Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

Abstract The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.

Download Full-text

Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

10.1101/2020.02.19.955781 ◽

2020 ◽

Cited By ~ 1

Author(s):

Miguel J N Ramos ◽

João L Coito ◽

David F Silva ◽

Jorge Cunha ◽

M Manuela R Costa ◽

...

Keyword(s):

Vitis Vinifera ◽

Reproductive Strategy ◽

Reference Genome ◽

Grapevine Genome ◽

Wine Production ◽

Male And Female ◽

Female Individual ◽

Wild Grapevine ◽

Good Material ◽

The Difference

ABSTRACTVitis is a relevant genus worldwide. The genome of a Vitis vinifera representative (PN40024) published in 2007 boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. vinifera domestication. Considering that grapevines for wine production (V. v. vinifera, hereafter vinifera) have evolved from V. v. sylvestris (hereafter sylvestris), or from a shared no-longer existing ancestor, both subspecies are quite close, but sylvestris has not been domesticated and still exist nowadays, preserving wild characteristics, making it a good material to provide insights into vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that sets them apart. While vinifera flowers are hermaphrodite with functional male and female organs, sylvestris is mostly dioecious. Male plants present flowers lacking functional carpels unable to produce grapes and female individuals have flowers with reflexed stamens producing infertile pollen but able to exhibit small and acidic grapes. In this paper, we describe the re-sequencing of the genomes from a male and a female individual of the wild sylvestris and its comparison against the reference vinifera genome.

Download Full-text

Host- and Species-Dependent Quasispecies Divergence of Severe Acute Respiratory Syndrome Coronavirus-2 in Non-human Primate Models

Frontiers in Microbiology ◽

10.3389/fmicb.2021.694897 ◽

2021 ◽

Vol 12 ◽

Author(s):

Eun-Ha Hwang ◽

Hoyin Chung ◽

Green Kim ◽

Hanseul Oh ◽

You Jung An ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Rhesus Macaques ◽

Vero Cells ◽

Frequency Variation ◽

Nucleotide Polymorphisms ◽

Human Beings ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Coding Regions ◽

Variant Analysis

Recently, newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been continuously reported worldwide. However, the precise evaluation of SARS-CoV-2 microevolution in host is very limited because the exact genetic information of infected virus could not be acquired in human researches. In this report, we performed deep sequencing for seed virus and SARS-CoV-2 isolated in eight cynomolgus and rhesus macaques at 3 days postinoculation and evaluated single-nucleotide polymorphisms (SNPs) in SARS-CoV-2 by variant analysis. A total of 69 single-nucleotide variants (SNVs) were present in the 5′-untranslated region (UTR), 3′-UTR, ORF1ab, S, ORF3a, ORF8, and N genes of the seed virus passaged in VERO cells. Between those present on the seed virus and those on each SARS-CoV-2 isolated from the lungs of the macaques, a total of 29 variants was identified in 4 coding proteins (ORF1ab, S, ORF3a, and N) and non-coding regions (5′- and 3′-UTR). Variant number was significantly different according to individuals and ranged from 2 to 11. Moreover, the average major frequency variation was identified in six sites between the cynomolgus monkeys and rhesus macaques. As with diverse SNPs in SARS-CoV-2, the values of viral titers in lungs were significantly different according to individuals and species. Our study first revealed that the genomes of SARS-CoV-2 differ according to individuals and species despite infection of the identical virus in non-human primates (NHPs). These results are important for the interpretation of longitudinal studies evaluating the evolution of the SARS-CoV-2 in human beings and development of new diagnostics, vaccine, and therapeutics targeting SARS-CoV-2.

Download Full-text

Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

Journal of Individual Differences ◽

10.1027/1614-0001.28.3.161 ◽

2007 ◽

Vol 28 (3) ◽

pp. 161-164 ◽

Cited By ~ 1

Author(s):

Rosalind Arden ◽

Nicole Harlaar ◽

Robert Plomin

Keyword(s):

Sex Differences ◽

Single Nucleotide Polymorphisms ◽

Cognitive Ability ◽

Dna Markers ◽

Community Sample ◽

Nucleotide Polymorphisms ◽

General Cognitive Ability ◽

Single Nucleotide ◽

The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

Download Full-text

Significant Associations of lncRNA H19 Genotypes with Susceptibility to Childhood Leukemia in Taiwan

Pharmaceuticals ◽

10.3390/ph14030235 ◽

2021 ◽

Vol 14 (3) ◽

pp. 235

Author(s):

Jen-Sheng Pei ◽

Chao-Chun Chen ◽

Wen-Shin Chang ◽

Yun-Chi Wang ◽

Jaw-Chyun Chen ◽

...

Keyword(s):

Confidence Interval ◽

Childhood Leukemia ◽

Healthy Controls ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Single Nucleotide ◽

Genotypic Distribution ◽

Heterozygous Variant ◽

Significant Difference ◽

The Difference

The purpose of our study was to investigate whether genetic variations in lncRNA H19 were associated with susceptibility to childhood leukemia. Two hundred and sixty-six childhood leukemia patients and 266 healthy controls were enrolled in Taiwan, and two single nucleotide polymorphisms (SNPs), rs2839698 and rs217727, in H19 were genotyped and analyzed. There was a significant difference in the genotypic distribution of rs2839698 between patients and healthy controls (p = 0.0277). Compared to the wild-type CC genotype, the heterozygous variant CT and homozygous variant TT genotypes were associated with significantly increased risks of childhood leukemia with an adjusted odd ratio (OR) of 1.46 (95% confidence interval (CI), 1.08–2.14, p = 0.0429) and 1.94 (95%CI, 1.15–3.31, p = 0.0169), respectively (pfor tread = 0.0277). The difference in allelic frequencies between childhood leukemia patients and controls was also significant (T versus C, adjusted OR = 1.53, 95%CI, 1.13–1.79, p = 0.0077). There were no significant differences in the genotypic and allelic distributions of rs217727 between cases and controls. Interestingly, the average level of H19 rs2839698 was statistically significantly higher for patients with CT and TT genotypes than from those with the CC genotype (p < 0.0001). Our results indicate that H19 SNP rs2839698, but not rs217727, may serve as a novel susceptibility marker for childhood leukemia.

Download Full-text

EPCO-02. GERMLINE SINGLE NUCLEOTIDE POLYMORPHISM rs55705857 AT 8q24 INTERACTS WITH SOMATIC IDH1 MUTATION TO ENHANCE HUMAN GLIOMA FORMATION

Neuro-Oncology ◽

10.1093/neuonc/noab196.001 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi1-vi1

Author(s):

Kristen Drucker ◽

Connor Yanchus ◽

Thomas Kollmeyer ◽

Asma Ali ◽

Decker Paul ◽

...

Keyword(s):

Fine Mapping ◽

Dna Interaction ◽

Genomic Region ◽

Idh1 Mutation ◽

Normal Brain ◽

Nucleotide Polymorphisms ◽

Human Glioma ◽

Single Nucleotide ◽

Coding Regions ◽

Chromatin Immunoprecipitation Sequencing

Abstract BACKGROUND Determination of the causation of germline single nucleotide polymorphisms (SNPs) located in non-coding regions of the genome is challenging. The genomic region of 8q24 has been identified as important in many kinds of cancer, linked to a topologically associated domain (TAD) encompassing MYC; this TAD contains a GWAS SNP (rs55705857) associated with IDH-mutant glioma. METHODS Germline genotyping data from 622 IDH-mutant glioma and 668 controls were used to fine map the rs55705857 locus by detailed haplotype analysis. Chromatin immunoprecipitation sequencing (ChIP-seq) of histone markers H3K4me1, H3K4me3, H3K27ac and H3K36me3 was performed on normal brain samples (n=8) and human glioma samples (n=11 IDH-wt and 52 IDH-mut). RNAseq from 9 normal and 83 brain tumors (n=26 IDH-wt and 55 IDH-mut) were used to assess differential gene expression. RESULTS Fine-mapping identified rs55705857 SNP as the most likely causative allele (OR=8.69; p<0.001) within 8q24 for the development of IDH-mutant glioma. At rs55705857, both H3K27ac and H3K4me1 in IDH-mutant vs IDH-wt tumors were increased 3.05- and 1.58-fold, respectively (DiffBind; p=5.81×10-7 and p=2.31×10-3). ChromHMM analysis of the marks indicated that promoter and enhancer functions were significantly increased, and the activity broadened at rs55705857 in IDH-mut gliomas compared to IDH-wt tumors and normal brain samples. This enhancement correlated with significant increased MYC expression in IDH-mut gliomas (p=3.1×10-13), as well as alterations of Myc signaling targets. Publicly available ATACseq, ChIPseq and long-range DNA interaction data demonstrated that the rs55705857 locus is open and interacts with the MYC promoter. CONCLUSIONS Fine-mapping of the 8q24 locus provided strong evidence that rs55705857 is the causative 8q24 locus associated with IDH-mut glioma. Functional experiments suggest that IDH mutation facilitates rs55705857 interaction with MYC to alter downstream MYC targets.

Download Full-text

Spatial genome architecture and the emergence of malignancy

Human Molecular Genetics ◽

10.1093/hmg/ddaa128 ◽

2020 ◽

Vol 29 (R2) ◽

pp. R197-R204 ◽

Cited By ~ 1

Author(s):

Adi Danieli ◽

Argyris Papantonis

Keyword(s):

Cell Cycle Progression ◽

Specific Gene ◽

Nucleotide Polymorphisms ◽

Drug Target Discovery ◽

Single Nucleotide ◽

Chromosome Conformation ◽

Chromosomal Structure ◽

Coding Regions ◽

Cell Type Specific ◽

Cancer Types

Abstract Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter–enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.

Download Full-text

Heterozygous Ile453Val codon mutation in exon 7, homozygous single nucleotide polymorphisms in intron 2 and 5 of cathepsin C are associated with Haim-Munk syndrome

European Journal of Dentistry ◽

10.4103/1305-7456.126250 ◽

2014 ◽

Vol 08 (01) ◽

pp. 079-084 ◽

Cited By ~ 6

Author(s):

Nalini Aswath ◽

Bhuminathan Swamikannu ◽

Sankar Narayanan Ramakrishnan ◽

Rajendran Shanmugam ◽

Jayakar Thomas ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Direct Sequencing ◽

Sequencing Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Heterozygous Condition ◽

South Indian ◽

The Subject ◽

First Time ◽

Intron 2

ABSTRACT Objective: In the present study, we have investigated the genetic status of CTSC gene in a HMS subject, who along with her parents belonged to non-Jewish South Indian Dravidian community. Materials and Methods: Genomic deoxyribonucleic acid isolated from the peripheral blood of the subject was amplified with CTSC exon specific primers and were analyzed by direct sequencing. Results: Sequencing analysis identified Ile453Val mutation within exon 7 of CTSC gene in heterozygous condition, and two single nucleotide polymorphisms (SNPs) within intron 2 and 5 in homozygous condition. Conclusion: The present study has identified for the first time the association of Ile453Val mutation within exon 7 and the two SNPs in a subject with HMS.

Download Full-text

Association of single-nucleotide polymorphisms in non-coding regions of the TLR4 gene with primary open angle glaucoma in a Mexican population

Ophthalmic Genetics ◽

10.1080/13816810.2016.1227454 ◽

2016 ◽

Vol 38 (4) ◽

pp. 325-329 ◽

Cited By ~ 8

Author(s):

Jose Navarro-Partida ◽

Beatriz Alvarado Castillo ◽

Abril Bernardette Martinez-Rizo ◽

Ramses Rosales-Diaz ◽

Jesus Bernardino Velazquez-Fernandez ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Primary Open Angle Glaucoma ◽

Open Angle Glaucoma ◽

Mexican Population ◽

Nucleotide Polymorphisms ◽

Open Angle ◽

Single Nucleotide ◽

Coding Regions ◽

Tlr4 Gene

Download Full-text

Characterization of single-nucleotide polymorphisms in coding regions of human genes

Nature Genetics ◽

10.1038/10290 ◽

1999 ◽

Vol 22 (3) ◽

pp. 231-238 ◽

Cited By ~ 1158

Author(s):

Michele Cargill ◽

David Altshuler ◽

James Ireland ◽

Pamela Sklar ◽

Kristin Ardlie ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Coding Regions ◽

Human Genes

Download Full-text

Linked mutations at adjacent nucleotides have shaped human population differentiation and protein evolution

10.1101/329292 ◽

2018 ◽

Author(s):

James G. D. Prendergast ◽

Carys Pugh ◽

Sarah E. Harris ◽

David A. Hume ◽

Ian J. Deary ◽

...

Keyword(s):

Human Population ◽

Single Mutation ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Mutational Spectra ◽

Coding Regions ◽

Selective Pressures ◽

Distinct Process ◽

Order Of Magnitude ◽

Mutational Processes

AbstractDespite the fundamental importance of single nucleotide polymorphisms (SNPs) to human evolution there are still large gaps in our understanding of the forces that shape their distribution across the genome. SNPs have been shown to not be distributed evenly, with directly adjacent SNPs found unusually frequently. Why this is the case is unclear. We illustrate how neighbouring SNPs that can’t be explained by a single mutation event (that we term here sequential dinucleotide mutations, SDMs) are driven by distinct mutational processes and selective pressures to SNPs and multinucleotide polymorphisms (MNPs). By studying variation across multiple populations, including a novel cohort of 1,358 Scottish genomes, we show that, SDMs are over twice as common as MNPs and like SNPs, display distinct mutational spectra across populations. These biases are though not only different to those observed among SNPs and MNPs, but also more divergent between human population groups. We show that the changes that make up SDMs are not independent, and identify a distinct mutational profile, CA → CG → TG, that is observed an order of magnitude more often than other SDMs, including others that involve the gain and subsequent deamination of CpG sites. This suggests these specific changes are driven by a distinct process. In coding regions particular SDMs are favoured, and especially those that lead to the creation of single codon amino acids. Intriguingly selection has favoured particular pathways through the amino acid code, with epistatic selection appearing to have disfavoured sequential non-synonymous changes.

Download Full-text