides (conserved 1, conserved 2, conserved 3) and identical nucleotides can be found. Conserved 1, conserved 2 and conserved 3 regions have high GC content, GC percentage is almost more than 60%. From our results, it seems that the more convenient host sites, intron sequences and secondary structures, or isolates for 18S and 28S rDNA intron insertion and deletion, the more popular they are. No matter 18S rDNA introns or 18S rDNA introns among tested isolates, complementary base pairing at the splicing sites in P1-IGS-P10 tertiary helix around 5'-end introns and exons were weak.

Allopatric Plant Pathogen Population Divergence following Disease Emergence.

Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.

Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka.

Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sri Lankan and the reference genotype strains of the DENV3 and DENV1 serotypes. The human- and mosquito-derived domain II, 3′ UTR were identical in nucleotide sequences within the serotypes isolated, indicating the conserved nature of the region during host switch. The sequence analysis revealed distinct variations in study isolates compared to so far recorded Sri Lankan isolates. However, despite single nucleotide variations, the maintenance of structural integrity was evident in related strains within the serotypes in the secondary structure analysis. The phylogenetic analysis revealed distinct clade segregation of the study sequences from so far reported Sri Lankan isolates and illustrated the phylogenetic relations of the study sequences to the available global isolates of respective serotypes.

Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

Echovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

The mRNA expression profile of the goat prion protein testis-specific (PRNT) gene and its associations with litter size

The goat PRNT gene was initially identified as a testis-specific gene with a role in spermatogenesis. In this study, we used quantitative real-time PCR (qPCR) to first determine the mRNA expression profile of this gene in different goat tissues. Surprisingly, we found that PRNT was expressed not only in the testis but also in nine other tissues in goats. Moreover, PRNT was weakly expressed in the testis, while its expression was strongest in the ovary. These results, combined with those of other studies, led us to hypothesize that the goat PRNT gene has a role in both male and female reproduction. We further used direct DNA sequencing to detect potential SNPs within this gene in Shaanbei whit cashmere (SBWC) rams and ewes, and identified three SNPs within the PRNT gene, namely, c.-58C > T, c.71A > G (p.Alanine24Valine), and c.102C > T (synonymous). In rams, c.-58C > T and c.102C > T were strongly linked with each other (D′ = 1.000, r2 = 0.504), whereas no significant association (P > 0.05) was found between the three SNPs and semen quality, which was consistent with the low expression of the PRNT gene in the testis. Interestingly, in ewes (n = 502), c.-58C > T and c.71A > G were also strongly linked with each other (D′ = 0.973, r2 = 0.537). Additionally, the c.71A > G locus, especially the AA genotype, had a significant influence on litter size (P = 0.006), consistent with the high PRNT expression in the ovary. Combined, the results of the expression profiling and analysis of the association between the SNPs and reproductive traits showed that two strongly linked nucleotide sequence variants within PRNT were significantly associated with goat litter size. These findings provide potential DNA markers for use in the marker-assisted selection (MAS) of goats with high-fertility traits.

Genetic and phylogenetic analysis of porcine circovirus type 2 on Jeju Island, South Korea, 2019-2020: evidence of a novel intergenotypic recombinant.

Porcine circovirus type 2 (PCV2) is the most ubiquitous viral pathogen of pigs and has persistently affected the global swine industry. Since first being identified in South Korea in 1999, the virus has undergone considerable genetic change and genotype shifts during the past two decades. These events have contributed to the coexistence of genotypes PCV2a, PCV2b, and PCV2d in Korean pig populations, which may promote viral recombination. The genotypic and phylogenetic characteristics of PCV2 strains circulating in pig herds on Jeju Island from 2019 to 2020 were the focus of this study. Genotype-specific PCR indicated that PCV2d is the dominant viral genotype and that coinfections with PCV2d and PCV2a (75%) or PCV2a and PCV2b (25%) are common in provincial pig herds. The complete genome sequences of 11 PCV2 strains, including three PCV2a, two PCV2b, and six PCV2d strains, were determined. A genomic comparison showed that all of the viruses had the highest nucleotide sequence identity to their corresponding genotypic reference strain. Notably, genetic and phylogenetic analysis revealed that one PCV2d strain, KNU-1931, exhibited nucleotide sequence variation in the ORF1 gene when compared to other PCV2d strains but showed a high degree of similarity to the PCV2b strains. Comprehensive recombination analysis suggested that KNU-1931 originated from natural recombination within ORF1 between PCV2b (the minor parent) and PCV2d (the major parent) strains. Our findings provide information about the frequency of genetic recombination between two different PCV2 genotypes circulating in the field domestically, illustrating the importance of continual intergenotypic recombination for viral fitness when multiple genotypes are present.

Nucleotide Sequence Variation in the Insulin-Like Growth Factor 1 Gene Affects Growth and Carcass Traits in New Zealand Romney Sheep.

Insulin-like growth factor 1 (IGF1) is a mediator of the effects of growth hormone and polymorphism in the IGF1 gene (IGF1) is reported to affect fat deposition in some livestock species. In this study, nucleotide sequence variation in three regions of ovine IGF1 (part of the 5′ flanking region, the exon 3 region, and the exon 4 region) was investigated in 848 New Zealand Romney lambs using PCR-single strand conformation polymorphism (SSCP) analyses to ascertain if single nucleotide polymorphisms (SNPs) existed. Six SNPs were identified across these three regions. The effect of the sequence variation in the exon 3 and exon 4 regions on growth and carcass traits were investigated. One of the PCR-SSCP sequence variants in the exon 3 region was associated with variation in hot carcass weight, carcass fat depth at the 12th rib measured using video imaging and the percentage proportion of leg lean meat, whereas the other was associated with variation in growth rate to weaning. No associations were detected for the other gene regions analyzed. The results suggest that polymorphism in exon 3 of ovine IGF1 has potential for use as a gene-marker for some carcass and growth traits.

Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

Massively parallel sequencing of 25 short tandem repeat loci including the SE33 marker in Koreans.

Massively parallel sequencing (MPS) technology has recently been introduced in research, clinical diagnostics, and forensics. MPS enables determination of the genotypes of multiple short tandem repeat (STR) markers and to determine nucleotide sequence variations, additionally. To improve STR analysis and a paternity index, a new, smaller-sized STR panel was designed that includes the SE33 locus. This study performed MPS using an STR panel including the SE33 marker in 101 Koreans. The concordance study was conducted by comparing the data obtained from the MPS assay with the results of a capillary electrophoresis (CE)-based method. In this study, an in-house MPS panel is designed that incorporates the 20 Combined DNA Index System (CODIS) loci and the Penta D, Penta E, and SE33 markers for enhanced discriminatory ability. The data obtained via MPS analysis were compared with CE data to confirm concordance. Fifty previously unreported alleles were detected through the MPS analysis. Three new SNP variations in the flanking region were also identified. Statistical analysis demonstrated that the SE33 marker was most effectively determined the match probability (PM) and typical paternity index (TPI). In the sensitivity study, concentrations as low as 80pg could be used to obtain full and concordant profiles. We designed a new, smaller-sized STR panel that includes the SE33 locus to improve STR analysis and the paternity index. Various new alleles were identified in SE33, indicating a high degree of polymorphism. The panel is expected to provide valid data for discrimination of unidentified bodies.

BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs

BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. We show two examples using Salmonella genomes: finding within minutes the presence of genes in the SPI-2 pathogenicity island in a collection of 926 genomes and identifying single nucleotide polymorphisms associated with fluoroquinolone resistance in three genes among 190,209 genomes. BlastFrost is available at https://github.com/nluhmann/BlastFrost/tree/master/data.