Number Of Nucleotide Differences Research Articles

The impact of surveillance and other factors on detection of emergent and circulating vaccine derived polioviruses.

Background: Circulating vaccine derived poliovirus (cVDPV) outbreaks remain a threat to polio eradication. To reduce cases of polio from cVDPV of serotype 2, the serotype 2 component of the vaccine has been removed from the global vaccine supply, but outbreaks of cVDPV2 have continued. The objective of this work is to understand the factors associated with later detection in order to improve detection of these unwanted events. Methods: The number of nucleotide differences between each cVDPV outbreak and the oral polio vaccine (OPV) strain was used to approximate the time from emergence to detection. Only independent emergences were included in the analysis. Variables such as serotype, surveillance quality, and World Health Organization (WHO) region were tested in a negative binomial regression model to ascertain whether these variables were associated with higher nucleotide differences upon detection. Results: In total, 74 outbreaks were analysed from 24 countries between 2004-2019. For serotype 1 (n=10), the median time from seeding until outbreak detection was572 (95% uncertainty interval (UI) 279-2016), for serotype 2 (n=59), 276 (95% UI 172-765) days, and for serotype 3 (n=5), 472 (95% UI 392-603) days. Significant improvement in the time to detection was found with increasing surveillance of non-polio acute flaccid paralysis (AFP) and adequate stool collection. Conclusions: cVDPVs remain a risk; all WHO regions have reported at least one VDPV outbreak since the first outbreak in 2000 and outbreak response campaigns using monovalent OPV type 2 risk seeding future outbreaks. Maintaining surveillance for poliomyelitis after local elimination is essential to quickly respond to both emergence of VDPVs and potential importations as low-quality AFP surveillance causes outbreaks to continue undetected. Considerable variation in the time between emergence and detection of VDPVs were apparent, and other than surveillance quality and inclusion of environmental surveillance,the reasons for this remain unclear.

The impact of surveillance and other factors on detection of emergent and circulating vaccine derived polioviruses

Background: Circulating vaccine derived poliovirus (cVDPV) outbreaks remain a threat to polio eradication. To reduce cases of polio from cVDPV of serotype 2, the serotype 2 component of the vaccine has been removed from the global vaccine supply, but outbreaks of cVDPV2 have continued. The objective of this work is to understand the factors associated with later detection in order to improve detection of these unwanted events. Methods: The number of nucleotide differences between each cVDPV outbreak and the oral polio vaccine (OPV) strain was used to approximate the time from emergence to detection. Only independent emergences were included in the analysis. Variables such as serotype, surveillance quality, and World Health Organization (WHO) region were tested in a negative binomial regression model to ascertain whether these variables were associated with higher nucleotide differences upon detection. Results: In total, 74 outbreaks were analysed from 24 countries between 2004-2019. For serotype 1 (n=10), the median time from seeding until outbreak detection was 284 (95% uncertainty interval (UI) 284-2008) days, for serotype 2 (n=59), 276 (95% UI 172-765) days, and for serotype 3 (n=5), 472 (95% UI 392-603) days. Significant improvement in the time to detection was found with increasing surveillance of non-polio acute flaccid paralysis (AFP) and adequate stool collection. Conclusions: cVDPVs remain a risk; all WHO regions have reported at least one VDPV outbreak since the first outbreak in 2000 and outbreak response campaigns using monovalent OPV type 2 risk seeding future outbreaks. Maintaining surveillance for poliomyelitis after local elimination is essential to quickly respond to both emergence of VDPVs and potential importations as low-quality AFP surveillance causes outbreaks to continue undetected. Considerable variation in the time between emergence and detection of VDPVs were apparent, and other than surveillance quality and inclusion of environmental surveillance, the reasons for this remain unclear.

The impact of surveillance and other factors on detection of emergent and circulating vaccine derived polioviruses

Background: Circulating vaccine derived poliovirus (cVDPV) outbreaks remain a threat to polio eradication. To reduce cases of polio from cVDPV of serotype 2, the serotype 2 component of the vaccine has been removed from the global vaccine supply, but outbreaks of cVDPV2 have continued. The objective of this work is to understand the factors associated with later detection in order to improve detection of these unwanted events. Methods: The number of nucleotide differences between each cVDPV outbreak and the oral polio vaccine (OPV) strain was used to approximate the time from emergence to detection. Only independent emergences were included in the analysis. Variables such as serotype, surveillance quality, and World Health Organization (WHO) region were tested in a negative binomial regression model to ascertain whether these variables were associated with higher nucleotide differences upon detection. Results: In total, 74 outbreaks were analysed from 24 countries between 2004-2019. For serotype 1 (n=10), the median time from seeding until outbreak detection was 284 (95% uncertainty interval (UI) 284-2008) days, for serotype 2 (n=59), 276 (95% UI 172-765) days, and for serotype 3 (n=5), 472 (95% UI 392-603) days. Significant improvement in the time to detection was found with increasing surveillance of non-polio acute flaccid paralysis (AFP) and adequate stool collection. Conclusions: cVDPVs remain a risk; all WHO regions have reported at least one VDPV outbreak since the first outbreak in 2000 and outbreak response campaigns using monovalent OPV type 2 risk seeding future outbreaks. Maintaining surveillance for poliomyelitis after local elimination is essential to quickly respond to both emergence of VDPVs and potential importations as low-quality AFP surveillance causes outbreaks to continue undetected. Considerable variation in the time between emergence and detection of VDPVs were apparent, and other than surveillance quality and inclusion of environmental surveillance, the reasons for this remain unclear.

The genetic diversity of the Vietnamese H’mong dog breed based on mitochondrial HV1 analysis

The H'mong docked tail is indigenous breed of dogs distributed in mountainous area of northern Vietnam. These dogs possess positive characteristics such as intelligence, agility, good health, good shape, human friendliness, ease of training and fully meet the criteria of a war dog. We had studied the diversity and origin of Vietnamese H’mong dogs based on the molecular data of the mitochondrial HV1 region. A total of seventy individual dogs were sampled from Lao Cai, Ha Giang and Hai Phong provinces of northern Vietnam and were sequenced. Among the targeted dogs, 29 haplotypes were recorded and divided into four main groups: A, B, C and E. In our study, nine new haplotypes were recorded and all of them belong to haplotype group A. Group A was the most common with 24 haplotypes (82.76%) followed by C, E and B with 2 (6.9%), 2 (6.9%) and 1 haplotypes (3.4%) respectively. The genetic variations in the H'mong dogs were high with nucleotide diversity (Pi = 0.03179), haplotype diversity (Hd = 0.95648) and average number of nucleotide differences (Kt = 5.18384) and the p-genetic distances range was from 0.2 to 2.9%. This study has provided a valuable platform for breeding and conservation and management of the species in Vietnam.

Genetic polymorphism of the extracellular region in surface associated interspersed 1.1 gene of Plasmodium falciparum field isolates from Thailand

BackgroundA novel variable surface antigens (VSAs), Surface-associated interspersed proteins (SUFRINs), is a protein that is modified on the surface of infected red blood cell (iRBC). Modified proteins on the iRBC surface cause severe malaria, which can lead to death throughout the life cycle of a malaria parasite. Previous study suggested that SURFIN1.1 is an immunogenic membrane-associated protein which was encoded by using the surf1.1 gene expressed during the trophozoite and schizont stages. This study aimed to identify the regions of SURFIN1.1 and investigate the genetic diversity of the extracellular region of the surf1.1 gene.MethodsA total of 32 blood samples from falciparum malaria cases that were diagnosed in Si Sa Ket Province, Thailand were collected. Plasmodium genomic DNA was extracted, and the extracellular region of surf1.1 gene was amplified using the polymerase chain reaction (PCR). A sequence analysis was then performed to obtain the number of haplotypes (H), the haplotype diversity (Hd), and the segregating sites (S), while the average number of nucleotide differences between two sequences (Pi); in addition, neutrality testing, Tajima’s D test, Fu and Li’s D* and F* statistics was also performed.ResultsFrom a total of 32 patient-isolated samples, 31 DNA sequences were obtained and analysed for surf1.1 gene extracellular region polymorphism. Researchers observed six distinct haplotypes in the current research area. Haplotype frequencies were 61.3%, 16.2%, and 12.9% for H1, H2, and H3, respectively. The remaining haplotype (H4-H6) frequency was 3.2% for each haplotype. Hd was 0.598 ± 0.089 with the Pi of 0.00381, and S was 15. The most common amino acid polymorphic site was E251Q; other sites included N48D, I49V, E228D, E235S, L265F, K267T, E276Q, and S288F. Fu and Li’s D* test value was − 1.24255, Fu and Li’s F* test value was − 1.10175, indicating a tendency toward negative balancing selection acting on the surf1.1 N-terminal region. The most polymorphic region was variable 2 (Var2) while cysteine-rich domain (CRD) was conserved in both the amino acid and nucleotide extracellular region of surf1.1 gene.ConclusionsThe Thai surf1.1 N-terminal region was well-conserved with only a few polymorphic sites remaining. In this study, the data regarding current bearing on the polymorphism of extracellular region of surf1.1 gene were reported, which might impact the biological roles of P. falciparum. In addition, may possibly serve as a suitable candidate for future development of SURFIN-based vaccines regarding malaria control.Graphic abstract

Genetic Diversity Analysis of Surface-Related Antigen (SRA) in Plasmodium falciparum Imported From Africa to China

Plasmodium falciparum surface-related antigen (SRA) is located on the surfaces of gametocyte and merozoite and has the structural and functional characteristics of potential targets for multistage vaccine development. However, little information is available regarding the genetic polymorphism of pfsra. To determine the extent of genetic variation about P. falciparum by characterizing the sra sequence, 74 P. falciparum samples were collected from migrant workers who returned to China from 12 countries of Africa between 2015 and 2019. The full length of the sra gene was amplified and sequenced. The average pairwise nucleotide diversities (π) of P. falciparum sra gene was 0.00132, and the haplotype diversity (Hd) was 0.770. The average number of nucleotide differences (k) for pfsra was 3.049. The ratio of non-synonymous (dN) to synonymous (dS) substitutions across sites (dN/dS) was 1.365. Amino acid substitutions of P. falciparum SRA could be categorized into 35 unique amino acid variants. Neutrality tests showed that the polymorphism of PfSRA was maintained by positive diversifying selection, which indicated its role as a potential target of protective immune responses and a vaccine candidate. Overall, the ability of the N-terminal of PfSRA antibodies to evoke inhibition of merozoite invasion of erythrocytes and conserved amino acid at low genetic diversity suggest that the N-terminal of PfSRA could be evaluated as a vaccine candidate against P. falciparum infection.

The impact of surveillance and other factors on detection of emergent and circulating vaccine derived polioviruses.

Background: Circulating vaccine derived poliovirus (cVDPV) outbreaks remain a threat to polio eradication. To reduce cases of polio from cVDPV of serotype 2, the serotype 2 component of the vaccine has been removed from the global vaccine supply, but outbreaks of cVDPV2 have continued. The objective of this work is to understand the factors associated with later detection in order to improve detection of these unwanted events. Methods: The number of nucleotide differences between each cVDPV outbreak and the oral polio vaccine (OPV) strain was used to approximate the time from emergence to detection. Only independent emergences were included in the analysis. Variables such as serotype, surveillance quality, and World Health Organization (WHO) region were tested in a negative binomial regression model to ascertain whether these variables were associated with higher nucleotide differences upon detection. Results: In total, 74 outbreaks were analysed from 24 countries between 2004 and 2019. For serotype 1 (n=10), the median time from seeding until outbreak detection was 284 (95% uncertainty interval (UI) 284-2008) days, for serotype 2 (n=59), 276 (95% UI 172-765) days, and for serotype 3 (n=5), 472 (95% UI 392-603) days. Significant improvement in the time to detection was found with increasing surveillance of non-polio acute flaccid paralysis (AFP) and adequate stool collection. Conclusions: cVDPVs remain a risk globally; all WHO regions have reported at least one VDPV outbreak since the first outbreak in 2001. Maintaining surveillance for poliomyelitis after local elimination is essential to quickly respond to both emergence of VDPVs and potential importations. Considerable variation in the time between emergence and detection of VDPVs were apparent, and other than surveillance quality and inclusion of environmental surveillance,the reasons for this remain unclear.

The identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR

Data were collected from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that the nucleotide sequences 16S rRNA region are highly similar to those of V. alginolyticus, V. azureus, V. fluvialis, V. natriengens and V. orientalis, which were published on Genbank and other, ranging from 98.05 to 100%. The digestive tract has the most common Vibrio strains (V. alginolyticus [16] V. azureus [7] and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained 1 to 3 toxin genes, except V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated that number of separate polymorphic sites (S), total number of mutant sites (Eta), number of haplotype (h), haplotype diversity (Hd), average number of nucleotide differences (k), nucleotide diversity (Pi) were 98 (S), 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980 × 10–3 ± 0.003 (Pi), respectively (P < 0,05). The G + C content above 1434 sites positions of nucleotide sequences accounted for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) hemorrhagic are V. azureus (27,67%), V. alginolyticus (50%), V. orientalis (6,67%) and V. fluvialis (16,67%). Through this result, we found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.

Разнообразие гаплотипов гена COI горбуши Оncorhynchus gorbuscha (Walbaum, 1792) бассейна реки Печоры

Pink salmon Oncorhynchus gorbuscha (Walba-um, 1792) is an anadromous epipelagic species that forms the basis of the Far East fishing in¬dustry. The result of the work on its acclimati¬zation carried out in the second half of the XX cen-tury was the rapid expansion of the area, in¬cluding the rivers of the European northeast of Russia. The findings of this species in the Pe¬chora river basin, which is the largest river sys¬tem in the area of distribution, allowed us to carry out a general morphological description of the pink salmon. The obtained values of the meristic characteris¬tics of the studied individuals indicate that they are close to the typical form of the pink salmon species. It is noted that the number of this spe¬cies in the Pechora River is extremely unstable. The analysis of the nucleotide sequences of the cytochrome oxidase subunit 1 gene (n = 71), carried out on the basis of our own data and in¬formation from the GenBank database, revealed 15 haplotypes. The average number of nucleo-tide differences per site (nucleotide diversity - Pi) was 0.00303 ± 0.000024. The transi¬tions/transversions ratio corresponded to the value of 2.4. The haplotype diversity value (Hd) is 0.823. In 11 tissue samples of pink salmon caught in the watercourses of the European northeast of Russia, 7 haplotypes of the COI gene were found, which is a fairly high ratio. An increase in the sample size will lead to the identification of even greater diversity for the studied gene in the acquired part of the range of the studied species. It is suggested that the main genetic effects of the «bottleneck» and «founder», characteristic of the populating by this species of a new territory, may not be ob¬served. The main reason is assumed to be a fairly large number of individuals from differ¬ent years of generations used in the process of introduction of pink salmon.

Genetic polymorphism of the N-terminal region in circumsporozoite surface protein of Plasmodium falciparum field isolates from Sudan

BackgroundMalaria caused by Plasmodium falciparum parasite is still known to be one of the most significant public health problems in sub-Saharan Africa. Genetic diversity of the Sudanese P. falciparum based on the diversity in the circumsporozoite surface protein (PfCSP) has not been previously studied. Therefore, this study aimed to investigate the genetic diversity of the N-terminal region of the pfcsp gene.MethodsA cross-sectional molecular study was conducted; 50 blood samples have been analysed from different regions in Sudan. Patients were recruited from the health facilities of Khartoum, New Halfa, Red Sea, White Nile, Al Qadarif, Gezira, River Nile, and Ad Damazin during malaria transmission seasons between June to October and December to February 2017–2018. Microscopic and nested PCR was performed for detection of P. falciparum. Merozoite surface protein-1 was performed to differentiate single and multiple clonal infections. The N-terminal of the pfcsp gene has been sequenced using PCR-Sanger dideoxy method and analysed to sequences polymorphism including the numbers of haplotypes (H), segregating sites (S), haplotypes diversity (Hd) and the average number of nucleotide differences between two sequences (Pi) were obtained using the software DnaSP v5.10. As well as neutrality testing, Tajima’s D test, Fu and Li’s D and F statistics.ResultsPCR amplification resulted in 1200 bp of the pfcsp gene. Only 21 PCR products were successfully sequenced while 29 were presenting multiple clonal P. falciparum parasite were not sequenced. The analysis of the N-terminal region of the PfCSP amino acids sequence compared to the reference strains showed five different haplotypes. H1 consisted of 3D7, NF54, HB3 and 13 isolates of the Sudanese pfcsp. H2 comprised of 7G8, Dd2, MAD20, RO33, Wellcome strain, and 5 isolates of the Sudanese pfcsp. H3, H4, and H5 were found in 3 distinct isolates. Hd was 0.594 ± 0.065, and S was 12. The most common polymorphic site was A98G; other sites were D82Y, N83H, N83M, K85L, L86F, R87L, R87F, and A98S. Fu and Li’s D* test value was − 2.70818, Fu and Li’s F* test value was − 2.83907, indicating a role of negative balancing selection in the pfcsp N-terminal region. Analysis with the global pfcsp N-terminal regions showed the presence of 13 haplotypes. Haplotypes frequencies were 79.4%, 17.0%, 1.6% and 1.0% for H1, H2, H3 and H4, respectively. Remaining haplotypes frequency was 0.1% for each. Hd was 0.340 ± 0.017 with a Pi of 0.00485, S was 18 sites, and Pi was 0.00030. Amino acid polymorphisms identified in the N-terminal region of global pfcsp were present at eight positions (D82Y, N83H/M, K85L/T/N, L86F, R87L/F, A98G/V/S, D99G, and G100D).ConclusionsSudanese pfcsp N-terminal region was well-conserved with only a few polymorphic sites. Geographical distribution of genetic diversity showed high similarity to the African isolates, and this will help and contribute in the deployment of RTS,S, a PfCSP-based vaccine, in Sudan.

Beta-tubulin and Actin gene phylogeny supports Phaeoacremoniumovale as a new species from freshwater habitats in China.

A new species of Phaeoacremonium, P.ovale (Togniniaceae), was isolated during a diversity study of freshwater fungi from Yunnan Province in China. Morphological and cultural studies of the fungus were carried out and its sexual and asexual morphs (holomorph) are introduced herein. This species is characterised by peculiar long-necked, semi-immersed ascomata with oval to ellipsoid ascospores and ellipsoid to ovoid conidia. Phylogenetic analyses of a combined TUB and ACT gene dataset revealed that strains of P.ovale constitute a strongly supported independent lineage and are related to P.griseo-olivaceum and P.africanum. The number of nucleotide differences, across the genes analysed, also supports establishment of P.ovale as a new species.

Genetic Characterization of Kazakh Native Sheep Breeds Using Mitochondrial DNA

In this study, we used mitochondrial (mt) DNA to reveal patterns of genetic diversity among six breeds of sheep native to Kazakhstan, including the Chu and Kalchengel types of Kazakh mutton-semifine-wool breed of sheep, Akzhayik, Edilbay, Kazakh fat-rumped semi-course-wool and South Kazakh Merino breeds. Mitochondrial DNA D-loop was studied in 64 samples to determine the genetic diversity of the local sheep breeds. The analysis identified 54 haplotypes and 113 polymorphic loci of mtDNA D-loop. For the studied breeds, haplotype diversity and nucleotide diversity were 0.993±0.005 and 0.039±0.001, respectively. The results indicated higher level of nucleotide diversity in the South Kazakh Merino (SKM) breed (0.047), while the lowest diversity was observed in the Edilbay breed (0.029). In addition, the average number of nucleotide differences (Kxy) and the average number of nucleotide substitutions (Dxy) were determined among the studied breeds. The minimal value of genetic distance was observed between Akzhayik mutton-wool and Kazakh fat-rumped semi-course-wool breeds (Kxy: 16.956 and Dxy: 0.039), while the maximum value was observed between the Edilbay and SKM breeds (Kxy: 24.600 and Dxy: 0.040). Phylogenetic analysis revealed the presence of three haplogroups, namely, A, B and C in the collected sample, while the haplogroups D and E were not found. The results indicated that 28 of 64 tested animals belong to haplogroup A (43.75%), whereas 25 of investigated animals were attributed to haplogroup B (39.06%) and 11 animals to haplogroup C (17.19%).

Population genetic structure of cotton pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) using mitochondrial cytochrome oxidase I (COI) gene sequences from India

Pink bollworm (PBW), Pectinophora gossypiella is one of the most destructive pest’s globally inflicting huge economic losses in cotton even during later stages of crop growth. In the present investigation, the population genetic structure, distribution, and genetic diversity of P. gossypiella in cotton growing zones of India using partial mitochondrial DNA cytochrome oxidase-I (COI) gene was addressed. The overall haplotype (Hd), number of nucleotide differences (K), and nucleotide diversity (π) were 0.3028, 0.327, and 0.00047, respectively which suggest that entire population exhibited low level of genetic diversity. Zone-wise clustering of population revealed that central zone recorded low level of Hd (0.2730) as compared to north (0.3619) and south (0.3028) zones. The most common haplotype (H1) reported in all 19 locations could be proposed as ancestral/original haplotype. This haplotype with one mutational step formed star-like phylogeny connected with 11 other haplotypes. The phylogenetic relationship studies revealed that most haplotypes of populations are closely related to each other. Haplotype 5 was exclusively present in Dharwad (South zone) shared with populations of Hanumangarh and Bathinda (North zone). The result indicated that there is no isolation by distance effect among the Indian populations of PBW. The present study reports a low genetic diversity among PBW populations of India and H1, as ancestral haplotype from which other haplotypes have evolved suggests that the migration and dispersal over long distance and invasiveness are major factors.

Comparison of 16S rDNA sequence among the phytoplasmas associated with wilt disease of coconut from different locations

In India, the wilt disease is a major threat to coconut plantations. The diagnost ic symptoms of disease are wilting of leaflets, yellowing and marginal necrosis of the older leaves. The phytoplasma associated with the disease was identified through molecular techniques that revealed that it belongs to 16SrXI -B group. In the present study phytoplasma DNA was extracted from coconut in three locations of South India to verify the presence of molecular variability in the 16S rDNA region. Diseased samples were collected, the DNA was amplified using custom designed semi-nested primers and the PCR products were cloned and sequenced. All sequences were trimmed and aligned and the sequence variation was analyzed by calculating the nucleotide diversity (Pi) using DnaSP V5 software. Based on Pi values, the nucleotide diversity was higher between the phytoplasmas from Kasaragod and Kayamkulam (0.0102) than between the phytoplasmas from Kayamkulam and Theni (0.0083). The average number of nucleotide difference was five out of 491 nucleot ides. Based on nucleotide identity, Kayamkulam phytoplasma shared 99% identity with Theni phytoplasma. The Kasaragod and Theni phytoplasmas shared 98% nucleot ideidentity. Moreover a Weligama leaf wilt phytoplasma from SriLanka resulted to be undistinguishable from the strain detected in Theni region (100% nucleotide identity). The 16S rDNA nucleotide variability of phytoplasmas between palms was 1.21% and within palms was 1.36%.

The complete mitogenome of the common dolphinfish (Coryphaena hippurus)

The complete mitochondrial genome of the dolphinfish (GeneBank accession number KF719178) structure is similar to that of other teleosts, has a total length of 15,733 bp, the base composition was as follows: A (28.78%), T (29.25%), C (25.45%) and G (16.50%), which demonstrated an A + T (58.04%) rich feature. It contains 13 protein-coding genes and 23 tRNA genes that range from 54 to 72 bp. We compared our mitogenome with the one reported by Miya and collaborators in 2013 and found that the average number of nucleotide differences was k: 47.000 resulting in a nucleotide diversity Pi(t) of 0.00299.

MtDNA variation within local human populations in Bosnia and Herzegovina

Being a crossroad of many ancient and recent historical migrations, Bosnia and Herzegovina (B&amp;H) represents unique spot of multicultural and social diversity. The main aim of this study was to assess genetic structure of three local populations of mountain area from central part of B&amp;H using mtDNA HVS-1 as an informative marker for population genetics studies. A 444 bp HVS-1 segment of control region of mtDNA extracted from buccal swabs was PCR amplified and sequenced. Haplotype and nucleotide diversity, average number of nucleotide differences, AMOVA and pairwise FST based on mtDNA haplotype and haplogroup frequencies were calculated. NJ tree was constructed based on pairwise FST results. Tajima?s D was calculated to evaluate population demographic status.

Investigation of the genetic diversity among native Turkish sheep breeds using mtDNA polymorphisms

A total of 135 unrelated sheep from nine Turkish native sheep breeds (Daglıc, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 ± 0.011, 0.01407 ± 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.

Genetic diversity and population genetic structure in giant earthworm Rhinodrilus alatus (Annelida: Clitellata: Glossoscolecidae)

Abstract Rhinodrilus alatus ( Righi, 1971 ) is a giant earthworm (“minhocucu”) endemic to Southeast Brazil savannah that has long been exploited as fishing bait, however such extractive activity results in social and environmental impacts as well as negative effects on the species. Genetic diversity, population genetic and geographic structures of R. alatus were characterized by sequencing of the mitochondrial gene cytochrome c oxidase I (COI) and a nuclear segment including 5.8S rRNA gene and the internal transcribed spacers 1 (ITS1) and 2 (ITS2). We sequenced 75 R. alatus and 6 Rhinodrilus motucu individuals collected at 21 sites. Genetic diversity was evaluated based on haplotype and nucleotide diversity, and average number of nucleotide differences. Population genetic and geographic structure was characterized with Mantel tests, spatial analysis of molecular variance (SAMOVA), and phylogenetic analysis (maximum likelihood, Bayesian inference, and median joining). High genetic diversity was found for this species with 53 haplotypes in the COI gene and 22 haplotypes for the ITS1-5.8S-ITS2 segment suggesting six and four lineages, respectively. Moderate population genetic structure was indicated by the spatial distribution of lineages and Mantel tests results. High genetic diversity associated with genetic and geographic population structure points to a low dispersal rate for the species, as described for other earthworms. We characterized less frequent lineages, which were collected on the periphery of the dispersal area of the species. Conservation of the largest possible number of lineages particularly those less common will be fundamental for maintaining the genetic diversity of the species.

The genetic diversity of mitochondrial DNA D-loop region of three geographical populations inTrionyx sinensis

Trionyx sinensis is regarded as a very important fishery animals with high economic value.However,the germplasm resources of Trionyx sinensis are exposed to admixture and degeneration due to the booming industry.The investigation of genetic diversity of Trionyx sinensis is beneficial to protect the germplasm resources.In the present study,the variation and genetic diversity of mtDNA D-loop region partial sequences in three geographical populations of Trionyx sinensis were analyzed by PCR combined with DNA sequencing and SSCP techniques.The average contents of A+T(65.4%)were higher than that of G+C(34.6%).A total of 7 variable sites(about 5.7% of the total nucleotides in the sequence)were detected in 25 individuals,and the value of si/sv was 2.76.The nucleotide diversity(π)of the 25 individuals was 0.019 95,and the average number of nucleotide differences(K) of them was 2.453.The 25 individuals belonged to 6 haplotypes according to the determined sequences.The haplotype diversity(Hd)was 0.707,and the average genetic distance(P) among the haplotypes of the species was 0.027.The analysis of phylogenetic tree with the method of UPGMA showed that the 6 haplotypes were clustered into three groups.Our data indicated that the variation and genetic diversity were high in the three populations of T.sinensis,in which the genetic diversity of Japanese population was richer than that of Huanghe and Huangsha population,and the genetic distance between Huangsha population and the other two populations was far.Moreover,we found that two types of electrophoretic patterns could be detected by PCR-SSCP,and all type Ⅱwere Japanese population,suggesting the effective application of PCR-SSCP method in 78 TT AA transversion mutation sites testing.

Bioinformatics analysis of metallothionein gene from &lt;i&gt;Agaricus bisporus, Ganoderma lucidum, Taiwanofungus camphorates&lt;/i&gt; and &lt;i&gt;Paxillus involutus&lt;/i&gt;

Metallothionein (MT) gene has an important role in the detoxification of toxic metals especially some heavy metals. Based on the published sequences of MT genes from Agaricus bisporus, Garnoderma lucidum, Taiwanofungus camphoratus and Paxillus involutus as a type of the edible or medical mushroom in NCBI database, their molecular structures, physiological functions and evolutionary relationship were analyzed using the bioinformatics methods. Results showed that AbMT, GlMT, TcMT and PiMT genes contained complete open reading frame (ORF) and their theoretical points of the last three encoding proteins were higher than 7.0. AbMT, GlMT, TcMT and PiMT were relatively rich in random coil and extended strand, but transmembrane helices and signal peptides were not found. 4 MTs were mainly localized in cell nucleus (over 60%) and their cellular functions might have some relation to central intermediary metabolism. Multiple sequence alignment indicated relatively high identity (more than 52%) and short genetic distances (lower than 0.900) among 4 MT nucleotide sequences. Abundant genetic diversity and strong codon bias were found based on the halotype diversity, average number of nucleotide differences, nucleotide diversity, effective number of codons, codon bias index and scaled chisquare. Simultaneously, we deduced that 4 MT genes during molecular evolution were under positive selection. The present study might provide basis for further investigation of MTs molecular mechanisms and genetic laws.