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1.
Gene ; 806: 145929, 2022 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-34461150

RESUMO

The body color of Neocaridina denticulate sinensis is a compelling phenotypic trait, in which a cascade of carotenoid metabolic processes plays an important role. The study was conducted to compare the transcriptome of cephalothoraxes among three pigmentation phenotypes (red, blue, and chocolate) of N. denticulate sinensis. The purpose of this study was to explore the candidate genes associated with different colors of N. denticulate sinensis. Nine cDNA libraries in three groups were constructed from the cephalothoraxes of shrimps. After assembly, 75022 unigenes were obtained in total with an average length of 1026 bp and N50 length of 1876 bp. There were 45977, 25284, 23605, 21913 unigenes annotated in the Nr, Swissprot, KOG, and KEGG databases, respectively. Differential expression analysis revealed that there were 829, 554, and 3194 differentially expressed genes (DEGs) in RD vs BL, RD vs CH, and BL vs CH, respectively. These DEGs may play roles in the absorption, transport, and metabolism of carotenoids. We also emphasized that electron transfer across the inner mitochondrial membrane (IMM) was a key process in pigment metabolism. In addition, a total of 6328 simple sequence repeats (SSRs) were also detected in N. denticulate sinensis. The results laid a solid foundation for further research on the molecular mechanism of integument pigmentation in the crustacean and contributed to developing more attractive aquatic animals.


Assuntos
Proteínas de Artrópodes/genética , Carotenoides/metabolismo , Decápodes/genética , Pigmentação/genética , Transcriptoma , Animais , Organismos Aquáticos , Proteínas de Artrópodes/classificação , Proteínas de Artrópodes/metabolismo , Transporte Biológico , Cor , Bases de Dados Genéticas , Decápodes/anatomia & histologia , Decápodes/metabolismo , Água Doce , Regulação da Expressão Gênica , Biblioteca Gênica , Ontologia Genética , Repetições de Microssatélites , Mitocôndrias/metabolismo , Membranas Mitocondriais/metabolismo , Anotação de Sequência Molecular , Característica Quantitativa Herdável
2.
BMC Bioinformatics ; 22(1): 429, 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34496768

RESUMO

BACKGROUND: With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across different fields, including population genetic diversity and structure analysis, the construction of genetic maps, and the investigation of intraspecies relationships. The development of accurate and efficient typing strategies for SSR-GBS is urgently needed and several tools have been published. However, to date, no suitable accurate genotyping method can tolerate single nucleotide variations (SNVs) in SSRs and flanking regions. These SNVs may be caused by PCR and sequencing errors or SNPs among varieties, and they directly affect sequence alignment and genotyping accuracy. RESULTS: Here, we report a new integrated strategy named the accurate microsatellite genotyping tool based on targeted sequencing (AMGT-TS) and provide a user-friendly web-based platform and command-line version of AMGT-TS. To handle SNVs in the SSRs or flanking regions, we developed a broad matching algorithm (BMA) that can quickly and accurately achieve SSR typing for ultradeep coverage and high-throughput analysis of loci with SNVs compatibility and grouping of typed reads for further in-depth information mining. To evaluate this tool, we tested 21 randomly sampled loci in eight maize varieties, accompanied by experimental validation on actual and simulated sequencing data. Our evaluation showed that, compared to other tools, AMGT-TS presented extremely accurate typing results with single base resolution for both homozygous and heterozygous samples. CONCLUSION: This integrated strategy can achieve accurate SSR genotyping based on targeted sequencing, and it can tolerate single nucleotide variations in the SSRs and flanking regions. This method can be readily applied to divergent sequencing platforms and species and has excellent application prospects in genetic and population biology research. The web-based platform and command-line version of AMGT-TS are available at https://amgt-ts.plantdna.site:8445 and https://github.com/plantdna/amgt-ts , respectively.


Assuntos
Repetições de Microssatélites , Nucleotídeos , Genótipo , Técnicas de Genotipagem , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites/genética
3.
J Insect Sci ; 21(5)2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34477874

RESUMO

Cuckoo bumble bees (Psithyrus) (Lepeletier, 1832) (Hymenoptera: Apidae) are a unique lineage of bees that depend exclusively on a host bumble bee species to provide nesting material, nutritional resources, and labor to rear offspring. In this study, we document usurpation incidence and population genetic data of Bombus insularis (Smith, 1861) (Hymenoptera: Apidae), a bumble bee species in the Psithyrus subgenus, on field-deployed B. huntii colonies in northern Utah, United States. Within 12 d of deploying B. huntii Greene, 1860 (Hymenoptera: Apidae) colonies at two field sites, 13 of the 16 colonies contained at least one established B. insularis female. Although our results demonstrate that field-deployed bumble bee colonies are highly susceptible to B. insularis usurpation, applying a fabricated excluder to prevent the inquiline from invading a colony was 100% effective. Sibship analysis using microsatellite genotype data of 59 B. insularis females estimates that they originated from at least 49 unique colonies. Furthermore, sibship analysis found siblings distributed between the field sites that were 7.04 km apart. Our result suggests that B. insularis females have the capacity to disperse across the landscape in search of host colonies at distances of at least 3.52 km and up to 7.04 km. Our study underscores the detrimental impact B. insularis usurpation has on the host bumble bee colony. As B. insularis significantly impacts the success of bumble bee colonies, we briefly discuss how the utilization of excluders may be useful for commercial bumble bee colonies that are used to pollinate open field crops.


Assuntos
Abelhas , Distribuição Animal , Animais , Abelhas/genética , Abelhas/fisiologia , Genética Populacional , Incidência , Repetições de Microssatélites/genética
4.
Zhongguo Zhong Yao Za Zhi ; 46(15): 3824-3831, 2021 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-34472255

RESUMO

The present study aimed to provide the protection strategies for wild germplasm resources of original plants of Viticis Fructus and a theoretical basis for the sustainable use of Viticis Fructus. The genetic diversity and genetic structures of the 232 indivi-duals in 19 populations of Vitex rotundifolia and V. trifolia were analyzed by eight SSR markers with tools such as Popgene32, GenAlex 6.502, and STRUCTURE. Bottleneck effect was detected for the population with more than 10 individuals. The results indicated that 42 and 26 alleles were detected from the populations of V. rotundifolia and V. trifolia, respectively, with average expected heterozygo-sities of 0.448 6 and 0.583 9, which are indicative of low genetic diversity. AMOVA revealed the obvious genetic variation of V. rotundifolia and V. trifolia within population(84.43%, P<0.01; 60.37%, P<0.01). Furthermore, in eight SSR loci, six from V. rotundifolia populations and two from V. trifolia populations failed to meet Hardy-Weinberg equilibrium expectations(P<0.05), which confirmed that the populations experienced bottleneck effect. As assessed by Mantel test, geographical distance posed slight impacts on the genetic variation between the populations of V. rotundifolia and V. trifolia. Principal component analysis(PCA) and STRUCTURE analysis demonstrated evident introgression of genes among various populations. The original plants of Viticis Fructus were confirmed low in genetic diversity and genetic differentiation level. Therefore, the protection of wild resources of original plants of Viticis Fructus should be strengthened to ensure its sustainable use.


Assuntos
Variação Genética , Vitex , Alelos , Frutas/genética , Geografia , Repetições de Microssatélites , Vitex/genética
5.
BMC Genomics ; 22(1): 623, 2021 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-34407764

RESUMO

BACKGROUND: The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. RESULTS: We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. CONCLUSIONS: The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.


Assuntos
Repetições de Microssatélites , Ursidae , Alelos , Animais , DNA , Genótipo , Ursidae/genética
6.
J Forensic Leg Med ; 82: 102223, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34343925

RESUMO

Human skin hosts a variety of microbes that can be transferred to surfaces ("touch microbiome"). These microorganisms can be considered as forensic markers similarly to "touch DNA". With this pilot study, we wanted to evaluate the transferability and persistence of the "touch microbiome" on a surface after the deposition of a fingerprint and its exposure for 30 days at room temperature. Eleven volunteers were enrolled in the study. Skin microbiome samples were collected by swabbing the palm of their hands; additionally, donors were asked to touch a glass microscope slide to deposit their fingerprints, that were then swabbed. Both human and microbial DNA was isolated and quantified. Amelogenin locus and 16 human STRs were amplified, whereas the V4 region of 16 S rRNA gene was sequenced using Illumina MiSeq platform. STR profiles were successfully typed for 5 out of 22 "touch DNA" samples, while a microbiome profile was obtained for 20 out of 22 "touch microbiome" samples. Six skin core microbiome taxa were identified, as well as unique donor characterizing taxa. These unique taxa may have relevance for personal identification studies and may be useful to provide forensic intelligence information also when "touch DNA" fails. Additional future studies including greater datasets, additional time points and a greater number of surfaces may clarify the applicability of "touch microbiome" studies to real forensic contexts.


Assuntos
Bactérias/classificação , Bactérias/genética , Impressões Digitais de DNA/métodos , Microbiota , RNA Ribossômico 16S/análise , Pele/microbiologia , Tato , Adulto , Idoso , Amelogenina/genética , DNA/isolamento & purificação , Conjuntos de Dados como Assunto , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Repetições de Microssatélites , Pessoa de Meia-Idade , Projetos Piloto , Análise de Sequência de RNA
7.
Molecules ; 26(16)2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34443469

RESUMO

The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.


Assuntos
DNA Forma Z/química , DNA Forma Z/genética , Evolução Molecular , Conformação de Ácido Nucleico , Proteínas/química , Proteínas/genética , Animais , Códon , DNA Forma Z/metabolismo , Genética , Humanos , Repetições de Microssatélites/genética , Proteínas/metabolismo
8.
Animal ; 15(9): 100317, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34340140

RESUMO

Mosaicism is frequently observed in aquaculture practices, and it adversely affects the production as well as the restoration programme of the sturgeon. The purpose of the present study was the induction of 2n/3n mosaic in sterlet, Acipenser ruthenus L., and compare their embryonic and larval development with diploid control sterlet. Microsatellite DNA loci genotyping was conducted for the identification of the genotypes and parentage analysis. Embryonic development was monitored in experimental groups at every 24 h interval. Identification of individual stages of embryonic development was recorded based on a 36-degree scale of development. Additionally, the BW and body length (LT) of experimental fishes were taken during 110 days of the rearing period. The Fulton's condition coefficient (F), length-weight parameters, and specific growth rate (SGR) coefficient were calculated. The analysis of embryonic development of the 2n/3n mosaic and the diploid control group did not show differences. However, higher mortality (88%) was observed in 2n/3n mosaic groups in comparison to the diploid control groups (55%). BW and body length of 2n/3n mosaic sterlet were slightly lower than the diploid control sterlet, but the differences were not statistically significant. F analysis did not confirm a lower growth performance of the fishes in the 2n/3n mosaic group. Microsatellite DNA loci genotyping confirmed both the incidence of polyspermy and retention of the second polar body. This paper presents the first report on embryonic development and growth performance of 2n/3n mosaic sturgeons.


Assuntos
Aquicultura , Peixes , Animais , Desenvolvimento Embrionário , Repetições de Microssatélites
9.
BMC Res Notes ; 14(1): 314, 2021 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-34399852

RESUMO

OBJECTIVE: Flathead catfish are rapidly expanding into nonnative waterways throughout the United States. Once established, flathead catfish may cause disruptions to the local ecosystem through consumption and competition with native fishes, including species of conservation concern. Flathead catfish often become a popular sport fish in their introduced range, and so management strategies must frequently balance the need to protect native and naturalized fauna while meeting the desire to maintain or enhance fisheries. However, there are currently few tools available to inform management of invasive flathead catfish (Pylodictis olivaris). We describe a suite of microsatellite loci that can be used to characterize population structure, predict invasion history, and assess potential mitigation strategies for flathead catfish. RESULTS: Our panel of 13 microsatellite loci were polymorphic and appear to be informative for population genetic studies of flathead catfish. We found moderate levels of diversity in four nonnative collections of flathead catfish in the Pennsylvania and Maryland sections of the Susquehanna River and the Schuylkill River, Pennsylvania. Analyses suggested patterns of genetic differentiation within- and among-rivers, highlighting the utility of this marker panel for understanding the structure and assessing the degree of connectivity among flathead catfish populations.


Assuntos
Ictaluridae , Animais , Ecossistema , Genética Populacional , Ictaluridae/genética , Repetições de Microssatélites/genética , Rios , Estados Unidos
10.
Trop Anim Health Prod ; 53(4): 434, 2021 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-34387779

RESUMO

The current context of climate change requires the conservation of local zoogenetic resources already very well adapted to the traditional breeding system, rough feeding, and heat and cold stress. This study assessed genetic diversity in local pigs in southern Benin, as a prerequisite for their sustainable use and sustainable management in Benin. A total of 69 individuals including 54 local pigs, 7 Large-White, and 8 hybrids (local pigs × Bush-pig) were genotyped by using 17 microsatellite markers. On the average, 8.94 alleles were detected per locus. Average expected and observed heterozygosities were respectively 0.51 and 0.46. Polymorphic information content was 0.61, and genetic diversity was 0.53. A phylogenetic tree gathered local pigs into three genetic clusters. Genetic structural analyses revealed introgression of Large-White's genes into the local pig's genome. Three groups were identified: hybrids (subpopulation 1), a mixture of Large-White and local pigs (subpopulation 2), and only local pigs (subpopulation 3). Symmetrical allelic distances were higher between subpopulations 1 and 2 (0.787) and then 1 and 3 (0.713). The same trend was detected for genetic distances between pairs of subpopulations. Genetic differentiation between subpopulations 2 and 3 was very weak as a consequence of high gene flow (10.82). Molecular variance analysis showed that 77% of genetic diversity within populations was related to variability between the individuals. These results showed that local pigs in southern Benin are threatened by genetic erosion and suggest prompt actions to implement sustainable conservation strategies.


Assuntos
Variação Genética , Repetições de Microssatélites , Alelos , Animais , Benin , Filogenia , Suínos/genética
11.
An Acad Bras Cienc ; 93(suppl 3): e20201649, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34378636

RESUMO

The objective of the present work was the molecular characterization of 11 parents and 101 hybrid progenies of conilon coffee, obtained through diallel crosses from the breeding program of the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (Incaper, ES, Brazil). The analyses were performed with 18 Simple Sequence Repeat (SSR) molecular markers, obtaining a total of 32 alleles. SSR markers were classified as moderately informative (PIC = 0.37), being efficient in characterizing individuals. High genetic diversity was verified in the 112 genotypes, based on the greater values of observed heterozygosity about to the expected heterozygosity (0.55 and 0.44, respectively), negative values for the fixation index (F) (-0.14), and the formation of distinct groups by UPGMA. These results indicate high genetic variability among the conilon coffee genitors, which remained similar and persisting in the progenies. The average dissimilarity between parents was 0.29 and between progenies 0.34. The progenies 38 and 40 and the parent P11 were considered the most divergent in the study. The genetic variability found can be explored in the genetic breeding of the conilon coffee and guide crossings between diversified and compatible genetic materials, for the composition of novel cultivars for the state of Espírito Santo.


Assuntos
Coffea/genética , Variação Genética , Genótipo , Hibridização Genética , Repetições de Microssatélites , Melhoramento Vegetal
12.
Nat Commun ; 12(1): 4843, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376693

RESUMO

Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3' ssDNA protrusions. By including so-called primase deserts in CRISPR/Cas9-induced DNA break configurations, we reveal that fill-in synthesis preferentially starts at the 3' tip, and find this activity to be dependent on 53BP1, and the CTC1-STN1-TEN1 (CST) and Shieldin complexes. This axis generates near-blunt ends specifically at DNA breaks with 3' overhangs, which are subsequently repaired by non-homologous end-joining. Our study provides a mechanistic explanation for a mutational signature abundantly observed in the genomes of species and cancer cells.


Assuntos
Quebras de DNA de Cadeia Dupla , DNA Polimerase I/metabolismo , DNA Primase/metabolismo , Repetições de Microssatélites/genética , Proteínas de Ligação a Telômeros/metabolismo , Animais , Sequência de Bases , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular , Células Cultivadas , Reparo do DNA por Junção de Extremidades , DNA Polimerase I/genética , DNA Primase/genética , DNA de Cadeia Simples , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Humanos , Camundongos , Complexos Multiproteicos/genética , Complexos Multiproteicos/metabolismo , Mutação , Telômero/genética , Telômero/metabolismo , Proteínas de Ligação a Telômeros/genética , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/genética , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/metabolismo
13.
Int J Mol Sci ; 22(13)2021 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-34209673

RESUMO

A cytokine storm, autoimmune features and dysfunctions of myeloid cells significantly contribute to severe coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Genetic background of the host seems to be partly responsible for severe phenotype and genes related to innate immune response seem critical host determinants. The C9orf72 gene has a role in vesicular trafficking, autophagy regulation and lysosome functions, is highly expressed in myeloid cells and is involved in immune functions, regulating the lysosomal degradation of mediators of innate immunity. A large non-coding hexanucleotide repeat expansion (HRE) in this gene is the main genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), both characterized by neuroinflammation and high systemic levels of proinflammatory cytokines, while HREs of intermediate length, although rare, are more frequent in autoimmune disorders. C9orf72 full mutation results in haploinsufficiency and intermediate HREs seem to modulate gene expression as well and impair autophagy. Herein, we sought to explore whether intermediate HREs in C9orf72 may be a risk factor for severe COVID-19. Although we found intermediate HREs in only a small portion of 240 patients with severe COVID-19 pneumonia, the magnitude of risk for requiring non-invasive or mechanical ventilation conferred by harboring intermediate repeats >10 units in at least one C9orf72 allele was more than twice respect to having shorter expansions, when adjusted for age (odds ratio (OR) 2.36; 95% confidence interval (CI) 1.04-5.37, p = 0.040). The association between intermediate repeats >10 units and more severe clinical outcome (p = 0.025) was also validated in an independent cohort of 201 SARS-CoV-2 infected patients. These data suggest that C9orf72 HREs >10 units may influence the pathogenic process driving more severe COVID-19 phenotypes.


Assuntos
Proteína C9orf72/genética , COVID-19/patologia , Repetições de Microssatélites , Adulto , Fatores Etários , Idoso , Esclerose Amiotrófica Lateral/genética , Esclerose Amiotrófica Lateral/patologia , COVID-19/genética , COVID-19/virologia , Feminino , Predisposição Genética para Doença , Genótipo , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Razão de Chances , Fatores de Risco , SARS-CoV-2/isolamento & purificação , Índice de Gravidade de Doença
14.
Int J Legal Med ; 135(5): 1675-1684, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34216266

RESUMO

The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.


Assuntos
Cromossomos Humanos Y/genética , Grupo com Ancestrais do Continente Europeu/genética , Variação Genética , Haplótipos , Europa (Continente)/etnologia , Migração Humana , Humanos , Repetições de Microssatélites , Filogenia , Filogeografia , Polimorfismo de Nucleotídeo Único
15.
Genes (Basel) ; 12(6)2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34200049

RESUMO

Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.


Assuntos
Cromossomos Humanos Y/genética , Haplótipos , Modelos Genéticos , Linhagem , Tempo , Triagem e Testes Direto ao Consumidor/estatística & dados numéricos , Testes Genéticos/estatística & dados numéricos , Humanos , Masculino , Repetições de Microssatélites , Taxa de Mutação , Polimorfismo Genético
16.
Forensic Sci Int ; 325: 110887, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34198074

RESUMO

In cases involving identification of missing persons, mass disasters and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA profiling. Standard methods for extraction of DNA from such samples involve grinding of the bone and teeth samples. Here, we present an extremely efficient protocol for recovery of DNA from bone samples by a method of scrapping. The study was carried out on 25 samples and it was found that the quantity of DNA isolated by the scrapping method was up to 1.131 ng/µl with a success rate of 93% as compared to a much lower yield of 0.359 ng/µl DNA isolated with a success rate of 28% through the grinding method. The scrapping method of DNA extraction has been proven to be extremely useful in forensic examination of challenging samples that had multiple failures using the traditional grinding method.


Assuntos
Impressões Digitais de DNA , DNA/análise , Fêmur/química , Repetições de Microssatélites , Manejo de Espécimes/métodos , Genética Forense/métodos , Humanos , Reação em Cadeia da Polimerase Multiplex
17.
Genetica ; 149(4): 239-251, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34231081

RESUMO

Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.


Assuntos
Genoma de Cloroplastos , Polimorfismo Genético , Prunus armeniaca/genética , Ecossistema , Espécies em Perigo de Extinção , Haplótipos , Repetições de Microssatélites , Sementes/genética
18.
Methods Mol Biol ; 2289: 199-219, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270072

RESUMO

Cork oak (Quercus suber L.) is a forest tree species of the family Fagaceae. It is characterized by long life cycles which hamper doubled haploid plant production to obtain homozygotes and pure lines. The time-consuming method of repeated backcrossings by conventional breeding techniques to produce pure lines is impractical in woody species. Nevertheless, biotechnology has offered new tools to make it possible. A doubled haploid plant or embryo is one that is developed by the doubling of a haploid set of chromosomes. A protocol to produce doubled haploids of cork oak has been developed through microspore embryogenesis. By a heat stress treatment, the microspores inside the anther leave the gametophytic pathway and react shifting their development to the sporophytic pathway by means of which haploid embryos are obtained. Chromosome duplication of haploids from cork oak anther cultures occurs either spontaneously or may be induced by the application of antimitotic agents (e.g., colchicine, oryzalin, amiprophos-methyl). Furthermore, a genetic test is designed through microsatellite markers to elucidate whether the diploid embryos obtained are originally haploids which spontaneously duplicated their genome, or alternatively those embryos are generated from the diploid tissue of the anther wall. Here we describe a detailed protocol to produce doubled haploid individuals from cork oak anther cultures by using temperature stress and antimitotic agents.


Assuntos
Flores/genética , Resposta ao Choque Térmico/genética , Quercus/genética , Diploide , Haploidia , Repetições de Microssatélites/genética , Melhoramento Vegetal/métodos , Sementes/genética , Temperatura
19.
Gene ; 800: 145845, 2021 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-34274465

RESUMO

The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.


Assuntos
Areca/genética , Perfilação da Expressão Gênica/métodos , Genoma de Planta , Genomas de Plastídeos , DNA Mitocondrial , Repetições de Microssatélites , Filogenia
20.
Science ; 372(6549)2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34324427

RESUMO

The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.


Assuntos
Repetições de Dinucleotídeos , Proteína 2 de Ligação a Metil-CpG/metabolismo , Repetições de Microssatélites , Nucleossomos/metabolismo , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/química , 5-Metilcitosina/metabolismo , Animais , Células Cultivadas , Cromatina/química , Cromatina/metabolismo , Cromatina/ultraestrutura , Citosina/química , Citosina/metabolismo , Metilação de DNA , Células-Tronco Embrionárias/metabolismo , Fibroblastos , Lobo Frontal/metabolismo , Proteína 2 de Ligação a Metil-CpG/química , Proteína 2 de Ligação a Metil-CpG/genética , Camundongos , Neurônios/metabolismo , Conformação de Ácido Nucleico , Oxirredução , Ligação Proteica , Domínios Proteicos , Síndrome de Rett/genética , Síndrome de Rett/metabolismo , Transcrição Genética
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