1
|
Lee DG, Kim SJ, Cho WC, Cho Y, Park JH, Lee J, Jung JY. Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs. Forensic Sci Int Genet 2023; 65:102875. [PMID: 37084624 DOI: 10.1016/j.fsigen.2023.102875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10-3 per generation, with an average mutation rate of 2.17 × 10-3 (95% CI, 1.5-3.1 × 10-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10-3 (95% CI, 2.3-3.7 × 10-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.
Collapse
Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, Wonju, South Korea; Department of forensics Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Yoonjung Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Busan Institute, Busan, South Korea
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, Jeju, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
| |
Collapse
|
2
|
Shabalala S, Ghai M, Okpeku M. Analysis of Y-STR diversity and DNA methylation variation among Black and Indian males from KwaZulu-Natal, South Africa. Forensic Sci Int 2023; 348:111682. [PMID: 37094501 DOI: 10.1016/j.forsciint.2023.111682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023]
Abstract
Y-chromosome short tandem repeats (Y-STRs) are essential in understanding genetic structure and diversity of human populations and, most importantly, in identification of male perpetrators in criminal investigations. DNA methylation differences have been reported in human populations and methylation pattern at the CpG sites found within or flanking the Y-STR sites could also aid in human identification. Studies based on DNA methylation (DNAm) at Y-STRs are currently limited. The current study aimed to analyze the Y-STR diversity in South African Black and Indian individuals living in KwaZulu-Natal, Durban, South Africa, with the Yfiler™ Plus Kit and to analyze DNAm patterns in Y-STR markers CpG sites. DNA from 247 stored saliva samples were isolated and quantified. Across the 27 Y-STR loci in the Yfiler™ Plus Kit, 253 alleles were observed in 113 South African Black and Indian males, 112 unique haplotypes were observed, and one haplotype appeared twice (two Black individuals). No statistically significant differences were observed in the genetic diversity between the two population groups (Fst = 0.028, p-value ≥ 0.05). The kit showed a high discrimination capacity (DC) of 0.9912 and an overall haplotype diversity (HD) = 0.9995 among the sampled population groups. DYS438 and DYS448 markers displayed 2 and 3 CpG sites, respectively. Based on the two-tailed Fisher's Exact test, there were no statistically significant differences in the DNAm levels at DYS438 CpGs of Black and Indian males (p > 0.05). The Yfiler™ Plus Kit can be considered highly discriminatory among South African Black and Indian males. Studies on the South African population using Yfiler™ Plus Kit are scarce. Hence, accumulating Y-STR data on the diverse South African population will enhance the representation of South Africa in STR databases. Knowing which Y-STR markers are significantly informative for South Africa is essential for developing Y-STR kits better suited for the different ethnic groups. And to the best of our knowledge, DNA methylation analysis in Y-STR for different ethnic groups has never been done before. Complementing Y-STR data with methylation knowledge could provide population-specific information for forensic identification.
Collapse
Affiliation(s)
- Sthabile Shabalala
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa.
| | - Moses Okpeku
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa
| |
Collapse
|
3
|
张 世, 蹇 慧, 王 倩, 王 威, 丁 艳, 张 宵, 徐 冬, 杜 冰, 金 波. [Polymorphism and Mutation Rate of 20 Rapidly Mutating Y-Chromosomal Short Tandem Repeats in Chinese Han Population of Sichuan Province]. Sichuan Da Xue Xue Bao Yi Xue Ban 2023; 54:367-373. [PMID: 36949700 PMCID: PMC10409182 DOI: 10.12182/20230260308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 03/24/2023]
Abstract
Objective To explore the applicability of 20 rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) in Chinese Han population of Sichuan province. Methods Two RM Y-STR multiple amplification systems (RM1, including DYF404S1, DYF399S1, DYS547, DYS526a/b, DYS626, DYF403S1a/b, and DYS612, and RM2, including DYS1003, DYS1007, DYR88, DYS712, DYS711, DYS724, and DYF1002, with 14 RM Y-STR loci in total) and Y41SE-V1.2 (including 6 RM Y-STR loci of DYS627, DYS576, DYF387S1, DYS518, DYS570, and DYS449, 30 ordinary Y-chromosomal short tandem repeats [Y-STR] loci, and 1 Indel locus) were used for the amplification and typing of 200 unrelated males and 260 father-son pairs. The polymorphisms and mutation rates of 20 RM Y-STRs and 30 ordinary Y-STRs in Chinese Han population of Sichuan province were investigated and compared. Results In the 200 unrelated males, the gene diversity (GD) of 20 RM Y-STR loci ranged from 0.7910 to 0.9975, and there were 200 haplotypes. Haplotype diversity (HD) was 1 and the discriminative capacity (DC) was 1. A total of 198 haplotypes were found in Y41se-v1.2 (the 30 Y-STRs), with 4 cases sharing two haplotypes, the haplotype diversity being 0.9999, and the discriminative capacity being 0.99. A total of 68 mutations were found at the 20 RM Y-STRs loci in the 260 father-son pairs, and there was slightly more increase than decrease of allele repeats (1.19∶1), with the mutation rate ranging from <3.85×10 -3 (95% C I: 0.00-1.41×10 -2) to 2.69×10 -2 (95% CI: 1.09×10 -2-5.47×10 -2), and the average mutation rate being 1.19×10 -2 (95% CI: 9.20×10 -3-1.51×10 -2). The 20 RM Y-STRs and the Y41SE-V1.2 (the 30 Y-STRs) could be used to distinguish 22.3% and 13.8% father-son pairs, respectively. Conclusion The 20 RM Y-STRs have high gene and haplotype diversity and paternal lineage differentiation rate in Chinese Han population of Sichuan province, showing great potential for application in Chinese Han population of Sichuan province.
Collapse
Affiliation(s)
- 世林 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 慧 蹇
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 倩 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 威 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 艳杰 丁
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 宵 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冬冬 徐
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冰 杜
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 波 金
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| |
Collapse
|
4
|
Queiroz PR, Posso MC, Martins ÉS, Grynberg P, Togawa R, Monnerat RG. Identification of cry genes in Bacillus thuringiensis by multiplex real-time PCR. J Microbiol Methods 2023; 205:106665. [PMID: 36592897 DOI: 10.1016/j.mimet.2022.106665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Bacillus thuringiensis is an important bacterium of the group Bacillus cereus sensu lato due to its insecticidal properties. This microorganism has high genetic variability and its strains produce different Cry toxins, known as δ-endotoxins, which are mainly responsible for its toxic effect on insects that are agricultural pests or vector human diseases. Each strain can express a variety of cry genes, out of a total of 789 cry genes described so far. The detection of these genes is very important to characterize strains, as they may indicate their toxic potential. Several methods have been used to characterize B. thuringiensis strains, but one of the most common techniques is Polymerase Chain Reaction (PCR) from primers that detect the presence of cry genes. This technique has been optimized to make real-time multiplex quantitative PCR (qPCR) assays faster, more efficient, and safer, because the presence of three genes can be detected in a single reaction. In this work, a multiplex assay was developed to identify the presence of genes from the cry1A, cry1C, and cry1F families whose respective toxins are present in both bioinsecticides, and commercial transgenic plants used to control caterpillars. Specific primers were designed to identify the families of the cited genes and the system was validated with samples that were sequenced by next-generation sequencing (NGS). The system was implemented and used to characterize 214 strains. Of these, eight were submitted to conventional PCR, and the results matched, again validating the system. Thus, the application of the proposed technique allows the reliable evaluation through this system to detect the presence of the genes of the families cry1A, cry1C, and cry1F in samples of B. thuringiensis.
Collapse
Affiliation(s)
- Paulo Roberto Queiroz
- CEUB 707/907 - Campus Universitário, SEPN - Asa Norte, Brasília, DF 70790-075, Brasil.
| | - Marina Cassago Posso
- Laboratório de Bactérias Entomopatogênicas, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brasil
| | | | - Priscila Grynberg
- Laboratório de Bioinformática, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brasil
| | - Roberto Togawa
- Laboratório de Bioinformática, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brasil
| | - Rose Gomes Monnerat
- Laboratório de Bactérias Entomopatogênicas, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brasil
| |
Collapse
|
5
|
Zhou K, Peng M, Deng N, Tan Z, Xiao N. Lactase bacteria in intestinal mucosa are associated with diarrhea caused by high-fat and high-protein diet. BMC Microbiol 2022; 22:226. [PMID: 36171559 PMCID: PMC9516839 DOI: 10.1186/s12866-022-02647-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Background Excessive fat and protein in food can cause diarrhea by disturbing the intestinal microecology. Lactase is a functional enzyme strongly associated with diarrhea, while lactase bacteria in the intestine are an important source of microbial lactase. Therefore, we reconnoiter the relationship between diarrhea induced by a high-fat and high-protein diet (HFHPD) and intestinal mucosal lactase bacteria from the perspective of functional genes. Result Operational Taxonomic Units (OTUs) were 23 and 31 in the normal group (NM) and model group (MD), respectively, and 11 of these were identical. The Chao1 and Observed specie indexes in the MD were higher than those in the NM, but this was not significant (P > 0.05). Meanwhile, the Principal coordinate analysis (PCoA) and Adonis test showed that the community structures of lactase bacteria in NM and MD were significantly different (P < 0.05). In taxonomic composition, lactase bacteria on the intestinal mucosa were sourced from Actinobacteria and Proteobacteria. Where Actinobacteria were higher in NM, and Proteobacteria were higher in MD. At the genus level, Bifidobacterium was the dominant genus (over 90% of the total). Compared to NM, the abundance of Bifidobacterium were lower in MD, while MD added sources for lactase bacteria of Rhizobium, Amycolatopsis, and Cedecea. Conclusions Our data demonstrate that HFHPD altered the community structure of lactase bacteria in the intestinal mucosa, decreased the abundance of the critical lactase bacteria, and promoted the occurrence of diarrhea.
Collapse
Affiliation(s)
- Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Maijiao Peng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Na Deng
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhoujin Tan
- Hunan Key Laboratory of TCM Prescription and Syndromes Translational Medicine, Changsha, Hunan, China.,College of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Nenqun Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China.
| |
Collapse
|
6
|
Mwangi JW, Okoth OR, Kariuki MP, Piero NM. Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes. J Genet Eng Biotechnol 2021; 19:142. [PMID: 34570295 PMCID: PMC8476662 DOI: 10.1186/s43141-021-00245-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. RESULTS Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). CONCLUSION These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.
Collapse
Affiliation(s)
- Jedidah Wangari Mwangi
- Department of Biochemistry, Microbiology and Biotechnology Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya.
| | - Oduor Richard Okoth
- Department of Biochemistry, Microbiology and Biotechnology Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| | | | - Ngugi Mathew Piero
- Department of Biochemistry, Microbiology and Biotechnology Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| |
Collapse
|
7
|
Joshi B, Lemtur S, Humtsoe M, Verma K, Kumawat RK, Kushwaha P, Kumar A, Srivastav KVV, Srivastava A, Shrivastava P. Genetic portrait of 23 Y-STR loci in the Naga tribes of Nagaland, India. Int J Legal Med 2021; 136:559-560. [PMID: 34292382 DOI: 10.1007/s00414-021-02662-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
To explore the genomic diversity and forensic characterization of Naga tribes, Nagaland, haplotypes for 23 Y-STR markers have been analyzed. In this study, 203 unrelated male individuals residing in the Northeast Indian state of Nagaland were selected. A total of 203 unique haplotypes were observed. The value of gene diversity (GD) and discrimination capacity (DC) was observed as 0.999999998927955 and 1 respectively. Forensic interest parameters viz., power of discrimination (PD), polymorphic information content (PIC), and matching probability (PM) were found to be 0.999999998695503, 0.999999976671191, and 1.3 × 10-9 respectively, for the studied population. Inter-population comparison study showed that the Naga tribes were found to have a distinct gene pool which is reflected in the neighbor-joining tree, principle coordinate analysis, and heat map. This is the first genetic study on Naga tribes based on 23 Y-STR markers. The Y chromosomal STR data will be useful for forensic DNA application and will enrich the existing Indian Y-STR database.
Collapse
Affiliation(s)
- Bhawana Joshi
- Department of Forensic Science, Faculty of Science, SGT University, Gurugram, 122505, Haryana, India
| | - Sentibenla Lemtur
- Department of Forensic Science, Faculty of Science, SGT University, Gurugram, 122505, Haryana, India
| | - Marlyn Humtsoe
- Department of Forensic Science, Faculty of Science, SGT University, Gurugram, 122505, Haryana, India
| | - Kapil Verma
- Crime Scene Management Division, Forensic Science Laboratory, Govt. of NCT of Delhi, 110085, Delhi, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Pushpesh Kushwaha
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India
| | - Akshay Kumar
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India
| | - Kunwar Veer Vikram Srivastav
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India
| | - Ankit Srivastava
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, 284128, U.P, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.
| |
Collapse
|
8
|
Sahoo S, Samal R, Behera S, Biswas S, Dixit S, Kumawat RK, Chaubey G, Bhasney V, Shrivastava P. Genomic insight into Y-STR diversity in the population of Odisha, India. Int J Legal Med 2021; 135:1771-2. [PMID: 33687496 DOI: 10.1007/s00414-021-02545-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
This study evaluated the haplotype diversity of 17 Y chromosomal genetic markers among 202 unrelated males who were randomly selected in the population of Odisha, India. Out of total 196 haplotypes observed in this study, 190 were unique haplotypes. Forensic relevant parameters, viz., gene diversity (GD) and discrimination capacity (DC), were calculated as 0.999999998 and 0.970 respectively, for the studied population. The highest genetic diversity was observed at the locus DYS385a/b (0.9541) and lowest at the locus DYS437 (0.3326) among all the studied Y chromosomal loci. The polymorphic information content (PIC), power of discrimination (PD), and matching probability (PM) was found to be 0.999999965, 0.999999998, and 1.6×10-9 for the tested Y STR loci. The genetic data observed in this study would enrich the existing Y STR data of the Indian population and would also be useful for forensic application.
Collapse
|
9
|
Gao G, Kan J, Jiang C, Ahmar S, Zhang J, Yang P. Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley. Funct Integr Genomics 2020; 21:31-42. [PMID: 33169329 DOI: 10.1007/s10142-020-00759-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 11/28/2022]
Abstract
Plant-specific TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1/2 (TCP) transcription factors have known roles in inflorescence architecture. In barley, there are two family members INTERMEDIUM-C (INT-c/HvTB1-1) and COMPOSITUM 1 (COM1/HvTCP24) which are involved in the manipulation of spike architecture, whereas the participation of TCP family genes in selection from wild (Hordeum vulgare subsp. spontaneum, Hs) to cultivated barley (Hordeum vulgare subsp. vulgare, Hv) remains poorly investigated. Here, by conducting a genome-wide survey for TCP-like sequences in publicly-released datasets, 22 HsTCP and 20 HvTCP genes encoded for mature proteins were identified and assigned into two classes (I and II) based on their functional domains and the phylogenetic analysis. Each counterpart of the orthologous gene in wild and cultivated barley usually represented a similarity on the transcriptional profile across the tissues. The diversity analysis of TCPs in 90 wild barley accessions and 137 landraces with geographically-referenced passport information revealed the detectable selection at three loci including INT-c/HvTB1-1, HvPCF2, and HvPCF8. Especially, the HvPCF8 haplotypes in cultivated barley were found correlating with their geographical collection sites. There was no difference observed in either transactivation activity in yeast or subcellular localization in Nicotiana benthamiana among these haplotypes. Nevertheless, the genome-wide diversity analysis of barley TCP genes in wild and cultivated populations provided insight for future functional characterization in plant development such as spike architecture.
Collapse
Affiliation(s)
- Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sunny Ahmar
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
10
|
Oh JS, Sa KJ, Hyun DY, Cho GT, Lee JK. Assessment of genetic diversity and population structure among a collection of Korean Perilla germplasms based on SSR markers. Genes Genomics 2020; 42:1419-30. [PMID: 33113112 DOI: 10.1007/s13258-020-01013-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/16/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Information on the genetic variation of genetic resource collections is very important for both the conservation and utilization of crop germplasms in genebanks. Var. frutescens of Perilla crop is extensively cultivated in South Korea as both an oil crop and a vegetable crop. OBJECTIVES We used SSR markers to evaluate the genetic diversity, genetic relationships, and population structure of 155 accessions of var. frutescens that have been selected as genetic resources for the development of leaf vegetable cultivars and preserved in the RDA-Genebank collection from South Korea. METHODS A total of 155 accessions of var. frutescens of Perilla crop collected in South Korea were obtained from the RDA-Genebank of the Republic of Korea. We selected 20 SSR markers representing the polymorphism of and adequately amplifying all the Perilla accessions. RESULTS The average GD and PIC values were 0.642 and 0.592, respectively, with ranges of 0.244-0.935 and 0.232- 0.931. The genetic variability in the southern region of South Korea was higher than that in the central region. The clustering patterns were not clearly distinguished between the accessions of var. frutescens from the central and southern regions of South Korea. CONCLUSION These results regarding the genetic diversity and population structure of the 155 accessions of var. frutescens of South Korea provide useful information for understanding the genetic variability of this crop and selecting and managing core germplasm sets in the RDA-Genebank of the Republic of Korea.
Collapse
|
11
|
Shang L, Ding G, Wu Y, Chen S, Sun H, Bai X, Zhang J, Li W. Population genetic data of 4 multicopy Y-STR markers in Chinese. Leg Med (Tokyo) 2020; 47:101788. [PMID: 32950019 DOI: 10.1016/j.legalmed.2020.101788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 11/23/2022]
Abstract
Novel Y chromosomal STR (Y-STR) markers have been continuously discovered during the past decades, promoting the widely application of Y-STRs in the area of forensic science. Here, four multicopy Y-STR markers were focused, including DYF383S1, DYF409S1, DYF411S1 and DYF371, which are rarely reported in China and differ in the number of copies on Y chromosome. Characterization of the markers was performed in population of Hunan province, China, based on sequence analysis. Allele nomenclature and allelic ladder were then developed to avoid the disunity of typing standard. To evaluate their forensic performance, gene diversity of the four loci was investigated in 548 unrelated male individuals from Hunan population. The number of haplotype was analyzed by both conservative (C-type) and expanded approach (E-type) for markers containing more than 2 copies. As detected, there were 7, 9, 13 alleles and 15, 22, 23 haplotypes for DYF383S1, DYF409S1 and DYF411S1, respectively. Thirty-two C-types and 56 E-types were found in DYF371, indicating the highest haplotype diversity (HD) among all tested loci (0.871 and 0.888 for C-type and E-type, respectively). Two other Y-STRs (DYF409S1, DYF411S1) also showed high haplotype diversity (>0.8) in the population. Combining the four loci, discrimination capacity reached 0.505 (C-type) or 0.533 (E-type), and the total HD values exceeded 0.991. The results inferred great potential of the multicopy markers to improve the resolution of paternal identification in China population.
Collapse
|
12
|
Daudi H, Shimelis H, Mathew I, Oteng‐Frimpong R, Ojiewo C, Varshney RK. Genetic diversity and population structure of groundnut ( Arachis hypogaea L.) accessions using phenotypic traits and SSR markers: implications for rust resistance breeding. Genet Resour Crop Evol 2020; 68:581-604. [PMID: 33505123 PMCID: PMC7811514 DOI: 10.1007/s10722-020-01007-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 08/30/2020] [Indexed: 05/27/2023]
Abstract
Groundnut (Arachis hypogaea L.) is a multi-purpose legume serving millions of farmers and their value chain actors globally. Use of old poor-performing cultivars contributes to low yields (< 1 t/ha) of groundnut in sub-Saharan Africa including Tanzania. The objectives of this study were to determine the extent of genetic variation among diverse groundnut collections using phenotypic traits and simple sequence repeat (SSR) markers to select distinct and complementary genotypes for breeding. One hundred and nineteen genotypes were evaluated under field conditions for agronomic traits and susceptibility to rust and leaf spot diseases. The study was conducted in two locations across two seasons. In addition, the 119 accessions were profiled with 13 selected SSR markers. Genotype and genotype by environment interaction effects were significant (p < 0.05) for days to flowering (DTF), late leaf spot score at 85 and 100 days after planting, pod yield (PDY), kernel yield (KY), hundred seed weight (HSW) and shelling percentage (SP). Principal components analysis revealed that plant stand, KY, SP, NPP (number of pods per plant), late leaf spot and rust disease scores accounted for the largest proportion of the total variation (71.9%) among the tested genotypes. Genotypes ICGV-SM 08587 and ICGV-SM 16579 had the most stable yields across the test environments. Moderate genetic variation was recorded with mean polymorphic information content of 0.34 and gene diversity of 0.63 using the SSR markers. The majority (74%) of genotypes showed high membership coefficients to their respective sub-populations, while 26% were admixtures after structure analysis. Much of the variation (69%) was found within populations due to genotypic differences. The present study identified genotypes ICGV-SM 06737, ICGV-SM 16575, ICG 12725 and ICGV-SM 16608 to be used for development of mapping population, which will be useful for groundnut improvement. This study provided a baseline information on characterization and selection of a large sample of groundnut genotypes in Tanzania for effective breeding and systematic conservation.
Collapse
Affiliation(s)
- Happy Daudi
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Tanzania Agricultural Research Institute-Naliendele, P.O. Box 509, Mtwara, Tanzania
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Isack Mathew
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| |
Collapse
|
13
|
Kumar A, Kumar R, Kumawat RK, Mathur B, Shrivastava P, Chaubey G, Yadav RK. Genetic portrait study for 23 Y-STR loci in the population of Rajasthan, India. Int J Legal Med 2020; 134:1691-1693. [PMID: 32548759 DOI: 10.1007/s00414-020-02339-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022]
Abstract
This study was conducted to come up with data on Y-STR markers for the population of Rajasthan comprising of the western arid region of India. Y-STR analysis is an established tool in forensic DNA casework and ancestry research. We analyzed 23 Y-STRs in randomly selected 310 unrelated individuals living within the geographical area of Rajasthan to establish parameters of forensic interest. Out of 310 haplotypes, 309 unique haplotypes were observed, which revealed a high discrimination capacity with a value of 0.997 for the studied loci. The gene diversity (GD) and haplotype diversity (HD) for the studied 23 Y STRs were found to be 0.664 and 0.666, respectively. In the population of Rajasthan, locus DYS385a/b showed the highest gene diversity with a value of 0.829 among all the studied loci. The studied population showed genetic relatedness with the populations of Madhya Pradesh, Uttar Pradesh, Jharkhand, and Himachal Pradesh.
Collapse
Affiliation(s)
- Anand Kumar
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India.
| | - Rajesh Kumar
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Baiju Mathur
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, UP, India
| | | |
Collapse
|
14
|
Wang G, Ren Y, Ng TB, Streit WR, Ye X. High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu. Biotechnol Lett 2019; 41:409-18. [PMID: 30644013 DOI: 10.1007/s10529-019-02646-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform. RESULTS A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity. CONCLUSIONS High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.
Collapse
|
15
|
Bengtsson-Palme J. The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always. Microbiome 2018; 6:125. [PMID: 29981578 PMCID: PMC6035801 DOI: 10.1186/s40168-018-0508-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/25/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments. RESULTS This study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well. CONCLUSIONS The results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.
Collapse
Affiliation(s)
- Johan Bengtsson-Palme
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI, 53715, USA.
- Centre for Antibiotic Resistance research (CARe) at University of Gothenburg, Gothenburg, Sweden.
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden.
| |
Collapse
|
16
|
Long C, Liu Y, He L, Tan Q, Yu Z, Xiao N, Tan Z. Bacterial lactase genes diversity in intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics. 3 Biotech 2018; 8:176. [PMID: 29556430 PMCID: PMC5847641 DOI: 10.1007/s13205-018-1191-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/01/2018] [Indexed: 01/01/2023] Open
Abstract
The current study aimed at exploring the diversity of bacterial lactase genes in the intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics and to provide experimental basis for antibiotics-induced diarrhea. Mice model of dysbacterial diarrhea was established by gastric perfusion with mixture of cephradine capsules and gentamicin sulfate (23.33 mL kg-1 d-1), twice a day and continuously for 5 days. Intestinal mucosa from jejunum to ileum was collected, and bacterial metagenomic DNA was extracted for Miseq metagenome sequencing to carry out diversity analysis. The results showed that specific operational taxonomic units (OTUs) were 45 in the control group and 159 in the model group. The Chao1, ACE, Shannon and Simpson indices in model group were significantly higher (P < 0.01 or P < 0.05) than control group. Principal component analysis (PCA) and box chart of the control group were relatively intensive, while in the model group, they were widely dispersed. Furthermore, the inter-group box area was higher than that in the intra-group. Compared with the model group, the abundance of bacterial lactase genes in Proteobacteria from the intestinal mucosa of the control group was higher, but lower in Actinobacteria and unclassified bacteria. At the genus level, the relative abundance of bacterial species and taxon units in model group was obviously increased (P < 0.05). Our results indicate that antibiotics increased the diversity and abundance of bacterial lactase genes in the intestinal mucosa, as the abundance of Betaproteobacteria, Cupriavidus, Ewingella, Methyloversatilis, Rhodocyclaceae and Rhodocyclales. In addition, antibiotics become an additional source for lactase genes of Ewingella, Methyloversatilis, Mycobacterium, Microbacterium, Beutenberqia and Actinomyces.
Collapse
Affiliation(s)
- Chengxing Long
- Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
- College of Mathematics and Finance, Hunan University of Humanities, Science and Technology, Loudi, 417000 China
| | - Yawei Liu
- Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
| | - Lu He
- Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
| | - Qinquan Tan
- School of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Zizhen Yu
- Rongjun Hospital of Hunan Province, Changsha, 410119 Hunan China
| | - Nenqun Xiao
- Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
| | - Zhoujin Tan
- Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
| |
Collapse
|
17
|
Long CX, He L, Guo YF, Liu YW, Xiao NQ, Tan ZJ. Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea. World J Gastroenterol 2017; 23:7584-7593. [PMID: 29204058 PMCID: PMC5698251 DOI: 10.3748/wjg.v23.i42.7584] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/14/2017] [Accepted: 09/26/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.
METHODS Following 2 d of adaptive feeding, 12 specific pathogen-free Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics (23.33 mL·kg-1·d-1) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units (OTUs) was carried out after amplification and sequencing.
RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups (P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.
CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.
Collapse
Affiliation(s)
- Cheng-Xing Long
- Lu-He, Yan-Fang Guo, Ya-Wei Liu, Nen-Qun Xiao, Zhou-Jin Tan, Department of Microbiology, Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
- College of Mathematics and Finance, Hunan University of Humanities, Science and Technology, Loudi 417000, Hunan Province, China
| | | | | | | | | | | |
Collapse
|
18
|
Li W, Song Y, Zhong Z, Huang X, Wang C, Li C, Yang H, Liu H, Ren Z, Lan J, Wu K, Peng G. Population genetics of Enterocytozoon bieneusi in captive giant pandas of China. Parasit Vectors 2017; 10:499. [PMID: 29047380 PMCID: PMC5648467 DOI: 10.1186/s13071-017-2459-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/08/2017] [Indexed: 01/21/2023] Open
Abstract
Background Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. Results We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E. bieneusi population genetics. For multilocus genotype (MLG) analysis of E. bieneusi-positive isolates, the MS1, MS3, MS4, and MS7 microsatellite and minisatellite loci were amplified and sequenced in 48, 45, 50 and 47 specimens, respectively, generating ten, eight, nine and five types. We successfully amplified 36 specimens and sequenced all five loci, forming 24 MLGs. Multilocus sequence analysis revealed a strong and significant linkage disequilibrium (LD), indicating a clonal population. This result was further supported by measurements of pairwise intergenic LD and a standardized index of association (ISA) from allelic profile data. The analysis in STRUCTURE suggested three subpopulations in E. bieneusi, further confirmed using right’s fixation index (FST). Subpopulations 1 and 2 exhibited an epidemic structure, whereas subpopulation 3 had a clonal structure. Conclusions Our results describe E. bieneusi population genetics in giant pandas for the first time, improving the current understanding E. bieneusi epidemiology in the studied region. These data also benefit future studies exploring potential transmission risks from pandas to other animals, including humans.
Collapse
Affiliation(s)
- Wei Li
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Yuan Song
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Zhijun Zhong
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Xiangming Huang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | | | - Caiwu Li
- Wolong Giant Panda Base, Aba, Sichuan Province, China
| | - Haidi Yang
- Wolong Giant Panda Base, Aba, Sichuan Province, China
| | - Haifeng Liu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Zhihua Ren
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Jingchao Lan
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | - Kongju Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | - Guangneng Peng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China.
| |
Collapse
|
19
|
Mahajan R, Zargar SM, Singh R, Salgotra RK, Farhat S, Sonah H. Population Structure Analysis and Selection of Core Set among Common Bean Genotypes from Jammu and Kashmir, India. Appl Biochem Biotechnol 2016; 182:16-28. [PMID: 27817047 DOI: 10.1007/s12010-016-2307-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
Understanding the genetic diversity of a crop is useful for its effective utilization in breeding programmes. For better understanding of the genetic variability in common bean, the first and foremost step is to study its genetic diversity. In the present investigation, 138 genotypes of common bean collected from various regions of Jammu and Kashmir, India, representing major common bean growing areas of this region, were evaluated using 23 SSRs. These SSRs were found highly polymorphic and possess high values for various parameters indicating their high discriminatory power. The average PIC value observed was 0.692, with 0.730 as average gene diversity value, and 0.267 as heterozygosity. Twenty-three SSRs produced a total of 251 alleles. The dendrogram generated with un-weighted neighbour joining cluster analysis grouped genotypes into three main clusters with various degrees of sub-clustering within the clusters. The model-based STRUCTURE analysis using 23 SSR markers identified a population with 3 sub-populations which corresponds to distance-based groupings with average F ST value and expected heterozygosity of 0.1497 and 0.6696, respectively, within the sub-population, as such high level of genetic diversity was observed within the population. Further, Core Hunter II was used to identify a core set of 96 diverse genotypes. This core set of diverse 96 genotypes is a potential resource for association mapping studies and can be used by breeders as a material to make desirable genetic crosses to generate elite varieties for the fulfilling global market needs. These findings have further implications in common bean breeding as well as conservation programs.
Collapse
Affiliation(s)
- Reetika Mahajan
- School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India
| | - Sajad Majeed Zargar
- Division of Biotechnology, S K University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
| | - Ravinder Singh
- School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India
| | - Romesh Kumar Salgotra
- School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India
| | - Sufia Farhat
- School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India
| | - Humaira Sonah
- Départment de phytologie-FSAA, Université Laval, Québec, QC, G1V 0A6, Canada
| |
Collapse
|
20
|
Kwon SY, Lee HY, Kim EH, Lee EY, Shin KJ. Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. Forensic Sci Int Genet 2016; 25:132-141. [PMID: 27591816 DOI: 10.1016/j.fsigen.2016.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 08/23/2016] [Accepted: 08/27/2016] [Indexed: 12/19/2022]
Abstract
Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories.
Collapse
Affiliation(s)
- So Yeun Kwon
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Eun Hye Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Eun Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| |
Collapse
|
21
|
Zhao W, Yu S, Yang Z, Zhang Y, Zhang L, Wang R, Zhang W, Yang F, Liu A. Genotyping of Enterocytozoon bieneusi (Microsporidia) isolated from various birds in China. Infect Genet Evol 2016; 40:151-154. [PMID: 26944443 DOI: 10.1016/j.meegid.2016.02.037] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/16/2016] [Accepted: 02/27/2016] [Indexed: 11/30/2022]
Abstract
Enterocytozoon bieneusi is a common opportunistic pathogen causing diarrhea in humans and animals. However, epidemiological data on E. bieneusi infections in birds are relatively scare worldwide, especially in China. To understand the prevalence and genetic diversity of E. bieneusi in birds and to assess the zoonotic potential of bird-derived E. bieneusi isolates, 194 fecal specimens from Gruidae, Anatidae and Columbidae in Heilongjiang Province, China, were analyzed by PCR and sequencing of the single internal transcribed spacer region of the rRNA gene. The average prevalence of E. bieneusi was 22.2%, with 12.5% for Gruidae, 15.9% for Anatidae and 44.0% for Columbidae. Altogether seven genotypes of E. bieneusi were identified, including four known genotypes-Peru6 (n=29), BEB6 (n=5), D (n=3) and EbpA (n=1)-and three novel genotypes named CHN-B1 (n=1), CHN-B2 (n=3) and CHN-B3 (n=1). All the known genotypes obtained here were previously detected in humans. All the novel genotypes were clustered into the zoonotic group 1 in phylogenetic analysis. The results indicate that these birds may play a potential role in the transmission of E. bieneusi to humans.
Collapse
Affiliation(s)
- Wei Zhao
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Siyang Yu
- Department of Laboratory Medicine, Xiangya Medical School, Central South University, Changsha, Hunan 410008, China
| | - Ziyin Yang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yichi Zhang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Weizhe Zhang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Fengkun Yang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aiqin Liu
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| |
Collapse
|
22
|
Raghunath R, Krishnamoorthy K, Balasubramanian L, Kunka Mohanram R. Genetic portrait of Tamil non-tribal and Irula tribal population using Y chromosome STR markers. Int J Legal Med 2015; 130:367-9. [PMID: 26024794 DOI: 10.1007/s00414-015-1207-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 11/28/2022]
Abstract
The 17 Y chromosomal short tandem repeat loci included in the AmpFlSTR® Yfiler™ PCR Amplification Kit were used to analyse the genetic diversity of 517 unrelated males representing the non-tribal and Irula tribal population of Tamil Nadu. A total of 392 unique haplotypes were identified among the 400 non-tribal samples whereas 111 were observed among the 117 Irula tribal samples. Rare alleles for the loci DYS458, DYS635 and YGATAH4.1 were also observed in both population. The haplotype diversity for the non-tribal and Irula tribal population were found to be 0.9999, and the gene diversity ranged from 0.2041 (DYS391) to 0.9612 (DYS385). Comparison of the test population with 26 national and global population using principal coordinate analysis (PCoA) and determination of the genetic distance matrix using phylogenetic molecular analysis indicate a clustering of the Tamil Nadu non-tribal and Irula tribal population away from other unrelated population and proximity towards some Indo-European (IE) and Asian population. Data are available in the Y chromosome haplotype reference database (YHRD) under accession number YA004055 for Tamil non-tribal and YA004056 for the Irula tribal group.
Collapse
Affiliation(s)
- Rajshree Raghunath
- Forensic Sciences Department, Mylapore, Chennai, Tamil Nadu, 600 004, India. .,Department of Biotechnology, SRM University, Kattankulathur, Chennai, Tamil Nadu, 603 203, India.
| | | | - Lakshmi Balasubramanian
- Forensic Sciences Department, Mylapore, Chennai, Tamil Nadu, 600 004, India.,Department of Biotechnology, SRM University, Kattankulathur, Chennai, Tamil Nadu, 603 203, India
| | | |
Collapse
|
23
|
Zhao W, Zhang W, Yang D, Zhang L, Wang R, Liu A. Prevalence of Enterocytozoon bieneusi and genetic diversity of ITS genotypes in sheep and goats in China. Infect Genet Evol 2015; 32:265-70. [PMID: 25818401 DOI: 10.1016/j.meegid.2015.03.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/16/2015] [Accepted: 03/21/2015] [Indexed: 11/30/2022]
Abstract
Enterocytozoon bieneusi is the most common microsporidia species, recognized in more than 90% cases of human microsporidiosis and has been found in a variety of animal hosts. To explore the prevalence of E. bieneusi in sheep and goats in China, genetic diversity and zoonotic potential of E. bieneusi, 193 fecal specimens from 138 sheep and 55 goats from eight farms in Heilongjiang Province, China were analyzed for the occurrence of E. bieneusi by PCR and sequencing of the single internal transcribed spacer (ITS) of the rRNA gene. The average prevalence of E. bieneusi was 22.3% (43/193), with 22.5% (31/138) for sheep versus 21.8% (12/55) for goats. Altogether 14 genotypes of E. bieneusi were identified, including six known genotypes-BEB6 (n=15), Peru6 (8), D (n=6), O (n=3), EbpC (n=2), and EbpA (n=1)-and eight novel genotypes named COS-I to COS-VII and COG-I (one each). Six of the genotypes were previously detected in humans. In phylogenetic analysis, the five novel genotypes COG-I and CCOS-IV to COS-VII were clustered into group 1 with zoonotic potential. These results indicate that these animals may play a potential role in the transmission of E. bieneusi to humans.
Collapse
Affiliation(s)
- Wei Zhao
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Weizhe Zhang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Dong Yang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Aiqin Liu
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| |
Collapse
|
24
|
Spagnuolo V, De Nicola F, Terracciano S, Bargagli R, Baldantoni D, Monaci F, Alfani A, Giordano S. Persistent pollutants and the patchiness of urban green areas as drivers of genetic richness in the epiphytic moss Leptodon smithii. J Environ Sci (China) 2014; 26:2493-2499. [PMID: 25499497 DOI: 10.1016/j.jes.2014.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 04/15/2014] [Accepted: 06/17/2014] [Indexed: 06/04/2023]
Abstract
We determined genetic variation and metal and polycyclic aromatic hydrocarbon concentrations in Leptodon smithii moss collected in holm oak stands at cities, outskirts and remote areas of Campania and Tuscany (Italy) to investigate if anthropogenic pressure (pollutant emissions and land use change) affects moss genetic richness. In both regions, metal and polycyclic aromatic hydrocarbon concentrations reflected the trend urban>outskirts>remote areas, excepting Tuscany remote site. In both regions, the moss gene diversity increased from urban to remote areas. The findings suggest the extent and the fragmentation of urban green areas, as drivers of moss genetic richness.
Collapse
Affiliation(s)
- Valeria Spagnuolo
- Department of Biology, University of Naples Federico II, via Cinthia 4, Naples 80126, Italy.
| | - Flavia De Nicola
- Department of Science and Technology, University of Sannio, Via Port'Arsa 11, Benevento 82100, Italy.
| | - Stefano Terracciano
- Department of Biology, University of Naples Federico II, via Cinthia 4, Naples 80126, Italy
| | - Roberto Bargagli
- Department of Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
| | - Daniela Baldantoni
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Fabrizio Monaci
- Department of Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
| | - Anna Alfani
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Simonetta Giordano
- Department of Biology, University of Naples Federico II, via Cinthia 4, Naples 80126, Italy
| |
Collapse
|
25
|
Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MMD, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LSD, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014; 12:12-23. [PMID: 24854874 PMCID: PMC4127773 DOI: 10.1016/j.fsigen.2014.04.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/19/2014] [Indexed: 02/05/2023]
Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
Collapse
Affiliation(s)
- Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Renato Salazar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | | | - Lorna H Santos
- Philippine National Police Crime Laboratory, Quezon City, Philippines
| | - Katja Anslinger
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Birgit Bayer
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | - Balazs Egyed
- GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Beate Balitzki
- Institut für Rechtsmedizin, Universität Basel, Switzerland
| | | | - David Ballard
- Department of Forensic and Analytical Science, King's College London, London, UK
| | | | - Xinia Barrantes
- Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
| | | | - Tina Wiest
- Landeskriminalamt Baden-Württemberg, Germany
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA
| | - Carey Davis
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
| | - Bruce Budowle
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Helen Burri
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | - Urs Borer
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | | | - Elizeu F Carvalho
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | - Patricia M Domingues
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | | | - Michael D Coble
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Carolyn R Hill
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Maria E D'Amato
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Sean Davison
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Ronny Decorte
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Maarten H D Larmuseau
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Claudio Ottoni
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Olga Rickards
- Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Jiang
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Tadeusz Dobosz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - Anna Jonkisz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - William E Frank
- Illinois State Police, Research & Development Laboratory, Springfield, USA
| | - Ivana Furac
- Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
| | - Christian Gehrig
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Vincent Castella
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Branka Grskovic
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Zagreb, Croatia
| | - Cordula Haas
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | - Jana Wobst
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | | | | | - Katsuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Di Zhou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Yan Li
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | - Shenglan Chen
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | | | | | - Zlatko Jakovski
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Tanja Ilievska
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Anja E Klann
- Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
| | | | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aikaterini Kondili
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Penelope Miniati
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Maria Vouropoulou
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Lejla Kovacevic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanovic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Iris Lindner
- Institut für Rechtsmedizin, Universität Rostock, Germany
| | - Issam Mansour
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Mouayyad Al-Azem
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Ansar El Andari
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Miguel Marino
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Sandra Furfuro
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Laura Locarno
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Pablo Martín
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Gracia M Luque
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | | | - Helena Moreira
- Departamento de Biologia, Universidade de Aveiro, Portugal
| | - Natsuko Mizuno
- National Research Institute of Police Science, Chiba, Japan
| | | | - Rodrigo S Moura Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
| | | | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Michael Kohl
- Institut für Rechtsmedizin, Universität Leipzig, Germany
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xianping Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | - Baowen Cheng
- Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
| | - Carolina Núñez
- BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
| | | | - Jill K Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Valerio Onofri
- Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | - Horolma Pamjav
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Antonia Volgyi
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Gusztav Barany
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Ryszard Pawlowski
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Agnieszka Maciejewska
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Susi Pelotti
- Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
| | - Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | - Christopher Phillips
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Jorge Cárdenas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Danel Rey-Gonzalez
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Francesca Brisighelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Department of Zoology, University of Oxford, Oxford, UK
| | - Ulises Toscanini
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - Andrea Piccinini
- Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
| | - Marilidia Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Stefania L Baldassarra
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | | | | | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Antti Sajantila
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Department of Forensic Medicine, University of Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Evelyn Guevara
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Jazelyn Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Maria Corazon De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Jae Joseph Russell Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Ulrike Schmidt
- Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
| | | | - Pekka Saukko
- Department of Forensic Medicine, University of Turku, Finland
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Miriam Sirker
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Iulia Skitsa
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Alexandra Ampati
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Tobi-Gail Smith
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
| | | | - Vlastimil Stenzl
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Thomas Capal
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Helena Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Stefania Turrina
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Domenico De Leo
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Andrea Verzeletti
- Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, UK
| | | | | | | | | | | | - Rita Y Y Yong
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.
| |
Collapse
|
26
|
Gao Y, Wang S, Xu D, Yu H, Wu L, Lin Q, Hu Y, Li X, He Z, Deng Y, Zhou J, Yang Y. GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient. Genom Data 2014; 2:132-4. [PMID: 26484083 PMCID: PMC4535962 DOI: 10.1016/j.gdata.2014.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/03/2014] [Accepted: 06/03/2014] [Indexed: 11/18/2022]
Abstract
To examine microbial responses to climate change, we used a microarray-based metagenomics tool named GeoChip 4.0 to profile soil microbial functional genes along four sites/elevations of a Tibetan mountainous grassland. We found that microbial communities differed among four elevations. Soil pH, temperature, NH4+–N and vegetation diversity were four major attributes affecting soil microbial communities. Here we describe in details the experiment design, the data normalization process, soil and vegetation analyses associated with the study published on ISME Journal in 2014 [1], whose raw data have been uploaded to Gene Expression Omnibus (accession number GSM1185243).
Collapse
Affiliation(s)
- Ying Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shiping Wang
- Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China
| | - Depeng Xu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hao Yu
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Linwei Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qiaoyan Lin
- Key Laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yigang Hu
- Key Laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Shapotou Desert Experiment and Research Station, Cold and Arid Regions and Environmental & Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiangzhen Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Ye Deng
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Corresponding author. Tel.: + 86 10 62784692; fax: + 86 10 62794006.
| |
Collapse
|
27
|
Abstract
BACKGROUND Genes encoding KIR receptors are clustered in one of the most variable regions of the human genome. KIR gene frequencies vary in worldwide populations and reveal high probability of individuals differing in their gene content. AIM This study aimed to investigate KIR diversity among the northern Indian population who share features with either Western Eurasian or East Asian populations. It sought to decipher how northern Indians are associated phylogenetically with global populations whilst also focusing on differentiation of populations. SUBJECTS AND METHODS This paper studied 867 northern Indians using PCR-SSP. Gene and genotypic frequencies were calculated, using statistical analyses. Findings were compared against 76 global populations of differing ethnicities. RESULTS This northern Indian population shared characteristics with Western Eurasian or Asian Indian populations, as is evident from genetic distance, clustered heatmap, phylogenetic assessment and principal component analysis. The findings are consistent with the demographic history of northern India, including specific features, such as presence of comparatively high KIR B-haplotype as compared to A-haplotype. CONCLUSION KIR frequencies and profiles of northern Indians were more similar to Western Eurasians, Africans and Asian Indians. This may suggest that KIR genes are under constant evolutionary pressures and selection, which may be linked to different invading pathogens.
Collapse
Affiliation(s)
- Swayam Prakash
- School of Biotechnology, Kalinga Institute of Industrial Technology University , Bhubaneswar, Odisha , India
| | | | | | | | | |
Collapse
|
28
|
Valadkhani Z, Kazemi F, Hassan N, Aghighi Z, Esmaili I, Talebi M. Gene Diversity of Trichomonas vaginalis Isolates. Iran J Parasitol 2011; 6:101-6. [PMID: 22347304 PMCID: PMC3279894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 07/29/2011] [Indexed: 10/24/2022]
Abstract
BACKGROUND Trichomonas vaginalis is protozoan parasite responsible for trichomoniasis and is more common in high-risk behavior group such as prostitute individuals. Interest in trichomoniasis is due to increase one's susceptibility to viruses such as herpes, human papillomavirus and HIV. The aim of this study was to find genotypic differences between the isolates. METHODS Forty isolates from prisoners' women in Tehran province were used in this study. The random amplified polymorphic DNA (RAPD) technique was used to determine genetic differences among isolates and was correlated with patient's records. By each primer the banding pattern size of each isolates was scored (bp), genetic differences were studied, and the genealogical tree was constructed by using NTSYS software program and UPGMA method. RESULTS The least number of bands were seen by using primer OPD8 and the most by using OPD3. Results showed no significant difference in isolates from different geographical areas in Iran. By using primer OPD1 specific amplified fragment with length 1300 base pair were found in only 8 isolates. All these isolates were belonged to addicted women; however, six belonged to asymptomatic patients and two to symptomatic ones. CONCLUSION There was not much genetic diversity in T vaginalis isolates from three different geographical areas.
Collapse
Affiliation(s)
- Z Valadkhani
- Dept. of Parasitology, Pasteur Institute of Iran, Tehran, Iran,Corresponding Author: Tel/Fax 021- 66968855.
| | - F Kazemi
- Dept. of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - N Hassan
- Dept. of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Z Aghighi
- Dept. of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - I Esmaili
- Tehran Prison HQ, Research Council of Tehran, Iran
| | - M Talebi
- Dept. of Agricultural Biotechnology, Collage of Agriculture, Isfahan University of Technology, Isfahan, Iran
| |
Collapse
|