1
|
Gahlyan RK, Vohra V, Chhotaray S, Kataria RS. Diversity assessment of a lesser known buffalo population from Central India and its comparative evaluation reveals presence of sufficient genetic variation and absence of selection. Anim Biotechnol 2024; 35:2305550. [PMID: 38270453 DOI: 10.1080/10495398.2024.2305550] [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] [Indexed: 01/26/2024]
Abstract
Planned breeding and conservation strategies for a lesser-known population require an assessment of complete genetic diversity and population structure analysis in addition to its morphometric characteristics. In the present study, a comparative analysis of the genetic structure of a rare buffalo population, namely Chhattisgarhi, was extensively studied using a panel of FAO-recommended microsatellite markers along with well-established breeds namely Murrah, Nili-Ravi, Gojri, Kalahandi, and Nagpuri. Mode shift analysis indicated the absence of genetic bottleneck in the recent past. Assessment of genetic diversity indices across all loci indicated the presence of sufficient genetic variation within and between populations. Analysis of molecular variance between the six different buffalo populations attributed 19.05% of the variations to between-population differentiation. Cluster analyses using DAPC and Bayesian approach along with the phylogenetic tree based on UPGMA grouped six populations into three groups. The Chhattisgarhi population was revealed to be genetically closer to Nagpuri and Kalahandi populations. The study reveals the presence of sufficient genetic diversity within the Chhattisgarhi population and indicates the absence of a systematic selection program. We suggest improvement and conservation programs should be planned for this breed in the near future through short-term selection.
Collapse
Affiliation(s)
- Rajesh Kumar Gahlyan
- Animal Genetics Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vikas Vohra
- Animal Genetics Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Supriya Chhotaray
- Animal Genetics Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - R S Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| |
Collapse
|
2
|
Li X, Li P, Tang W, Zheng J, Fan F, Jiang X, Li Z, Fang Y. Simultaneous determination of subspecies and geographic origins of 110 rice cultivars by microsatellite markers. Food Chem 2024; 445:138657. [PMID: 38354640 DOI: 10.1016/j.foodchem.2024.138657] [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: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Rice varieties of different subspecies types (indica rice and japonica rice) across various geographical origins (Hunan, Jiangsu, and Northeast China) were monitored using microsatellite markers (simple sequence repeats, SSR). 110 representative rice cultivars were collected from the main crop areas. Multiple methods including clustering analysis (neighbor-joining (NJ) method, unweighted pair-group method with arithmetic mean (UPGMA) method), principal component analysis (PCA) and model-based grouping were applied. The study revealed that 25 pairs of SSR markers exhibited a broad range of polymorphism information content (PIC) values, ranging from 0.240 to 0.830. Furthermore, our study successfully achieved a higher overall mean correct rate of 99.09% in determining the geographical origin of rice. Simultaneously, it accurately classified indica rice and japonica rice. These findings are significant as they provide an SSR fingerprint of 110 high-quality rice cultivars, serving as a valuable scientific resource for the detection of rice adulteration and traceability of its origin.
Collapse
Affiliation(s)
- Xinyue Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Peng Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Wenqian Tang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Jiayu Zheng
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Xiaoyi Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Ziqian Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Yong Fang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China.
| |
Collapse
|
3
|
Ablondi M, Stocco G, Cortellari M, Carta A, Summer A, Negro A, Grande S, Crepaldi P, Cipolat-Gotet C, Biffani S. Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds. J Anim Breed Genet 2024; 141:278-290. [PMID: 38058229 DOI: 10.1111/jbg.12839] [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: 06/26/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023]
Abstract
Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle. A major difficulty during this transition period is the need of SNP data for parents and offspring, which in most cases is not yet feasible due to the genotyping cost. To overcome the unavailability of same genotyping platform during the transition period, in this study we aimed to assess the feasibility of a MS imputation pipeline from SNPs in four native sheep dairy breeds: Comisana (N = 331), Massese (N = 210), Delle Langhe (N = 59) and Sarda (N = 1003). Those sheep were genotyped for 11 MS and with the Ovine SNP50 Bead Chip. Prior to imputation, a quality control (QC) was performed, and SNPs located within a window of 2 Mb from each MS were selected. The core of the developed pipeline was made up of three steps: (a) storing of both MS and SNP data in a Variant Call Format file, (b) masking MS information in a random sample of individuals (10%), (c) imputing masked MS based on non-missing individuals (90%) using an imputation program. The feasability of the proposed methodology was assessed also among different training - testing split ratio, population size, number of flanking SNPs as well as within and among breeds. The accuracy of the MS imputation was assessed based on the genotype concordance as well as at parentage verification level in a subset of animals in which assigned parents' MS were available. A total of 8 MS passed the QC, and 505 SNPs were located within the ±2 Mb window from each MS, with an average of 63 SNPs per MS. The results were encouraging since when excluding the worst imputed MS (OARAE129), and regardless on the analyses performed (within and across breeds) for all breeds, we achieved an overall concordance rate over 94%. In addition, on average, the imputed offspring MS resulted in equivalent parentage outcome in 94% of the cases when compared to verification using original MS, highlighting both the feasibility and the eventual practical advantage of using this imputation pipeline.
Collapse
Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, Università degli studi di Parma, Parma, Italy
| | - Giorgia Stocco
- Department of Veterinary Science, Università degli studi di Parma, Parma, Italy
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, Sassari, Italy
| | - Andrea Summer
- Department of Veterinary Science, Università degli studi di Parma, Parma, Italy
| | - Alessio Negro
- Ufficio Studi, Associazione Nazionale della Pastorizia, Rome, Italy
| | - Silverio Grande
- Ufficio Studi, Associazione Nazionale della Pastorizia, Rome, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | | | - Stefano Biffani
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biologia e Biotecnologia Agraria (IBBA), Milan, Italy
| |
Collapse
|
4
|
Ochoa-Aristizábal AM, Márquez EJ. Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia. PLoS One 2024; 19:e0302273. [PMID: 38625982 DOI: 10.1371/journal.pone.0302273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/29/2024] [Indexed: 04/18/2024] Open
Abstract
Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.
Collapse
Affiliation(s)
- Ana Maria Ochoa-Aristizábal
- Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Facultad de Ciencias Universidad Nacional de Colombia - Sede Medellín, Medellín, Antioquia, Colombia
| | - Edna Judith Márquez
- Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Facultad de Ciencias Universidad Nacional de Colombia - Sede Medellín, Medellín, Antioquia, Colombia
| |
Collapse
|
5
|
Tajeddin N, Arabfard M, Alizadeh S, Salesi M, Khamse S, Delbari A, Ohadi M. Novel islands of GGC and GCC repeats coincide with human evolution. Gene 2024; 902:148194. [PMID: 38262548 DOI: 10.1016/j.gene.2024.148194] [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: 08/21/2023] [Revised: 10/29/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored. RESULTS In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions. CONCLUSION We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.
Collapse
Affiliation(s)
- N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| |
Collapse
|
6
|
Purificacion M, Shah RBM, De Meeûs T, Bakar SB, Savantil AB, Yusof MM, Amalin D, Nguyen H, Sulistyowati E, Budiman A, Ekayanti A, Niogret J, Ravel S, Vreysen MJB, Abd-Alla AMM. Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae). PLoS One 2024; 19:e0297662. [PMID: 38603675 PMCID: PMC11008836 DOI: 10.1371/journal.pone.0297662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 04/13/2024] Open
Abstract
The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.
Collapse
Affiliation(s)
- Marynold Purificacion
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Roslina Binti Mohd Shah
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Thierry De Meeûs
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
- IRD, UMR Intertryp, Cirad, Campus International de Baillarguet, Montpellier, France
| | | | - Anisah Bintil Savantil
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Meriam Mohd Yusof
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Divina Amalin
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Hien Nguyen
- Plant Protection Research Institute, Duc Thang, Hanoi, Vietnam
| | | | - Aris Budiman
- Indonesian Coffee and Cocoa Research Institute, Jember, Indonesia
| | - Arni Ekayanti
- Mars Cocoa Research Centre, Mars Wrigley, Sulawesi Selatan, Indonesia
| | - Jerome Niogret
- Mars Wrigley, Centre for Tropical Environmental & Sustainability Science, James Cook University Nguma-bada Campus, Smithfield, Australia
| | - Sophie Ravel
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Adly M. M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| |
Collapse
|
7
|
Uppili B, Faruq M. STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. Database (Oxford) 2024; 2024:baae020. [PMID: 38602506 PMCID: PMC11008502 DOI: 10.1093/database/baae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/10/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Short Tandem Repeats (STRs) are genetic markers made up of repeating DNA sequences. The variations of the STRs are widely studied in forensic analysis, population studies and genetic testing for a variety of neuromuscular disorders. Understanding polymorphic STR variation and its cause is crucial for deciphering genetic information and finding links to various disorders. In this paper, we present STRIDE-DB, a novel and unique platform to explore STR Instability and its Phenotypic Relevance, and a comprehensive database of STRs in the human genome. We utilized RepeatMasker to identify all the STRs in the human genome (hg19) and combined it with frequency data from the 1000 Genomes Project. STRIDE-DB, a user-friendly resource, plays a pivotal role in investigating the relationship between STR variation, instability and phenotype. By harnessing data from genome-wide association studies (GWAS), ClinVar database, Alu loci, Haploblocks in genome and Conservation of the STRs, it serves as an important tool for researchers exploring the variability of STRs in the human genome and its direct impact on phenotypes. STRIDE-DB has its broad applicability and significance in various research domains like forensic sciences and other repeat expansion disorders. Database URL: https://stridedb.igib.res.in.
Collapse
Affiliation(s)
- Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
- CSIR-HRDC Campus, Academy for Scientific and Innovative Research, Ghaziabad 201002, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
| |
Collapse
|
8
|
Ning Y, Liu D, Gu J, Zhang Y, Roberts NJ, Guskov VY, Sun J, Liu D, Gong M, Qi J, He Z, Shi C, Jiang G. The genetic status and rescue measure for a geographically isolated population of Amur tigers. Sci Rep 2024; 14:8088. [PMID: 38582794 PMCID: PMC10998829 DOI: 10.1038/s41598-024-58746-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 04/02/2024] [Indexed: 04/08/2024] Open
Abstract
The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.
Collapse
Affiliation(s)
- Yao Ning
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Dongqi Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jiayin Gu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Yifei Zhang
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Nathan James Roberts
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Valentin Yu Guskov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences (FSCEATB FEB RAS), Vladivostok, Russian Federation
| | - Jiale Sun
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Dan Liu
- Siberian Tiger Park, Harbin, 150028, Heilongjiang, China
| | - Ming Gong
- Siberian Tiger Park, Harbin, 150028, Heilongjiang, China
| | - Jinzhe Qi
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zhijian He
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Chunmei Shi
- College of Mathematics and Computer Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Guangshun Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.
| |
Collapse
|
9
|
Srithawong S, Muisuk K, Prakhun N, Tungpairojwong N, Kutanan W. Forensic efficiency and genetic polymorphisms of 12 X-chromosomal STR loci in Northeastern Thai populations. Mol Genet Genomics 2024; 299:42. [PMID: 38568251 DOI: 10.1007/s00438-024-02134-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Northeastern Thailand comprises one-third of the country and is home to various populations, with Lao Isan constituting the majority, while others are considered minority groups. Previous studies on forensic short tandem repeats (STRs) in Thailand predominantly focused on autosomal STRs but there was a paucity of X-STRs, exclusively reported from the North and Central regions of the country. In this study, we have newly established a 12 X-STRs from a total of 896 samples from Northeastern Thailand, encompassing Lao Isan as the major group in the region, alongside nine minor populations (Khmer, Mon, Nyahkur, Bru, Kuy, Phutai, Kalueang, Nyaw, and Saek). Across all ten populations, the combined powers of discrimination in both genders were high and the combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were also high (> 0.99999). DXS10148 emerged as the most informative marker, while DXS7423 was identified as the least informative. Genetic comparison based on X-STRs frequency supported genetic distinction of cerain minor groups such as Kuy, Saek and Nyahkur from other northeastern Thai groups as well as genetic differences according to the geographic region of Thai groups (Northeast, North and Central). In sum, the overall results on population genetics are in agreement with earlier reports on other genetic systems, indicating the informativeness of X-STRs for use in anthropological genetics studies. From a forensic perspective, despite the limitations of small sample sizes for minority groups, the present results contribute to filling the gap in the reference X-STRs database of the major group Lao Isan, providing valuable frequency data for forensic applications in Thailand and neighboring countries.
Collapse
Affiliation(s)
- Suparat Srithawong
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Kanha Muisuk
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nonglak Prakhun
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | | | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.
- Department of Biology, Faculty of Science, Naresuan University, Pitsanulok, Thailand.
| |
Collapse
|
10
|
Fišarová L, Šurinová M, Jarošová A, Krejčík J, Vosátka M. Evidence of the Ability of Microsatellite Method to Distinguish Cannabis Strains with High Cannabinoid Content. Cannabis Cannabinoid Res 2024; 9:513-522. [PMID: 36695671 DOI: 10.1089/can.2022.0272] [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] [Indexed: 01/26/2023] Open
Abstract
Introduction: Cannabis is a plant with high potential for use in several sectors of the industry; however, it is also a controversial crop due to its tetrahydrocannabinol (THC) content. Moreover, the plant has a rather unclarified classification. Traditionally, two types of Cannabis have been distinguished, hemp as a source of fiber and low THC content, and marijuana with high THC levels, which is used as a drug. With the increasing use of CBD strains and wide range of commercially used THC strains, it is becoming paramount to be able to develop an easy and reliable method for Cannabis strain differentiation. The use of simple sequence repeat markers, or microsatellites, seems to be an applicable choice. Materials and Methods: In this study, 52 strains of Cannabis with variable cannabinoid content were collected from growers from different geographical regions and analyzed using 17 different microsatellite markers. For more precise differentiation, five strains were selected and a higher number of individuals of each were analyzed. Results: Fragment analysis and cluster analysis showed that when one to three individual plants per strain were analyzed, the method was able to classify these samples into distinguishable groups with similar gene structure. They also revealed that when a larger sample set was used (10 individual plants per strain), highly specific strain clusters could be fully discriminated. Conclusion: Our study involved the highest number of cannabinoid-rich strains up to now and showed that the microsatellite method can be used to reliably differentiate Cannabis strains and show their relationships.
Collapse
Affiliation(s)
- Lenka Fišarová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Mária Šurinová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Andrea Jarošová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Josef Krejčík
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Miroslav Vosátka
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| |
Collapse
|
11
|
Oketch JW, Wain LV, Hollox EJ. A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples. PLoS One 2024; 19:e0300545. [PMID: 38558075 PMCID: PMC10984476 DOI: 10.1371/journal.pone.0300545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.
Collapse
Affiliation(s)
- John W. Oketch
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
12
|
Kim KR, Kim KY, Song HY. Genetic Structure and Diversity of Hatchery and Wild Populations of Yellow Catfish Tachysurus fulvidraco (Siluriformes: Bagridae) from Korea. Int J Mol Sci 2024; 25:3923. [PMID: 38612732 PMCID: PMC11011370 DOI: 10.3390/ijms25073923] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from -0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco.
Collapse
Affiliation(s)
- Kang-Rae Kim
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan 31538, Republic of Korea;
| | - Keun-Yong Kim
- Department of Genetic Analysis, AquaGenTech Co., Ltd., Busan 48300, Republic of Korea;
| | - Ha Yoon Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, Geumsan 32762, Republic of Korea
| |
Collapse
|
13
|
Zeye MMJ, Ouedraogo SY, Bado P, Zoure AA, Djigma FW, Wu X, Simpore J. Forensic autosomal and gonosomal short tandem repeat marker reference database for populations in Burkina Faso. Sci Rep 2024; 14:7369. [PMID: 38548827 PMCID: PMC10979005 DOI: 10.1038/s41598-024-58179-4] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/26/2024] [Indexed: 04/01/2024] Open
Abstract
Tandem repeat genetic profiles used in forensic applications varies between populations. Despite the diversity and security issues in the Sahel that require the identification of victims (soldiers and civilians), Burkina Faso (BF) remains understudied. To fill this information gap, 396 unrelated individuals from BF were genotyped using a MICROREADER 21 ID System kit. All 20 short tandem repeat (STR) loci tested passed the Hardy-Weinberg equilibrium (HWE) test. The combined powers of exclusion for duos (CPE duos) and trios (CPE trios) for the 20 tested loci were 0.9999998 and 0.9999307, respectively. The probability that two individuals would share the same DNA profiles among the BF population was 9.80898 × 10-26. For the X-chromosome STR analysis, 292 individuals were included in this study using a MICROREADER 19X Direct ID System kit. Among the 19 loci, no significant deviations from HWE test were observed in female samples after Bonferroni correction (p < 0.05/19 = 0.0026), except for loci GATA165B12 and DXS7423. The results showed that the combined power of exclusion (CPE) and the combined power of discrimination in females (CPDF) and males (CPDM) were 0.999999760893, 0.999999999992, and 1, respectively. Comparison with other African sub-populations showed that geographical proximity is a reliable indicator of genetic relatedness.
Collapse
Affiliation(s)
- Moutanou Modeste Judes Zeye
- Department of Medical Parasitology, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
- Laboratory of Molecular Biology and Genetics (LMBG) (Labiogene), University Joseph KI-ZERBO, CERBA/LABIOGENE, 01, BP 364, Ouagadougou 01, Burkina Faso
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Serge Yannick Ouedraogo
- Department of Oncology, School of Clinical Medicine, Shandong Cancer Hospital, Shandong First Medical University, Shandong Academy of Medical Sciences, 6699 Qingdao Road, Huaiyin District, Jinan, 250000, Shandong, People's Republic of China
- Laboratory of Molecular Biology and Genetics (LMBG) (Labiogene), University Joseph KI-ZERBO, CERBA/LABIOGENE, 01, BP 364, Ouagadougou 01, Burkina Faso
| | - Prosper Bado
- Laboratory of Molecular Biology and Genetics (LMBG) (Labiogene), University Joseph KI-ZERBO, CERBA/LABIOGENE, 01, BP 364, Ouagadougou 01, Burkina Faso
| | - Abdou Azaque Zoure
- Department of Biomedical and Public Health, Research Institute of Health Sciences (IRSS/CNRST), 03 BP 7192, Ouagadougou 01, Burkina Faso
| | - Florencia W Djigma
- Laboratory of Molecular Biology and Genetics (LMBG) (Labiogene), University Joseph KI-ZERBO, CERBA/LABIOGENE, 01, BP 364, Ouagadougou 01, Burkina Faso
| | - Xiang Wu
- Department of Medical Parasitology, School of Basic Medical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LMBG) (Labiogene), University Joseph KI-ZERBO, CERBA/LABIOGENE, 01, BP 364, Ouagadougou 01, Burkina Faso.
| |
Collapse
|
14
|
Koshiishi Y, Wada K. Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq. Sci Rep 2024; 14:6982. [PMID: 38523157 PMCID: PMC10961305 DOI: 10.1038/s41598-024-57032-y] [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: 12/05/2023] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
The emu is a novel poultry species in Japan. However, Japanese farmed emu populations have reduced genetic diversity owing to inbreeding. We have previously suggested that there are genetic resources in the Tohoku Safari Park (TSP) and Fuji/Kakegawa Kachoen Garden Park (FGP/KGP) to extend the genetic diversity of commercial emu farms based on microsatellite (SSR) and mitochondrial DNA. However, those markers provide relatively poor information. Thus, we investigated the genetic structure of farmed Japanese populations based on a large-scale genotyping system using RAD-seq and verified the usefulness of TSP and FGP/KGP as genetic resources for expanding genetic diversity. Admixture, phylogenetic, and principal component analyses based on 28,676 SNPs showed that TSP individuals were ancestors in the Okhotsk Emu Farm (OEF). FGP/KGP individuals showed a unique genetic component that differed from that of the others. We have previously reported that the mitochondrial haplotypes of FGP/KGP were shared with an isolated wild population in eastern Australia. These results suggest that FGP/KGP individuals originated from an eastern Australia isolated population different from other populations including ancestral of OEF/TSP. Our results would provide information for the development of Japanese emu farms and industry and for the conservation of genetic resources in the Australian wild emu.
Collapse
Affiliation(s)
- Yuichi Koshiishi
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502, Japan.
| | - Kenta Wada
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
| |
Collapse
|
15
|
Kamdem NG, Sergeant S, Vercruysse C, Deblauwe V, Sonké B, Hardy OJ. Development and characterization of nuclear microsatellite markers for the African walnut Coula edulis Baill (Coulaceae). Mol Biol Rep 2024; 51:438. [PMID: 38520482 DOI: 10.1007/s11033-024-09373-0] [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: 10/17/2023] [Accepted: 02/21/2024] [Indexed: 03/25/2024]
Abstract
PREMISE OF THE STUDY Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow. METHODS AND RESULTS A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa. CONCLUSIONS The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts.
Collapse
Affiliation(s)
- Narcisse Guy Kamdem
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. D. Roosevelt 50, Brussels, B-1050, Belgium.
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, B.P. 047, Yaounde, Cameroon.
| | - Saskia Sergeant
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. D. Roosevelt 50, Brussels, B-1050, Belgium
| | - Camille Vercruysse
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. D. Roosevelt 50, Brussels, B-1050, Belgium
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and Sustainability, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture (IITA), Yaoundé, Cameroon
| | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, B.P. 047, Yaounde, Cameroon
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. D. Roosevelt 50, Brussels, B-1050, Belgium
| |
Collapse
|
16
|
López-Armenta M, Álvarez-Sánchez ME, León-Campos C, Gonzalez-Sobrino BZ, Rangel-Villalobos H, Muñoz-Valle JF, Sánchez-Méndez AD, Aguilar-Velázquez JA. Analysis of 26 STR loci (PowerPlex® Fusion 6C System) in a mestizo population from Mexico city. Mol Biol Rep 2024; 51:430. [PMID: 38517597 DOI: 10.1007/s11033-024-09390-z] [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: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
BACKGROUND Short tandem repeats (STRs) are the most widely used genetic markers in forensic genetics. Therefore, it is essential to document genetic population data of new kits designed for human identification purposes to enable laboratories to use these genetic systems to interpret and solve forensic casework. However, in Mexico, there are no studies with the PowerPlex Fusion 6C System, which includes 26 STRs (23 autosomal STRs and 3 Y-STRs). METHODS AND RESULTS 600 DNA samples from Mexico City were subjected to genotyping using the PowerPlex Fusion 6C System. For autosomal STRs, 312 different alleles were observed. Combined PE and PD were 99.999999809866% and 99.99999999999999999999999818795%, respectively. Genetic distances and AMOVA test showed low but significant differentiation between Mexican populations. CONCLUSIONS The results reported in this work demonstrate the efficacy of this system for human identification purposes in the population studied and justify its possible application in other Mexican Mestizo populations.
Collapse
Affiliation(s)
- Mauro López-Armenta
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
- Instituto de Servicios Periciales y Ciencias Forenses (INCIFO), Poder Judicial de la Ciudad de México, Ciudad de México, México
| | | | - Carolina León-Campos
- Instituto de Servicios Periciales y Ciencias Forenses (INCIFO), Poder Judicial de la Ciudad de México, Ciudad de México, México
| | | | - Héctor Rangel-Villalobos
- Intituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán, Jalisco, México
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México.
| |
Collapse
|
17
|
Bretschneider A, Mazanec J, Wittmeier P, Flux AL, Schmidt D, Hummel S. X-chromosomal STRs in aDNA kinship analysis. Anthropol Anz 2024; 81:131-138. [PMID: 37580949 DOI: 10.1127/anthranz/2023/1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 08/16/2023]
Abstract
The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.
Collapse
Affiliation(s)
- Anna Bretschneider
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Janine Mazanec
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Patrick Wittmeier
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Anna Lena Flux
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Diane Schmidt
- Hessisches Landeskriminalamt, Hölderlinstraße 1-5, 65187, Wiesbaden, Germany
| | - Susanne Hummel
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| |
Collapse
|
18
|
de Sousa RPC, Furo IDO, Silva-Oliveira GC, de Sousa-Felix RC, Bessa-Brito CD, Mello RC, Sampaio I, Artoni RF, de Oliveira EHC, Vallinoto M. Comparative cytogenetics of microsatellite distribution in two tetra fishes Astyanax bimaculatus (Linnaeus, 1758) and Psalidodon scabripinnis (Jenyns, 1842). PeerJ 2024; 12:e16924. [PMID: 38525285 PMCID: PMC10960527 DOI: 10.7717/peerj.16924] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/19/2024] [Indexed: 03/26/2024] Open
Abstract
Background The main cytogenetic studies of the Characidae family comprise the genera Astyanax and Psalidodon involving the use of repetitive DNA probes. However, for the microsatellite classes, studies are still scarce and the function of these sequences in the genome of these individuals is still not understood. Thus, we aimed to analyze and compare the distribution of microsatellite sequences in the species Astyanax bimaculatus and Psalidodon scabripinnis. Methods We collected biopsies from the fins of A. bimaculatus and P. scabripinnis to perform cell culture, followed by chromosome extraction, and mapped the distribution of 14 microsatellites by FISH in both species. Results and Discussion The diploid number observed for both species was 2n = 50, with an acrocentric B microchromosome in A. bimaculatus and a metacentric B chromosome in P. scabripinnis. Regarding FISH, 11 probes hybridized in the karyotype of A. bimaculatus mainly in centromeric regions, and 13 probes hybridized in P. scabripinnis, mainly in telomeric regions, in addition to a large accumulation of microsatellite hybridization on its B chromosome. Conclusion Comparative FISH mapping of 14 microsatellite motifs revealed different patterns of distribution both in autosomes and supernumerary chromosomes of A. bimaculatus and P. scabripinnis, suggesting independent evolutionary processes in each of these species, representing excellent data on chromosome rearrangements and cytotaxonomy.
Collapse
Affiliation(s)
| | | | | | | | | | - Raynara Costa Mello
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Seção do Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Instituto de Ciências Naturais e Exatas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Marcelo Vallinoto
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| |
Collapse
|
19
|
Kumar A, Panda AK, Usmani AA, Yadav P, Panwar A, Badola R, Hussain SA, Gupta SK. Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis. Sci Rep 2024; 14:5920. [PMID: 38467641 PMCID: PMC10928089 DOI: 10.1038/s41598-024-54816-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.
Collapse
Affiliation(s)
- Ajit Kumar
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Ashish Kumar Panda
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Aftab Alam Usmani
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Prabhaker Yadav
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
- Department of System Biology, Centre for Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Anshu Panwar
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Ruchi Badola
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Syed Ainul Hussain
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India
| | - Sandeep Kumar Gupta
- Wildlife Institute of India, P.O. Box # 18, Chandrabani, Dehra Dun, Uttarakhand, 248001, India.
| |
Collapse
|
20
|
Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819. Leg Med (Tokyo) 2024; 67:102390. [PMID: 38190775 DOI: 10.1016/j.legalmed.2023.102390] [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: 09/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.
Collapse
Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| |
Collapse
|
21
|
Hymus CM, Baxter FO, Ta H, Tran T, de Sousa C, Mountford NS, Tay JW. A comparison of six adhesive tapes as tape lifts for efficient trace DNA recovery without the transfer of PCR inhibitors. Leg Med (Tokyo) 2024; 67:102330. [PMID: 37802731 DOI: 10.1016/j.legalmed.2023.102330] [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: 06/06/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Tape-lifting is a non-destructive method employed in the laboratory to recover and collect trace DNA evidence from crime scene exhibits with porous surfaces. The success of tape-lifting is a balance between capturing the biological material and compatibility with downstream DNA extraction processes to ensure efficient release of the tape-lifted material during DNA extraction. In this study, six commercially available low-, regular- and high-tack adhesive tapes were evaluated. The low-tack S183 tape and the highly adhesive S-Hold tape were compared for DNA recovery efficiency from different materials commonly encountered in casework. All tape-lifts were processed using PrepFiler Express™ BTA and AutoMate Express™ Forensic DNA extraction systems, DNA samples quantitated by Quantifiler TRIO, amplified using Powerplex® 21 and VeriFiler™ PLUS (VFP), and analysed on a 3500xl genetic analyser to evaluate the quality of the resultant STR profiles obtained. The more adhesive S-Hold tape recovered comparable or more DNA than the low-tack S183 tape from the majority of materials tested. However, STR profiles obtained from S183 tape-lifts were of markedly higher quality compared to S-Hold tape-lifts. This was most evident for towel, denim and printed chiffon, where S-Hold samples exhibited severe PCR inhibition, with VFP internal quality markers confirming the presence of inhibitors. The findings suggest that strong adhesion is not necessarily beneficial for tape-lifting, as the low tack S183 tape was able to efficiently recover cellular material from the surface of porous substrates commonly encountered in casework, while avoiding the co-transfer of PCR-inhibitory substances from the sampled material.
Collapse
Affiliation(s)
- Colby M Hymus
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Fiona O Baxter
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Hoan Ta
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Teresa Tran
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Clare de Sousa
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Nicholas S Mountford
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Jasmine W Tay
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia.
| |
Collapse
|
22
|
Berumen J, Orozco L, Gallardo-Rincón H, Juárez-Torres E, Barrera E, Cruz-López M, Benuto RE, Ramos-Martinez E, Marin-Madina M, Alvarado-Silva A, Valladares-Salgado A, Peralta-Romero JJ, García-Ortiz H, Martinez-Juarez LA, Montoya A, Alvarez-Hernández DA, Alegre-Diaz J, Kuri-Morales P, Tapia-Conyer R. Association of tyrosine hydroxylase 01 (TH01) microsatellite and insulin gene (INS) variable number of tandem repeat (VNTR) with type 2 diabetes and fasting insulin secretion in Mexican population. J Endocrinol Invest 2024; 47:571-583. [PMID: 37624484 PMCID: PMC10904573 DOI: 10.1007/s40618-023-02175-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/05/2023] [Indexed: 08/26/2023]
Abstract
PURPOSE A variable number of tandem repeats (VNTR) in the insulin gene (INS) control region may be involved in type 2 diabetes (T2D). The TH01 microsatellite is near INS and may regulate it. We investigated whether the TH01 microsatellite and INS VNTR, assessed via the surrogate marker single nucleotide polymorphism rs689, are associated with T2D and serum insulin levels in a Mexican population. METHODS We analyzed a main case-control study (n = 1986) that used univariate and multivariate logistic regression models to calculate the risk conferred by TH01 and rs689 loci for T2D development; rs689 results were replicated in other case-control (n = 1188) and cross-sectional (n = 1914) studies. RESULTS TH01 alleles 6, 8, 9, and 9.3 and allele A of rs689 were independently associated with T2D, with differences between sex and age at diagnosis. TH01 alleles with ≥ 8 repeats conferred an increased risk for T2D in males compared with ≤ 7 repeats (odds ratio, ≥ 1.46; 95% confidence interval, 1.1-1.95). In females, larger alleles conferred a 1.5-fold higher risk for T2D when diagnosed ≥ 46 years but conferred protection when diagnosed ≤ 45 years. Similarly, rs689 allele A was associated with T2D in these groups. In males, larger TH01 alleles and the rs689 A allele were associated with a significant decrease in median fasting plasma insulin concentration with age in T2D cases; the reverse occurred in controls. CONCLUSION Larger TH01 alleles and rs689 A allele may potentiate insulin synthesis in males without T2D, a process disabled in those with T2D.
Collapse
Affiliation(s)
- J Berumen
- Facultad de Medicina, Unidad de Investigación en Medicina Experimental, Universidad Nacional Autónoma de México, 06720, Mexico City, México.
| | - L Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Secretaria de Salud, 14610, Mexico City, México
| | - H Gallardo-Rincón
- Departamento de Soluciones Operativas, Fundación Carlos Slim, 11529, Mexico City, Mexico.
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, 44340, Guadalajara, Jalisco, México.
| | - E Juárez-Torres
- Laboratorio Huella Génica, Unidad de Diabetes, 06600, Mexico City, Mexico
| | - E Barrera
- Facultad de Medicina, Unidad de Investigación en Medicina Experimental, Universidad Nacional Autónoma de México, 06720, Mexico City, México
| | - M Cruz-López
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, México
| | - R E Benuto
- Laboratorio Huella Génica, Unidad de Diabetes, 06600, Mexico City, Mexico
| | - E Ramos-Martinez
- Facultad de Medicina, Unidad de Investigación en Medicina Experimental, Universidad Nacional Autónoma de México, 06720, Mexico City, México
| | - M Marin-Madina
- Laboratorio Huella Génica, Unidad de Diabetes, 06600, Mexico City, Mexico
| | - A Alvarado-Silva
- Laboratorio Huella Génica, Unidad de Diabetes, 06600, Mexico City, Mexico
| | - A Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, México
| | - J J Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, México
| | - H García-Ortiz
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Secretaria de Salud, 14610, Mexico City, México
| | - L A Martinez-Juarez
- Departamento de Soluciones Operativas, Fundación Carlos Slim, 11529, Mexico City, Mexico
- Center for Humanitarian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - A Montoya
- Departamento de Soluciones Operativas, Fundación Carlos Slim, 11529, Mexico City, Mexico
| | - D A Alvarez-Hernández
- Departamento de Soluciones Operativas, Fundación Carlos Slim, 11529, Mexico City, Mexico
| | - J Alegre-Diaz
- Facultad de Medicina, Unidad de Investigación en Medicina Experimental, Universidad Nacional Autónoma de México, 06720, Mexico City, México
| | - P Kuri-Morales
- Proyecto OriGen, Instituto Tecnologico y de Estudios Superiores de Monterrey, Monterrey, México
| | - R Tapia-Conyer
- Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, 04510, Mexico City, México
| |
Collapse
|
23
|
Lan Q, Cai M, Xu H, Bai X, Shen C, Zhu B. Developmental validation of a custom-designed Multi-InDel panel: A five-dye multiplex amplification system for challenging DNA samples. Electrophoresis 2024; 45:489-504. [PMID: 38037290 DOI: 10.1002/elps.202300192] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
The continual investigation of novel genetic markers has yielded promising solutions for addressing the challenges encountered in forensic DNA analysis. In this study, we have introduced a custom-designed panel capable of simultaneously amplifying 41 novel Multi-insertion/deletion (Multi-InDel) markers and an amelogenin locus using the capillary electrophoresis platform. Through a developmental validation study conducted in accordance with guidelines recommended by the Scientific Working Group on DNA Analysis Methods, we demonstrated that the new Multi-InDel system exhibited the sensitivity to produce reliable genotyping profiles with as little as 62.5 pg of template DNA. Accurate and complete genotyping profiles could be obtained even in the presence of specific concentrations of PCR inhibitors. Furthermore, the maximum amplicon size for this system was limited to under 220 bp in the genotyping profile, resulting in its superior efficiency compared to commercially available short tandem repeat kits for both naturally and artificially degraded samples. In the context of mixed DNA analysis, the Multi-InDel system was proved informative in the identification of two-person DNA mixture, even when the template DNA of the minor contributor was as low as 50 pg. In conclusion, a series of performance evaluation studies have provided compelling evidence that the new Multi-InDel system holds promise as a valuable tool for forensic DNA analysis.
Collapse
Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chunmei Shen
- Department of Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
| |
Collapse
|
24
|
Ren H, Zhang J, Yang T, Zhang X, Liu J, Chen C, Shi Y, Chen Y, Jia L, Simayijiang H, Yan J. Analysis of homozygous allele mismatches in paternity tests with massively parallel sequencing. Electrophoresis 2024; 45:480-488. [PMID: 38037297 DOI: 10.1002/elps.202300130] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/12/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
In paternity testing, short tandem repeats (STRs) allele mismatches are often detected. Nowadays, polymerase chain reaction- and capillary electrophoresis (CE)-based STR genotyping is the most commonly used method to distinguish alleles based on their length. However, it could not detect alleles of the same size with sequence differences. Massively parallel sequencing (MPS) can determine not only allele sizes but also sequences, which could explain the causes of allele mismatches. Additionally, more types of genetic markers can be detected in a single assay, which increases the discriminatory power and facilitates the analysis of paternity tests. In this study, we analyzed 11 cases with homozygous allele mismatches from routine DNA trio paternity tests using the CE platform. Samples were sequenced using the ForenSeq DNA Signature Prep Kit and the MiSeq FGx Sequencing System. The results show that of the eight father-child mismatch cases and three mother-child mismatch cases, five cases with D5S818 and D8S1179 and one case at D13S317 were classified as non-amplification. The other three cases and two cases could be defined as mutations. This study suggests that MPS-based STR genotyping can provide additional information that allows more accurate interpretation of allelic mismatches in paternity testing.
Collapse
Affiliation(s)
- He Ren
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, Academy of Forensic Science, Shanghai, P. R. China
- Beijing Police College, Beijing, P. R. China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Tingting Yang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Chong Chen
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, P. R. China
| | - Yan Shi
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, P. R. China
| | - Ying Chen
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, P. R. China
| | - Li Jia
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, P. R. China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| |
Collapse
|
25
|
Sawada M, Hida T, Kamiya T, Minowa T, Kato J, Okura M, Idogawa M, Tokino T, Uhara H. Effects of temozolomide on tumor mutation burden and microsatellite instability in melanoma cells. J Dermatol 2024; 51:409-418. [PMID: 37658676 DOI: 10.1111/1346-8138.16925] [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: 06/23/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The efficacy of combination therapy with an immune checkpoint inhibitor (ICI) and cytotoxic chemotherapeutic agents has been investigated in cancer, including melanoma. Before ICIs were introduced, dacarbazine or temozolomide (TMZ) were used to treat melanoma. Several studies using glioma or colorectal cancer cells showed that TMZ can increase the tumor mutation burden (TMB) and induce mismatch repair (MMR) deficiency associated with microsatellite instability (MSI). These could increase immunoreactivity to an ICI, but this has not been evaluated in melanoma cells. We investigated the effects of TMZ on MSI status and TMB in melanoma cells. To evaluate the TMB, we performed whole-exome sequencing using genomic DNA from the human melanoma cell lines Mel18, A375, WM266-4, G361, and TXM18 before and after TMZ treatment. Polymerase chain reaction amplification of five mononucleotide repeat markers, BAT25, BAT26, NR21, NR24, and MONO27, was performed, and we analyzed changes in the MSI status. In all cell lines, the TMB was increased after TMZ treatment (the change amount of TMB with ≤ 5% variant allele frequency [VAF] was 18.0-38.3 mutations per megabase) even in the condition without obvious cytological damage. MSI after TMZ treatment was not observed in any cells. TMZ increased TMB but did not change MSI status in melanoma cells.
Collapse
Affiliation(s)
- Masahide Sawada
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tokimasa Hida
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takafumi Kamiya
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomoyuki Minowa
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Junji Kato
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masae Okura
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masashi Idogawa
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hisashi Uhara
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
26
|
Moracho E, Klein EK, Oddou-Muratorio S, Hampe A, Jordano P. Highly clustered mating networks in naturally fragmented riparian tree populations. Mol Ecol 2024; 33:e17285. [PMID: 38288563 DOI: 10.1111/mec.17285] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024]
Abstract
Understanding how spatial patterns of mating and gene flow respond to habitat loss and geographical isolation is a crucial aspect of forest fragmentation genetics. Naturally fragmented riparian tree populations exhibit unique characteristics that significantly influence these patterns. In this study, we investigate mating patterns, pollen-mediated gene flow, and genetic diversity in relict populations of Frangula alnus in southern Spain by testing specific hypotheses related to the riparian habitat. We employ a novel approach that combines paternity analysis, particularly suited for small and isolated populations, with complex network theory and Bayesian models to predict mating likelihood among tree pairs. Our findings reveal a prevalence of short-distance pollination, resulting in spatially driven local mating clusters with a distinct subset of trees being highly connected in the mating network. Additionally, we observe numerous pollination events over distances of hundreds of metres and considerable pollen immigration. Local neighbourhood density is the primary factor influencing within-population mating patterns and pollen dispersal; moreover, mating network properties reflect the population's size and spatial configuration. Conversely, among-population pollen dispersal is mainly determined by tree size, which influences floral display. Our results do not support a major role of directional pollen dispersal in longitudinal trends of genetic diversity. We provide evidence that long-term fragmented tree populations persist in unique environments that shape mating patterns and impose constraints to pollen-mediated gene flow. Nevertheless, even seemingly strongly isolated populations can maintain functional connectivity over extended periods, especially when animal-mediated mating networks promote genetic diversity, as in this riparian tree species.
Collapse
Affiliation(s)
- Eva Moracho
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Etienne K Klein
- Ecologie des Forêts Méditerranéennes, UR 629, INRA, Avignon, France
- Biostatistique et Processus Spatiaux, UR 546, INRA, Avignon, France
| | | | - Arndt Hampe
- INRA, UMR1202 BIOGECO, Cestas, France
- Univ. Bordeaux, UMR1202 BIOGECO, Talence, France
| | - Pedro Jordano
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- Dept. Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| |
Collapse
|
27
|
Ma D, Lin Y, Zhang R, Wang S, Hu W, Ye M, Gao H, Wang L, Song Y, Guo H. Effect of uniparental disomy in parentage testing. Leg Med (Tokyo) 2024; 67:102381. [PMID: 38154315 DOI: 10.1016/j.legalmed.2023.102381] [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: 04/22/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Uniparental disomy (UPD) is a rare type of chromosomal aberration that may hinder the analysis of kinship during forensic identification. Here, we investigated these genetic findings to avoid false exclusions during parentage testing. Thirty-nine fluorescently labeled, autosomal short tandem repeats (STR) were amplified in three cases, to detect parent-child relationships. Twenty-three fluorescently labeled Y-chromosome STRs were also employed. These were subjected to capillary electrophoresis. The parentage index was calculated by the bipartite or tripartite model. Single nucleotide polymorphism (SNP) microarrays were performed to further investigate the genetic mechanisms. The conclusions supported the biological mother-child relationship in three cases. However, in all cases, the alleged father and child had three autosomal STR markers, constrained to a single chromosome, which did not conform to Mendelian inheritance rules. The genotyping of 23 Y-chromosome STRs did not reveal any violations of Mendelian law. The combination of STR profiling and SNP microarrays suggested that two children had maternal UPD of chromosome 7, whilst one had UPD of chromosome 2. After excluding the three incompatible loci, the conclusions supported the biological father-child relationship in all cases. The same results were obtained when parentage testing of trios was used. Uniparental disomy may complicate the judgment of kinship in parentage testing. The possibility of UPD should be considered when incompatible STR loci are found on the same chromosome. Genetic evidence obtained through additional molecular techniques can provide better interpretation of kinship in the presence of UPD and avoid false exclusions of biological relationships.
Collapse
Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - YuMei Lin
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - RuanZhang Zhang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Shayan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Wenlong Hu
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Mei Ye
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China.
| |
Collapse
|
28
|
Dierig L, Kunz SN, Wiegand P. Comparison of massively parallel sequencing to capillary electrophoresis for short tandem repeat genotyping of trace DNA. Electrophoresis 2024; 45:451-462. [PMID: 38085164 DOI: 10.1002/elps.202300145] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 03/20/2024]
Abstract
In forensic genetics, massively parallel sequencing (MPS) offers several advantages over the current golden standard, capillary electrophoresis (CE): additional sequence information, shorter amplicon lengths, and the simultaneous analysis of many markers. These benefits result in a reduced number of reactions necessary while improving the amount of data obtained, thereby conserving valuable sample extracts. This proves particularly advantageous for the analysis of trace DNA. This study assessed the suitability of MPS for short tandem repeat (STR) typing of low template samples compared with results obtained through CE. The MPS genotypes showed higher concordance to reference genotypes, with donor alleles being more frequently assigned to be the major contributor, meeting the requirements for database entry. However, the MPS workflow is more time-consuming and associated with higher costs.
Collapse
Affiliation(s)
- Lisa Dierig
- Institute of Legal Medicine, Ulm University, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Ulm University, Ulm, Germany
| |
Collapse
|
29
|
Lizano AMD, Kim KM, Juinio-Meñez MA, Ravago-Gotanco R. Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers. Sci Rep 2024; 14:4886. [PMID: 38418859 PMCID: PMC10901784 DOI: 10.1038/s41598-024-54987-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35-2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex.
Collapse
Affiliation(s)
- Apollo Marco D Lizano
- Faculty of Biosciences & Aquaculture, Nord University, Bodø, Norway.
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines.
| | - Kenneth M Kim
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
| | | | - Rachel Ravago-Gotanco
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
| |
Collapse
|
30
|
Yadav J, Jasrotia P, Jaglan MS, Sareen S, Kashyap PL, Kumar S, Yadav SS, Singh G, Singh GP. Unravelling the novel genetic diversity and marker-trait associations of corn leaf aphid resistance in wheat using microsatellite markers. PLoS One 2024; 19:e0289527. [PMID: 38386640 PMCID: PMC10883527 DOI: 10.1371/journal.pone.0289527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/17/2023] [Indexed: 02/24/2024] Open
Abstract
The study was conducted to identify novel simple sequence repeat (SSR) markers associated with resistance to corn aphid (CLA), Rhopalosiphum maidis L. in 48 selected bread wheat (Triticum aestivum L.) and wild wheat (Aegilops spp. & T. dicoccoides) genotypes during two consecutive cropping seasons (2018-19 and 2019-20). A total of 51 polymorphic markers containing 143 alleles were used for the analysis. The frequency of the major allele ranged from 0.552 (Xgwm113) to 0.938 (Xcfd45, Xgwm194 and Xgwm526), with a mean of 0.731. Gene diversity ranged from 0.116 (Xgwm526) to 0.489 (Xgwm113), with a mean of 0.354. The polymorphic information content (PIC) value for the SSR markers ranged from 0.107 (Xgwm526) to 0.370 (Xgwm113) with a mean of 0.282. The results of the STRUCTURE analysis revealed the presence of four main subgroups in the populations. Analysis of molecular variance (AMOVA) showed that the between-group difference was around 37 per cent of the total variation contributed to the diversity by the whole germplasm, while 63 per cent of the variation was attributed between individuals within the group. A general linear model (GLM) was used to identify marker-trait associations, which detected a total of 23 and 27 significant new marker-trait associations (MTAs) at the p < 0.01 significance level during the 2018-19 and 2019-20 crop seasons, respectively. The findings of this study have important implications for the identification of molecular markers associated with CLA resistance. These markers can increase the accuracy and efficiency of aphid-resistant germplasm selection, ultimately facilitating the transfer of resistance traits to desirable wheat genotypes.
Collapse
Affiliation(s)
- Jayant Yadav
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Poonam Jasrotia
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | | | - Sindhu Sareen
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Prem Lal Kashyap
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sudheer Kumar
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | | | - Gyanendra Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Gyanendra Pratap Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| |
Collapse
|
31
|
Tao R, Dong X, Zhen X, Xia R, Qu Y, Liu S, Zhang S, Li C. Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit. Mol Genet Genomics 2024; 299:9. [PMID: 38374461 DOI: 10.1007/s00438-024-02121-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.
Collapse
Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, 201108, China
| | - Xiaoyuan Zhen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, 100088, China.
| | - Suhua Zhang
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China.
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
32
|
Fandade V, Singh P, Singh D, Sharma H, Thakur G, Saini S, Kumar P, Mantri S, Bishnoi OP, Roy J. Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat (Triticum spp). Gene 2024; 896:148039. [PMID: 38036075 DOI: 10.1016/j.gene.2023.148039] [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: 09/09/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Wheat (Triticum aestivum L.) is a crucial global staple crop, and is consistently being improved to enhance yield, disease resistance, and quality traits. However, the development of molecular markers is a challenging task due to its hexaploid genome. Molecular marker system such as simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) are helpful for breeding, but SNP has limitations due to its development cost and its conversion to breeder markers. The study proposed an in-silico approach, by utilizing the low-cost transcriptome sequencing of two parental lines, 'TAC 75' and 'WH 1105', to identify polymorphic SSRs for mapping in a recombinant inbred line (RIL) population. This study introduces a new approach to bridge wheat genetics intricacies and next-generation sequencing potential. It presents a comprehensive genome-wide SSR distribution using IWGSC CS RefSeq v2.1 genome assembly and to identify 189 polymorphic loci through in-silico strategy. Of these, 54.76% showed polymorphism between parents, surpassing the traditional low polymorphic success rate. A RIL population screening validated these markers, demonstrating the fitness of identified markers through chi-square tests. The designed SSRs were also validated for genetic diversity analysis in a subset of 37 Indian wheat genotypes and cross-transferability in the wild/relative wheat species. In diversity analysis, a subset of 38 markers revealed 95 alleles (2.5 allele/locus), indicating substantial genetic variation. Population structure analysis unveiled three distinct groups, supported by phylogenetic and PCoA analyses. Further the polymorphic SSRs were also analyzed for SSR-gene association using gene ontology analysis. By utilizing the developing seed transcriptome data within parental lines, the study has enhanced the polymorphic SSR identification precision and facilitated in the RIL population. The undertaken study pioneers the use of transcriptome sequencing and genetic mapping to overcome challenges posed by the intricate wheat genome. This approach offers a cost-effective, less labour-intensive alternative to conventional methods, providing a platform for advancing wheat breeding research.
Collapse
Affiliation(s)
- Vikas Fandade
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Pradeep Singh
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Dalwinder Singh
- Department of Anatomy and cell biology, University of Western Ontario, London, Canada.
| | - Himanshu Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Garima Thakur
- Protection for Plant Varieties and Farmers Rights Authority, New Delhi, India.
| | - Shivangi Saini
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - Prashant Kumar
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.
| | - Shrikant Mantri
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| | - O P Bishnoi
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar- 125004, India.
| | - Joy Roy
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali-140306, Punjab, India.
| |
Collapse
|
33
|
Xiao Y, Yu X, Wang Y, Song G, Liu M, Wang D, Wang H. A novel immune-related gene signature for diagnosis and potential immunotherapy of microsatellite stable endometrial carcinoma. Sci Rep 2024; 14:3738. [PMID: 38355782 PMCID: PMC10867009 DOI: 10.1038/s41598-024-53338-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
An immune-related gene signature (IRGS) was established to better understand the molecular and immunologic characteristics of microsatellite instable (MSI) and microsatellite stable (MSS) endometrial carcinoma (EC), and provide potential immunotherapy directions for MSS patients. Top 20 immune-related hub genes were screened by weight gene coexpression network analysis (WGCNA), and an IRGS was further established through Cox regression analysis. The molecular and immune characteristics were clarified in IRGS high and low risk groups. Expression and MS status validation of the IRGS were conducted through quantitative real-time Polymerase Chain Reaction (rt-qPCR) and immunohistochemistry (IHC) analysis. The IRGS includes 2 oncogenes (AGTR1 and HTR3C) and 2 tumor suppressor genes (CD3E and SERPIND1). Patients in IRGS high-risk group were more with MSS status, higher tumor grade, later FIGO stage, serous histology and elder ages compared with IRGS low-risk group (P < 0.05). Besides, patients in MSS group were more FIGO stages II-IV (42.7% vs. 26%), serous histology (35.7% vs. 5.3%) and with higher IRGS risk score (1.51 ± 3.11 vs. 1.02 ± 0.67) (P < 0.05) than patients in MSI group. Furthermore, patients in IRGS high-risk group had higher tumor purity, more Macrophages M1 and Macrophages M2 infiltrating, higher proportion of Macrophages M2 and Dendritic cells activated, lower proportion of T cells regulatory (Tregs), lower tumor mutation burden (TMB). Correspondingly, subjects in IRGS low-risk group had higher immunphenoscores than IRGS high-risk group. The relative mRNA level of AGTR1 and HTR3C were gradually increase, while CD3E and SERPIND1 were reversed in rt-qPCR. Through IHC experiments, AGTR1(69.2% vs 30%, P = 0.074) and HTR3C (76.9% vs 30%, P = 0.024) had higher positive staining rates in ECs than non-ECs. While SERPIND1 (84.6% vs 20%, P = 0.003) and CD3E (61.5% vs 40%, P = 0.000) had higher positive staining rates in non-ECs. IRGS is a potential diagnostic and prognostic biomarker for EC. IRGS low risk group might benefit from immune checkpoint inhibitors, while IRGS high risk group deserve other potential immunotherapy.
Collapse
Affiliation(s)
- Yunyun Xiao
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China
| | - XiaoChuan Yu
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China
| | - Yaping Wang
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Guangyao Song
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Ming Liu
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Daqing Wang
- Department of Oncology, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China.
| | - Huali Wang
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China.
| |
Collapse
|
34
|
Freitas I, Velo-Antón G, Lopes S, Muñoz-Merida A, Martínez-Freiría F. Isolation and characterization of polymorphic microsatellite loci for the three Iberian vipers, Vipera aspis, V. Latastei and V. seoanei by Illumina MiSeq sequencing. Mol Biol Rep 2024; 51:294. [PMID: 38334910 PMCID: PMC10857953 DOI: 10.1007/s11033-024-09263-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND European vipers (genus Vipera) are a well-studied taxonomic group, but the low resolution of nuclear sanger-sequenced regions has precluded thorough studies at systematic, ecological, evolutionary and conservation levels. In this study, we developed novel microsatellite markers for the three Iberian vipers, Vipera aspis, V. latastei and V. seoanei, and assessed their polymorphism in north-central Iberian populations. METHODS AND RESULTS Genomic libraries were developed for each species using an Illumina Miseq sequencing approach. From the 70 primer pairs initially tested, 48 amplified reliably and were polymorphic within species. Cross-species transferability was achieved for 31 microsatellites loci in the three target species and four additional loci that were transferable to one species only. The 48 loci amplified in average seven alleles, and detected average expected and observed heterozygosities of 0.7 and 0.55, in the three genotyped populations/species (26 V. aspis, 20 V. latastei and 10 V. seoanei). CONCLUSIONS Our study provides a selection of 48 polymorphic microsatellite markers that will contribute significantly to current knowledge on genetic diversity, gene flow, population structure, demographic dynamics, systematics, reproduction and heritability in these species, and potentially in other congeneric taxa.
Collapse
Affiliation(s)
- Inês Freitas
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4099-002, Portugal.
| | - Guillermo Velo-Antón
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- Facultad de Biología, Edificio de Ciencias Experimentales, Universidad de Vigo, Bloque B, Planta 2, Laboratorio 39 (Grupo GEA), Vigo, E-36310, Spain
| | - Susana Lopes
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Antonio Muñoz-Merida
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Fernando Martínez-Freiría
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| |
Collapse
|
35
|
Verbiest MA, Lundström O, Xia F, Baudis M, Bilgin Sonay T, Anisimova M. Short tandem repeat mutations regulate gene expression in colorectal cancer. Sci Rep 2024; 14:3331. [PMID: 38336885 PMCID: PMC10858039 DOI: 10.1038/s41598-024-53739-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
Short tandem repeat (STR) mutations are prevalent in colorectal cancer (CRC), especially in tumours with the microsatellite instability (MSI) phenotype. While STR length variations are known to regulate gene expression under physiological conditions, the functional impact of STR mutations in CRC remains unclear. Here, we integrate STR mutation data with clinical information and gene expression data to study the gene regulatory effects of STR mutations in CRC. We confirm that STR mutability in CRC highly depends on the MSI status, repeat unit size, and repeat length. Furthermore, we present a set of 1244 putative expression STRs (eSTRs) for which the STR length is associated with gene expression levels in CRC tumours. The length of 73 eSTRs is associated with expression levels of cancer-related genes, nine of which are CRC-specific genes. We show that linear models describing eSTR-gene expression relationships allow for predictions of gene expression changes in response to eSTR mutations. Moreover, we found an increased mutability of eSTRs in MSI tumours. Our evidence of gene regulatory roles for eSTRs in CRC highlights a mostly overlooked way through which tumours may modulate their phenotypes. Future extensions of these findings could uncover new STR-based targets in the treatment of cancer.
Collapse
Affiliation(s)
- Max A Verbiest
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Oxana Lundström
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Feifei Xia
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tugce Bilgin Sonay
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - Maria Anisimova
- Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
36
|
Das G, Das SP, Bit A, Sahoo L, Swain SK, Raghavendra CH, Krishnaprasoon NP, Sahoo SK, Das P. Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree. Mol Biol Rep 2024; 51:290. [PMID: 38329563 DOI: 10.1007/s11033-023-09188-5] [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: 09/13/2023] [Accepted: 12/20/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The Deccan mahseer, Tor khudree (Sykes, 1839) is a potential game and food fish species belonging to the family cyprinidae and is categorized as endangered. Its distribution is restricted to southern part of India, specifically to Peninsular Rivers. This study is first to assess the genetic diversity and differentiation in Tor khudree by developing novel simple sequence repeat (SSR) markers. METHODS AND RESULTS Low depth next generation sequencing followed by sequence analysis in MISA software identified 187,649 SSRs. The novel fourteen validated SSR loci were used for population genetic analysis. All of the SSR loci were highly informative with mean PIC > 0.5. High mean allelic richness (9.29) observed heterozygosity (0.98) and expected heterozygosity (0.79) were observed across the loci. However, genetic differentiation was low but significant (0.052). Negative FIS values were observed in both locus-wise and populations indicating the presence of high heterozygosity. Intrapopulation variation was found to be high (96.29%). The population structure revealed two genetic stocks. CONCLUSIONS The results from the present study including the highly polymorphic markers developed would be a useful resource for further research on population genetics and conservation genetics of the species.
Collapse
Affiliation(s)
- Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | | | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Subrat Kumar Swain
- Institute of Medical Sciences & SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India
| | | | - N P Krishnaprasoon
- PMFGR Centre of ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Kochi, India
| | - Sangram Ketan Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
- Aquaculture Productions and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
| |
Collapse
|
37
|
Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (Bethesda) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
Collapse
Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| |
Collapse
|
38
|
Abuelmaali SA, Mashlawi AM, Ishak IH, Wajidi MFF, Jaal Z, Avicor SW, Kassim NFA. Population genetic structure of Aedes aegypti subspecies in selected geographical locations in Sudan. Sci Rep 2024; 14:2978. [PMID: 38316804 PMCID: PMC10844603 DOI: 10.1038/s41598-024-52591-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024] Open
Abstract
Although knowledge of the composition and genetic diversity of disease vectors is important for their management, this is limiting in many instances. In this study, the population structure and phylogenetic relationship of the two Aedes aegypti subspecies namely Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf) in eight geographical areas in Sudan were analyzed using seven microsatellite markers. Hardy-Weinberg Equilibrium (HWE) for the two subspecies revealed that Aaa deviated from HWE among the seven microsatellite loci, while Aaf exhibited departure in five loci and no departure in two loci (A10 and M201). The Factorial Correspondence Analysis (FCA) plots revealed that the Aaa populations from Port Sudan, Tokar, and Kassala clustered together (which is consistent with the unrooted phylogenetic tree), Aaf from Fasher and Nyala populations clustered together, and Gezira, Kadugli, and Junaynah populations also clustered together. The Bayesian cluster analysis structured the populations into two groups suggesting two genetically distinct groups (subspecies). Isolation by distance test revealed a moderate to strong significant correlation between geographical distance and genetic variations (p = 0.003, r = 0.391). The migration network created using divMigrate demonstrated that migration and gene exchange between subspecies populations appear to occur based on their geographical proximity. The genetic structure of the Ae. aegypti subspecies population and the gene flow among them, which may be interpreted as the mosquito vector's capacity for dispersal, were revealed in this study. These findings will help in the improvement of dengue epidemiology research including information on the identity of the target vector/subspecies and the arboviruses vector surveillance program.
Collapse
Affiliation(s)
- Sara A Abuelmaali
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, 11115, Sudan
| | - Abadi M Mashlawi
- Department of Biology, College of Science, Jazan University, P.O. Box. 114, Jazan, 45142, Kingdom of Saudi Arabia
| | - Intan Haslina Ishak
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | | | - Zairi Jaal
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Silas Wintuma Avicor
- Molecular Entomology Research Group, Universiti Sains Malaysia, 11800, Penang, Malaysia
- Entomology Division, Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | - Nur Faeza Abu Kassim
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
39
|
Salinas-Pineda L, Berumen J, Lopez Armenta M, Leon Campos C, Rangel-Villalobos H, Juarez-Torres E, Huerta-Pacheco NS, Aguilar-Velazquez JA, Villavicencio-Queijeiro A, Guardado-Estrada M. Forensic parameters and population structure based on 21 autosomal STRs with the investigator 24plex QS in mestizos from the Mexico City population. Leg Med (Tokyo) 2024; 66:102344. [PMID: 37977100 DOI: 10.1016/j.legalmed.2023.102344] [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: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Allele frequencies and forensic parameters for 21 STR autosomal markers (CSF1PO, D10S1248, D12S391, D13S317,D16S539, D18S51, D19S433, D1S1656,D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, FGA, SE33, TH01, TPOX and vWA) were reported in 289 unrelated individuals from Mexico City, Mexico. In addition, an interpopulation analysis was performed including other world populations. In brief, the established population database of 21 autosomal STR markers in the present work is adequate for human identification purposes.
Collapse
Affiliation(s)
- Lizette Salinas-Pineda
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jaime Berumen
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mauro Lopez Armenta
- Laboratorio de Genética, Instituto de Servicios Periciales y Ciencias Forenses del Poder Judicial de la CDMX, Ciudad de México, Mexico
| | - Carolina Leon Campos
- Laboratorio de Genética, Instituto de Servicios Periciales y Ciencias Forenses del Poder Judicial de la CDMX, Ciudad de México, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Mexico
| | | | - N Sofia Huerta-Pacheco
- CONACHYT-Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jose Alonso Aguilar-Velazquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico; Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico
| | - Alexa Villavicencio-Queijeiro
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| |
Collapse
|
40
|
Kim KR, Park SY, Kim H, Kim J, Hong JM, Kim SY, Yu JN. Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea. Genes Genomics 2024; 46:187-202. [PMID: 38240922 DOI: 10.1007/s13258-023-01479-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/23/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level. OBJECTIVE Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina. METHODS Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers. RESULTS The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754. CONCLUSION Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.
Collapse
Affiliation(s)
- Kang-Rae Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - So Young Park
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Heesoo Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jiyeon Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong Min Hong
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Sun-Yu Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong-Nam Yu
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea.
| |
Collapse
|
41
|
Tachikawa K, Shimizu T, Imai T, Ko R, Kawai Y, Omae Y, Tokunaga K, Frith MC, Yamano Y, Mitsuhashi S. Cost-Effective Cas9-Mediated Targeted Sequencing of Spinocerebellar Ataxia Repeat Expansions. J Mol Diagn 2024; 26:85-95. [PMID: 38008286 DOI: 10.1016/j.jmoldx.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/28/2023] Open
Abstract
Hereditary repeat diseases are caused by an abnormal expansion of short tandem repeats in the genome. Among them, spinocerebellar ataxia (SCA) is a heterogeneous disease, and currently, 16 responsible repeats are known. Genetic diagnosis is obtained by analyzing the number of repeats through separate testing of each repeat. Although simultaneous detection of candidate repeats using current massively parallel sequencing technologies has been developed to avoid complicated multiple experiments, these methods are generally expensive. This study developed a cost-effective SCA repeat panel [Flongle SCA repeat panel sequencing (FLO-SCAp)] using Cas9-mediated targeted long-read sequencing and the smallest long-read sequencing apparatus, Flongle. This panel enabled the detection of repeat copy number changes, internal repeat sequences, and DNA methylation in seven patients with different repeat expansion diseases. The median (interquartile range) values of coverage and on-target rate were 39.5 (12 to 72) and 11.6% (7.5% to 16.5%), respectively. This approach was validated by comparing repeat copy number changes measured by FLO-SCAp and short-read whole-genome sequencing. A high correlation was observed between FLO-SCAp and short-read whole-genome sequencing when the repeat length was ≤250 bp (r = 0.98; P < 0.001). Thus, FLO-SCAp represents the most cost-effective method for conducting multiplex testing of repeats and can serve as the first-line diagnostic tool for SCA.
Collapse
Affiliation(s)
- Keiji Tachikawa
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Takahiro Shimizu
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Takeshi Imai
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Riyoko Ko
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan; Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Yoshihisa Yamano
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan; Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Satomi Mitsuhashi
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan.
| |
Collapse
|
42
|
Li S, Kou PW, Xu YK, Liu CL, Sun XC, Li B, Huang WJ. [Development and application of SSR markers of Saposhnikovia divaricata based on transcriptome]. Zhongguo Zhong Yao Za Zhi 2024; 49:717-727. [PMID: 38621875 DOI: 10.19540/j.cnki.cjcmm.20231013.103] [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] [Indexed: 04/17/2024]
Abstract
Transcriptome sequencing was employed to mine the simple sequence repeat(SSR) locus information of Saposhnikovia divaricata and design specific primers, which aimed to provide a basis for the research on the genetic diversity of S. divaricata germplasm resources. The seed purity, 1 000-seed weight, germination rate, and seed vigor were determined. MISA was used to obtain the SSR locus information from 12 606 unigene longer than 1 kb in the transcriptome database. Forty-three pairs of SSR primers designed in Primer 3 were used to analyze the polymorphism of 28 S. divaricata samples of different sources. The results showed that there were differences in the seed purity, 1 000-seed weight, germination rate, vigor, and seed length and width among S. divaricata samples of different sources. Particularly, the germination rate and seed vigor had significant differences, and HB-ZJK1, NMG-CF4, NMG-BT, NMG-HLE1, and NMG-CF2 had significantly higher 1 000-seed weight, germination rate, and seed vigor than the samples of other sources. Among the 86 233 unigene, 12 606(14.62%) unigene contained 15 958 SSR loci, with one SSR locus every 5 009 bp on average. The SSR loci were mainly single nucleotide and dinucleotide repeats, which were dominated by G/C and TC/AG, respectively. All the primers were screened by using 28 S. divaricata sample from different habitats, and the primers corresponding to the amplification products with clear bands and stable polymorphism were obtained. The clustering results of the biological characteristics and genetic diversity of the 28 S. divaricata samples were basically consistent, and the samples of the same origin(HB-AG1, HB-AG2, HB-ZJK1, and HB-ZJK2) generally gathered together and had close genetic relationship. The SSRs in S. divaricata transcriptome has high frequency, rich types, and high polymorphism, which provides candidate molecular markers for the germplasm identification, genetic map construction, and molecular-assisted breeding.
Collapse
Affiliation(s)
- Shuang Li
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Pei-Wen Kou
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Yi-Ke Xu
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Chang-le Liu
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Xiao-Chun Sun
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Bo Li
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| | - Wen-Jing Huang
- State Key Laboratory of Research and Development of Characteristic Resources of Qin Medicine (Cultivation), Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine Xianyang 712083, China
| |
Collapse
|
43
|
He S, Yuan C, Zhang P, Wang H, Luo D, Dai X. Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers. BMC Plant Biol 2024; 24:77. [PMID: 38287273 PMCID: PMC10823706 DOI: 10.1186/s12870-024-04759-5] [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] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND Rhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources. RESULTS In the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity. CONCLUSIONS This is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.
Collapse
Affiliation(s)
- Shuang He
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China
| | - Congjun Yuan
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China.
| | - Panli Zhang
- Guizhou Forestry School, Guiyang, 550200, Guizhou, China
| | - Haodong Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Dali Luo
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Xiaoyong Dai
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China
| |
Collapse
|
44
|
Lu J, Toro C, Adams DR, Moreno CAM, Lee WP, Leung YY, Harms MB, Vardarajan B, Heinzen EL. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC Genomics 2024; 25:115. [PMID: 38279154 PMCID: PMC10811831 DOI: 10.1186/s12864-023-09935-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. RESULTS Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. CONCLUSIONS LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.
Collapse
Affiliation(s)
- Jinfeng Lu
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA.
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mathew B Harms
- Department of Neurology, Division of Neuromuscular Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Badri Vardarajan
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA
| | - Erin L Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
45
|
Almerekova S, Yermagambetova M, Jumanov S, Abugalieva S, Turuspekov Y. Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan. PLoS One 2024; 19:e0295550. [PMID: 38271463 PMCID: PMC10810545 DOI: 10.1371/journal.pone.0295550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/24/2023] [Indexed: 01/27/2024] Open
Abstract
Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.
Collapse
Affiliation(s)
- Shyryn Almerekova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Moldir Yermagambetova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Smatulla Jumanov
- Aksu-Zhabagly Nature Reserve, Zhabagly, Turkestan Region, Kazakhstan
| | - Saule Abugalieva
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Yerlan Turuspekov
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
46
|
Mussmann SM, Wilson WD. Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi. Mol Biol Rep 2024; 51:210. [PMID: 38270754 DOI: 10.1007/s11033-023-09094-w] [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: 07/01/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Masked Bobwhite (Colinus virginianus ridgwayi) is a critically-endangered New World quail species endemic to Sonoran Desert grasslands of North America. It suffered severe population declines during the nineteenth and twentieth centuries, with its persistence now reliant upon a captive breeding program that requires careful genetic management to maintain extant genetic diversity. Although nuclear microsatellite DNA markers existed for the closely related Northern Bobwhite (C. virginianus), none were available for Masked Bobwhite to inform necessary management decisions. METHODS AND RESULTS Paired-end Illumina© sequencing was conducted to screen the Masked Bobwhite genome for microsatellite loci. We identified 18 loci exhibiting high polymorphism and limited deviations from genetic equilibrium expectations. These loci were amplified in 78 individuals. Familial relationships were reconstructed via sibship methods and compared to manually-curated pedigree data. Thirteen of fifteen full-sibling groups in the pedigree were exactly reconstructed (86.6%). Three other full-sibling groups partially matched pedigree relationships with high statistical confidence, and likely represented pedigree inaccuracies. Four additional full-sibling pairs were identified with low statistical confidence and likely resulted from analytical artifacts. CONCLUSIONS The novel microsatellite loci accurately reconstructed parent-offspring and sibling relationships. These loci will be useful for guiding genetic management decisions and identifying pedigree inaccuracies in the captive breeding program.
Collapse
Affiliation(s)
- Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Rd., Dexter, NM, 88230, USA.
- Abernathy Fish Technology Center, U.S. Fish and Wildlife Service, 1440 Abernathy Creek Rd., Longview, WA, 98632, USA.
| | - Wade D Wilson
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Rd., Dexter, NM, 88230, USA
| |
Collapse
|
47
|
Thelingwani RS, Jonhera CA, Masimirembwa C. Analysis of data and common mutations encountered during routine parentage testing in Zimbabwe. Sci Rep 2024; 14:1385. [PMID: 38228706 DOI: 10.1038/s41598-024-51987-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
We analyzed parentage data collected over a ten-year period in a Zimbabwean DNA testing laboratory. Parentage case types, prevalence, exclusion data, mutations rates and observed genotyping irregularities were analyzed. We report analysis results from 1303 cases. DNA extraction and STR typing was conducted using standard commercial kits. Paternity was the most requested test (87.37%) followed by the indirect biological kinship tests (7.01%). Duo paternity (motherless) was the most common paternity test for both regular and court cases. We observed 367 paternity exclusions from 1135 cases, giving an overall paternity exclusion rate of 32.33%. Maternity had the lowest exclusion rate (8.33%), with criminal cases having the highest paternity (61.11%) and maternity (33.33%) exclusion rates. The number of mismatched STR loci ranged from 2-12 for duo cases and 4-18 for the trio cases. FGA, D2S1338, D18S51 and D2S441 were the most informative markers for exclusion. We detected 30 mutations out of 837 cases with an estimated paternal and maternal mutation rate of 0.0021 and 0.0011 respectively. Triallelic patterns were only observed at the TPOX locus with allele 10 and 11 being the extra alleles transmitted. Our report provides forensic parameters which can improve parentage and forensic analysis in Zimbabwe.
Collapse
Affiliation(s)
- Roslyn Stella Thelingwani
- Forensic Science Unit, Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe.
- CradleOmics, Block C, Wilkins Hospital Complex, Harare, Zimbabwe.
| | - Catherine Ashley Jonhera
- Forensic Science Unit, Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
| | - Collen Masimirembwa
- Forensic Science Unit, Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
| |
Collapse
|
48
|
Orazov A, Yermagambetova M, Myrzagaliyeva A, Mukhitdinov N, Tustubayeva S, Turuspekov Y, Almerekova S. Plant height variation and genetic diversity between Prunus ledebouriana (Schlecht.) YY Yao and Prunus tenella Batsch based on using SSR markers in East Kazakhstan. PeerJ 2024; 12:e16735. [PMID: 38223754 PMCID: PMC10788089 DOI: 10.7717/peerj.16735] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Background Genetic differences between isolated endemic populations of plant species and those with widely known twin species are relevant for conserving the biological diversity of our planet's flora. Prunus ledebouriana (Schlecht.) YY Yao is an endangered and endemic species of shrub almond from central Asia. Few studies have explored this species, which is closely related and morphologically similar to the well-known Prunus tenella Batsch. In this article, we present a comparative analysis of studies of three P. ledebouriana populations and one close population of P. tenella in Eastern Kazakhstan in order to determine the particular geographic mutual replacement of the two species. Methods The populations were collected from different ecological niches, including one steppe population near Ust-Kamenogorsk (P. tenella) and three populations (P. ledebouriana) in the mountainous area. Estimation of plant height using a t-test suggested a statistically significant difference between the populations and the two species (P < 0.0001). DNA simple sequence repeat (SSR) markers were applied to study the two species' genetic diversity and population structure. Results A total of 19 polymorphic SSR loci were analyzed, and the results showed that the population collected in mountainous areas had a lower variation level than steppe populations. The highest level of Nei's genetic diversity index was demonstrated in the 4-UK population (0.622) of P. tenella. The lowest was recorded in population 3-KA (0.461) of P. ledebouriana, collected at the highest altitude of the four populations (2,086 meters above sea level). The total genetic variation of P. ledebouriana was distributed 73% within populations and 27% between populations. STRUCTURE results showed that two morphologically similar species diverged starting at step K = 3, with limited population mixing. The results confirmed the morphological and genetic differences between P. tenella and P. ledebouriana and described the level of genetic variation for P. ledebouriana. The study's results proved that the steppe zone and mountain altitude factor between P. tenella and isolated mountain samples of P. ledebouriana.
Collapse
Affiliation(s)
- Aidyn Orazov
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Moldir Yermagambetova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anar Myrzagaliyeva
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
| | - Nashtay Mukhitdinov
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Shynar Tustubayeva
- School of Natural Sciences, Astana International University, Astana, Kazakhstan
| | - Yerlan Turuspekov
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Shyryn Almerekova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
49
|
Fu R, Zhao L, Chen C, Wang J, Lu D. Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut. Biomolecules 2024; 14:79. [PMID: 38254679 PMCID: PMC10813778 DOI: 10.3390/biom14010079] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.
Collapse
Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| |
Collapse
|
50
|
Salas-Castañeda MR, Saavedra-Sotelo NC, Cruz-Barraza JA, Bisbal-Pardo CI, Rocha-Olivares A. Novel microsatellite markers suggest significant genetic isolation in the Eastern Pacific sponge Aplysina gerardogreeni. Mol Biol Rep 2024; 51:87. [PMID: 38183556 PMCID: PMC10771372 DOI: 10.1007/s11033-023-09043-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 10/25/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND The Eastern Tropical Pacific (ETP) harbors a great diversity of Porifera. In particular, the Aplysina genus has acquired biotechnological and pharmacological importance. Nevertheless, the ecological aspects of their species and populations have been poorly studied. Aplysina gerardogreeni is the most conspicuous verongid sponge from the ETP, where it is usually found on rocky-coralline ecosystems. We evaluated the polymorphism levels of 18 microsatellites obtained from next-generation sequencing technologies. Furthermore, we tested the null hypothesis of panmixia in A. gerardogreeni population from two Mexican-Pacific localities. METHODS AND RESULTS A total of 6,128,000 paired reads were processed of which primer sets of 18 microsatellites were designed. The loci were tested in 64 specimens from Mazatlan, Sinaloa (N = 32) and Isabel Island, Nayarit (N = 32). The microsatellites developed were moderately polymorphic with a range of alleles between 2 and 11, and Ho between 0.069 and 0.785. Fifteen loci displayed significant deviation from the Hardy-Weinberg equilibrium. No linkage disequilibrium was detected. A strong genetic structure was confirmed between localities using hierarchical Bayesian analyses, principal coordinates analyses, and fixation indices (FST = 0.108*). All the samples were assigned to their locality; however, there was a small sign of mixing between localities. CONCLUSIONS Despite the moderate values of diversity in microsatellites, they showed a strong signal of genetic structure between populations. We suggest that these molecular markers can be a relevant tool to evaluate all populations across the ETP. In addition, 17 of these microsatellites were successfully amplified in the species A. fistularis and A. lacunosa, meaning they could also be applied in congeneric sponges from the Caribbean Sea. The use of these molecular markers in population genetic studies will allow assessment of the connectivity patterns in species of the Aplysina genus.
Collapse
Affiliation(s)
- Manuel Ricardo Salas-Castañeda
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad Universitaria Coyoacán, C.P. 04510, Mexico City, Mexico
- Unidad Académica Mazatlán, Instituto Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena s/n, CP 82000, Mazatlán, Sinaloa, Mexico
| | - Nancy C Saavedra-Sotelo
- Facultad de Ciencias del Mar, Universidad Autónoma de Sinaloa (UAS), Mazatlán, Sinaloa, Mexico
| | - José Antonio Cruz-Barraza
- Unidad Académica Mazatlán, Instituto Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena s/n, CP 82000, Mazatlán, Sinaloa, Mexico.
| | - Celia Isabel Bisbal-Pardo
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Axayácatl Rocha-Olivares
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| |
Collapse
|