scholarly journals Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

2019 ◽  
Vol 23 (2) ◽  
pp. 135-139
Author(s):  
S. S. Gatzkaya ◽  
E. V. Evtushenko
Keyword(s):  
Nucleotide Diversity ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Nucleotide Polymorphisms ◽  
Mean Values ◽  
Geographic Ranges ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Commercial Breeding ◽  
The Mean

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

scholarly journals Analysis of Primary Structural Determinants That Distinguish the Centromere-Specific Function of Histone Variant Cse4p from Histone H3

1999 ◽  
Vol 19 (9) ◽  
pp. 6130-6139 ◽  
Author(s):  
Kevin C. Keith ◽  
Richard E. Baker ◽  
Yinhuai Chen ◽  
Kendra Harris ◽  
Sam Stoler ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Histone H3 ◽  
Biochemical Properties ◽  
Chromosome Loss ◽  
Structural Determinants ◽  
Histone Fold ◽  
Chromosome Transmission ◽  
Histone Fold Domain ◽  
N Terminus ◽  
Nested Deletions

ABSTRACT Cse4p is a variant of histone H3 that has an essential role in chromosome segregation and centromere chromatin structure in budding yeast. Cse4p has a unique 135-amino-acid N terminus and a C-terminal histone-fold domain that is more than 60% identical to histone H3 and the mammalian centromere protein CENP-A. Cse4p and CENP-A have biochemical properties similar to H3 and probably replace H3 in centromere-specific nucleosomes in yeasts and mammals, respectively. In order to identify regions of Cse4p that distinguish it from H3 and confer centromere function, a systematic site-directed mutational analysis was performed. Nested deletions of the Cse4p N terminus showed that this region of the protein contains at least one essential domain. The C-terminal histone-fold domain of Cse4p was analyzed by changing Cse4p amino acids that differ between Cse4p and H3 to the analogous H3 residues. Extensive substitution of contiguous Cse4p residues with H3 counterparts resulted in cell lethality. However, all large lethal substitution alleles could be subdivided into smaller viable alleles, many of which caused elevated rates of mitotic chromosome loss. The results indicate that residues critical for wild-type Cse4p function and high-fidelity chromosome transmission are distributed across the entire histone-fold domain. Our findings are discussed in the context of the known structure of H3 within the nucleosome and compared with previous results reported for CENP-A.

scholarly journals Single Nucleotide Polymorphisms in the Promoter of CYP19 Gene in Cattle Bred in Iraq

2020 ◽  
Vol 33 (1) ◽  
pp. 89-97
Author(s):  
Salah H. Faraj ◽  
Asaad Y. Ayied ◽  
Khalaf A. H. Al-Rishdy
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Diversity ◽  
Animal Species ◽  
Haplotype Diversity ◽  
Evolutionary Relationship ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cyp19 Gene

The present study was undertaken to characterize the genetic diversity of the aromatase cytochrome P450 (CYP19) gene in 34 cows (15 local, 14 Holstein, and 5 Crosses) in Iraq. The objectives of the present study are to detect SNPs (mutations) in promoter p1.1 of the CYP19 gene in cattle bred in Iraq using sequencing techniques. We identified five single-nucleotide polymorphisms (SNP) loci of the CYP19 gene that were detected, namely G933T, G994C, A1044G, A1062T, and C1468A. The results showed the presence of 3, 4, and 2 polymorphic sites leading to the construction of 4, 5, and 3 different haplotypes for Holstein, local, and crosses respectively. Haplotype diversity were 0.791, 0.752, and 0.700 respectively. While nucleotide diversity was 0.0017, 0.0022, and 0.0013 respectively. Besides, we carried out a phylogenetic analysis of these sequences to address the evolutionary relationship between the animal species. These fragments were assigned in the GenBank database under the accession numbers: LC490756, LC490757, LC491437, LC491438, LC491439, LC491588, and LC491589.

scholarly journals Gene Genealogies Reveal High Nucleotide Diversity and Admixture Haplotypes Within Three Alternaria Species Associated with Tomato and Potato

2020 ◽  
Vol 110 (8) ◽  
pp. 1449-1464
Author(s):  
Tika B. Adhikari ◽  
Thomas Ingram ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Nucleotide Diversity ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Its Region ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Alternaria Species ◽  
Neutrality Tests ◽  
Species Specific

Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. alternata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson’s theta were higher in A. alternata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. alternata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. alternata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlH1 to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaH1, AsAlH2/AsAlH3, and AsAlH4 and consisted exclusively of A. alternata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp.

scholarly journals Single-Nucleotide Polymorphisms in Soybean

Genetics ◽  
2003 ◽  
Vol 163 (3) ◽  
pp. 1123-1134 ◽  
Author(s):  
Y L Zhu ◽  
Q J Song ◽  
D L Hyten ◽  
C P Van Tassell ◽  
L K Matukumalli ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Dna ◽  
Nucleotide Diversity ◽  
Genomic Sequence ◽  
Haplotype Diversity ◽  
Pcr Primers ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cultivated Soybean

Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

scholarly journals Histone-Histone Interactions and Centromere Function

2000 ◽  
Vol 20 (15) ◽  
pp. 5700-5711 ◽  
Author(s):  
Lynn Glowczewski ◽  
Peirong Yang ◽  
Tatyana Kalashnikova ◽  
Maria Soledad Santisteban ◽  
M. Mitchell Smith
Keyword(s):  
Mitotic Chromosome ◽  
Histone H3 ◽  
Temperature Sensitive ◽  
Histone H4 ◽  
Cooperative Interactions ◽  
Histone Fold ◽  
Centromere Function ◽  
Chromosome Transmission ◽  
Histone Fold Domain ◽  
Allele Specific

ABSTRACT Cse4p is a structural component of the core centromere ofSaccharomyces cerevisiae and is a member of the conserved CENP-A family of specialized histone H3 variants. The histone H4 allelehhf1-20 confers defects in core centromere chromatin structure and mitotic chromosome transmission. We have proposed that Cse4p and histone H4 interact through their respective histone fold domains to assemble a nucleosome-like structure at centromeric DNA. To test this model, we targeted random mutations to the Cse4p histone fold domain and isolated three temperature-sensitive cse4alleles in an unbiased genetic screen. Two of the cse4alleles contain mutations at the Cse4p-H4 interface. One of these requires two widely separated mutations demonstrating long-range cooperative interactions in the structure. The third cse4allele is mutated at its helix 2-helix 3 interface, a region required for homotypic H3 fold dimerization. Overexpression of wild-type Cse4p and histone H4 confer reciprocal allele-specific suppression ofcse4 and hhf1 mutations, providing strong evidence for Cse4p-H4 protein interaction. Overexpression of histone H3 is dosage lethal in cse4 mutants, suggesting that histone H3 competes with Cse4p for histone H4 binding. However, the relative resistance of the Cse4p-H4 pathway to H3 interference argues that centromere chromatin assembly must be highly regulated.

scholarly journals Extremely low genetic variability within and among locations of the greenfish holothurianStichopus chloronotusBrandt, 1835 in Okinawa, Japan

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2410 ◽  
Author(s):  
Taha Soliman ◽  
Okuto Takama ◽  
Iria Fernandez-Silva ◽  
James D. Reimer
Keyword(s):  
Sea Cucumber ◽  
Nucleotide Diversity ◽  
East Coast ◽  
Histone H3 ◽  
Haplotype Diversity ◽  
Conservation Policies ◽  
16S Ribosomal Dna ◽  
Southern Japan ◽  
Stichopus Chloronotus ◽  
Management And Conservation

The greenfish sea cucumberStichopus chloronotusis an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction.Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies ofS. chloronotusin southern Japan.

scholarly journals A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS

2021 ◽  
Vol 20 (1) ◽  
pp. 1-11
Author(s):  
S.O. DUROSARO ◽  
B.T. OSHINOWO ◽  
A.C. AKPOJO ◽  
L.T. OLUYOMBO ◽  
I.C. NWOSU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Polymorphisms ◽  
Indigenous Chickens ◽  
Loop Region ◽  
D Loop ◽  
Selective Forces ◽  
Loss Of Diversity

Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.

DNA Barcoding Reveals Intra-Species Genetic Diversity of Amphiesma stolatum

2021 ◽  
Vol 9 (2) ◽  
pp. 139-145
Author(s):  
Lalbiak zuala ◽  
◽  
H.T. Lalremsanga ◽  
Lalrin sanga ◽  
Lalmuan sanga ◽  
...  
Keyword(s):  
16S Rrna ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Northeast India ◽  
Morphological Data ◽  
Cox1 Gene ◽  
History Museum ◽  
The Mean ◽  
Elevational Range ◽  
First Time

Amphiesma stolatum is a widely distributed snake species. But the intra-species genetic information is still limited from India. This paper provides the first-time barcode data of A. stolatum (cox1 and 16s rRNA) sampled from Mizoram State, India. We compare the newly generated sequences with the conspecies sequences from the Indo-Malayan region, and establishes its phylogenetic relationship with its sister genera. We diagnosed a total of five haplotypes from the cox1 gene fragment with 0.844 and 0.004 as the haplotype diversity (hd) and nucleotide diversity (Pi), respectively. The specimens from Mizoram showed a Kimura 2 parameter genetic distance of 0.21% (16s rRNA) and 1.05–1.22% (cox1) with the sequences from Guangdong Province, China; 1.22% (cox1) with the sequences from Hubei Province, China; 0.87–1.05% (cox1) with that from Taiwan; 8.05% with the specimen vouchered in the Natural History Museum, London. The mean intra-specific K2P distances are 4% and 0.36% in 16s rRNA and cox1, respectively. We also contribute new distributional records and elevational range, with notes on additional morphological data and occurrence of the two distinct morphs in Mizoram, Northeast India.

scholarly journals A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Xueqin Liu ◽  
Pu Zhang ◽  
Gongying Zhang ◽  
Sichen Li ◽  
Long Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Hydropathy Index ◽  
Altitude Adaptation ◽  
Nucleotide Divergence ◽  
Tibetan Chicken

To obtain a full understanding of the genetic diversity of the cytochrome oxidase III gene(COX-III)and its association with high altitude adaptation in Tibetan chickens, we sequencedCOX-IIIin 12 chicken populations (155 Tibetan chickens and 145 other domestic chickens). We identified a total of 11 single nucleotide polymorphisms (SNPs) and 12 haplotypes (Ha1–Ha12). Low genetic diversity (haplotype diversity = 0.531 ± 0.087, nucleotide diversity = 0.00125) was detected forCOX-III, and haplotype diversity of Tibetan chicken populations (0.750 ± 0.018) was markedly higher than lowland chicken populations (0.570 ± 0.028). Obvious genetic differentiation (nucleotide divergence = 0.092~0.339) and conspicuous gene communication (gene flow = 0.33~32.22) among 12 populations suggested that Tianfu black-bone fowl (white feather) was possibly introduced from Tibetan chicken. SNP m.10587 T>C affects the specific functions of the COX enzyme. Haplotype Ha3 was found in Tibetan chickens, and SNP m.10115G>A caused an amino acid substitution (Val62Ile) associated with phospholipid binding, while mutations m.10017C>A and m.10555G>A and the previously reported SNP m.10065T>C reduced the hydropathy index to some extent. Together, this indicates that the mitochondrial membrane is more hydrophobic in Tibetan chickens.

scholarly journals Assembly of CENP-A into Centromeric Chromatin Requires a Cooperative Array of Nucleosomal DNA Contact Sites

1997 ◽  
Vol 136 (3) ◽  
pp. 501-513 ◽  
Author(s):  
Richard D. Shelby ◽  
Omid Vafa ◽  
Kevin F. Sullivan
Keyword(s):  
Cell Cycle ◽  
Histone H3 ◽  
Structural Elements ◽  
Histone Fold ◽  
Contact Sites ◽  
Nucleosomal Dna ◽  
Histone Fold Domain ◽  
Cycle Dependent

We investigated the requirements for targeting the centromeric histone H3 homologue CENP-A for assembly at centromeres in human cells by transfection of epitope-tagged CENP-A derivatives into HeLa cells. Centromeric targeting is driven solely by the conserved histone fold domain of CENP-A. Using the crystal structure of histone H3 as a guide, a series of CENPA/histone H3 chimeras was constructed to test the role of discrete structural elements of the histone fold domain. Three elements were identified that are necessary for efficient targeting to centromeres. Two correspond to contact sites between histone H3 and nucleosomal DNA. The third maps to a homotypic H3–H3 interaction site important for assembly of the (H3/H4)2 heterotetramer. Immunoprecipitation confirms that CENP-A self-associates in vivo. In addition, targeting requires that CENP-A expression is uncoupled from histone H3 synthesis during S phase. CENP-A mRNA accumulates later in the cell cycle than histone H3, peaking in G2. Isolation of the gene for human CENP-A revealed a regulatory motif in the promoter region that directs the late S/G2 expression of other cell cycle–dependent transcripts such as cdc2, cdc25C, and cyclin A. Our data suggest a mechanism for molecular recognition of centromeric DNA at the nucleosomal level mediated by a cooperative series of differentiated CENP-A–DNA contact sites arrayed across the surface of a CENP-A nucleosome and a distinctive assembly pathway occurring late in the cell cycle.

Sign in / Sign up

Export Citation Format

Share Document