scholarly journals PbGP43 Genotyping Using Paraffin-embedded Biopsies of Human Paracoccidioidomycosis Reveals a Genetically Distinct Lineage in the Paracoccidioides Brasiliensis Complex

2021 ◽  
Author(s):  
Giannina Ricci ◽  
Emeline Boni Campanini ◽  
Angela Satie Nishikaku ◽  
Rosana Puccia ◽  
Mariangela Ester Alencar Marques ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Paracoccidioides Brasiliensis ◽  
Haplotype Network ◽  
Histopathological Diagnosis ◽  
Gene Products ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Ffpe Samples ◽  
Distinct Lineage ◽  
Phylogenetic Lineages

Abstract Paracoccidioidomycosis (PCM) is a systemic mycosis caused by a group of cryptic species embedded in the Paracoccidioides brasiliensis complex and Paracoccidioides lutzii. Four species were recently inferred to belong to the P. brasiliensis complex, but the high genetic diversity found in both human and environmental samples have suggested that the number of lineages may be higher.This study aimed to assess the 43-kilodalton glycoprotein genotypes (PbGP43) in paraffin-embedded samples from PCM patients to infer the phylogenetic lineages of the P. brasiliensis complex responsible for causing the infection.Formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with histopathological diagnosis of PCM were analyzed. DNAs were extracted and amplified for a region of the second exon of the PbGP43 gene. Products were sequenced and aligned with other PbGP43 sequences available. A haplotype network and the phylogenetic relationships among sequences were inferred. Amino acid substitutions were investigated regarding the potential to modify physicochemical properties in the proteins.Six phylogenetic lineages were identified as belonging to the P. brasiliensis complex. Two lineages did not group with any of the four recognized species of the complex, and, interestingly, one of them comprised only FFPE samples. A coinfection involving two lineages was found. Five parsimony-informative sites were identified and three of them showed radical non-synonymous substitutions with the potential to promote changes in the protein.This study expands the knowledge regarding the genetic diversity existing in the P. brasiliensis complex and shows the potential of FFPE samples in species identification and in detecting coinfections.

scholarly journals Genetic diversity of the Green Turtle (Testudines: Cheloniidae: Chelonia mydas (Linnaeus, 1758)) population nesting at Kosgoda Rookery, Sri Lanka

2017 ◽  
Vol 9 (6) ◽  
pp. 10261
Author(s):  
E. M.L. Ekanayake ◽  
T. Kapurusinghe ◽  
M. M. Saman ◽  
D. S. Rathnakumara ◽  
P. Samaraweera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Green Turtle ◽  
Chelonia Mydas ◽  
Sea Turtle ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Hardy Weinberg Equilibrium ◽  
Turtle Population ◽  
The Mean

We determined the genetic diversity of the Green Turtle Chelonia mydas (Linneaus, 1758) nesting at Kosgoda rookery, the second largest sea turtle aggregation on the southwestern coast of Sri Lanka.  Skin tissue samples were collected from 68 nesting females and genetic diversity was estimated using six microsatellite loci.  High genetic diversity was observed within the population as all loci analyzed were highly polymorphic with a total of 149 alleles observed.  The mean number of alleles per locus was 24.7 and the mean observed and expected heterozygosity across all loci were 0.75 and 0.93, respectively.  It appears that five out of six loci were not in Hardy-Weinberg equilibrium, while micro-checker analysis suggested that the Kosgoda Green Turtle population was possibly in equilibrium.  The viability of a population is unlikely to be reduced if high genetic diversity is maintained within it.  Although the Green Turtle population nesting at Kosgoda is small compared to other nesting rookeries in the world, the high genetic diversity observed suggests that the population may not be undergoing a bottleneck.

Multilocus sequence typing (MLST) analysis of 104Clostridium difficilestrains isolated from China

2012 ◽  
Vol 141 (1) ◽  
pp. 195-199 ◽  
Author(s):  
Q. YAN ◽  
J. ZHANG ◽  
C. CHEN ◽  
H. ZHOU ◽  
P. DU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clostridium Difficile ◽  
Multilocus Sequence Typing ◽  
Geographical Origin ◽  
Host Population ◽  
High Genetic Diversity ◽  
Dominant Type ◽  
Mlst Analysis ◽  
Phylogenetic Lineages ◽  
Sequence Types

SUMMARYThe phylogenetic and epidemic relationships of 104 clinical isolatesof Clostridium difficilefrom three hospitals of different geographical and population sources in China were investigated by multilocus sequence typing. Twenty-two sequence types (STs) were identified, four of which, ST117, ST118, ST119 and ST129, were novel. No geographically specific and host population-specific phylogenetic lineages were found and there was no correlation between geographical origin or host population and strain genotype. ST37 was the dominant type in our survey but the four novel STs underline the high genetic diversity and unique polymorphisms inC. difficilefrom China.

scholarly journals Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amer Al-Jawabreh ◽  
Suheir Ereqat ◽  
Kamal Dumaidi ◽  
Hanan Al-Jawabreh ◽  
Abedelmajeed Nasereddin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Haplotype Network ◽  
Health Concern ◽  
Diversity Analysis ◽  
High Genetic Diversity ◽  
Genetic Diversity Analysis ◽  
First Time

Abstract Objectives SARS-CoV-2, severe respiratory syndrome coronavirus-2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS-CoV-2 in Palestine in fall 2020. Results To achieve these aims, whole genome sequencing of SARS-CoV-2, phylogenetic analysis, haplotype networking and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS-CoV-2 genome sequences, in which cluster-I comprised the majority of clusters by 90%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster-I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima’s D and Fu-Li’s-F tests (− 2.11 and 2.74, respectively), highest number of mutations (Eta = 120), highest number of haplotypes (h = 17), and highest average number of nucleotide differences between any two sequences (S = 118). The study confirmed the high genetic diversity among the Palestinian of SARS-CoV-2 which possessed high number of mutations including one which was reported for the first time.

scholarly journals Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia

DEPIK ◽  
2014 ◽  
Vol 3 (1) ◽  
Author(s):  
Nebuchadnezzar Akbar ◽  
Neviaty P Zamani ◽  
Hawis H Madduppa
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Yellowfin Tuna ◽  
Conservation Strategy ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Chain Reactions ◽  
Polymerase Chain ◽  
Two Populations

Abstract. Yellowfin tuna (Thunnus albacores) is a large, pelagic, and migratory species of tuna that inhabits Moluccas Sea in Indonesia, and most sea environment worldwide. However, high fishing activities tend to happen in the Indonesia region and catch product appear to be decreasing. A better understanding of yellowfin tuna genetic diversity is required to plan better conservation strategy of tuna. The study was conducted to infer the genetic diversity of yellowfin tuna (T. albacores) in the Moluccas Sea. A total of 41 tissue samples of yellowfin tuna were collected from two regions in the Moluccas Sea (North Moluccas and Ambon) during an expedition in February 2013. The results showed that genetic diversity and nucleotide diversity of yellowfin tuna from North Moluccas population was 0.984 and 0.021, respectively; while in Ambon population, the genetic and nucleotide diversities were 1.00 and 0.018, respectively. The high genetic diversity (0.990) and nucleotide diversity (0.020) between two populations were observed. Based on phylogenetic analysis, no genetic differentiation between the two populations in Moluccas Sea was revealed .Keywords :  Population genetics; Haplotype diversity; Coral Triangle; Phylogenetics; Polymerase Chain Reactions (PCRs) Abstrak. Tuna sirip kuning (Thunnus albacores) adalah ikan komersial penting dan ditemukan di Laut Maluku, Indonesia. Tetapi, aktivitas penangkapan ikan tuna sirip kuning dapat menurunkan kualitas dan kuantitas stok ikan, sehingga perlu adanya pengkajian keragaman genetik ikan tuna sirip kuning. Pemahaman yang baik tentang keragaman genetika dibutuhkan untuk merencanakan strategi konservasi tuna yang lebih baik. Penelitian ini bertujuan untuk mengetahui keragaman genetik  ikan tuna sirip kuning dari dua populasi di Laut Maluku. Sebanyak 41 sampel jaringan dari tuna sirip kuning dikumpulkan dari dua populasi di Laut Maluku (Maluku Utara dan Ambon) selama ekspedisi pada bulan Februari 2013. Hasil penelitian menunjukkan bahwa keragaman genetik populasi tuna sirip kuning pada perairan Maluku Utara dan Ambon masing-masing sebesar 0,984 dan 1,00 sedangkan nilai keragaman nukleotida masing-masing bernilai 0,021 dan 0,018. Nilai keragaman genetik dan keragaman nukloetida yang tinggi didaptkan antar kedua populasi masing-masing sebesar 0,990 dan 0,020. Berdasarkan analisis filogenetik, dua populasi di Laut Maluku ini memiliki kedekatan secara genetik.Kata kunci : Genetika populasi; Keragaman haplotipe; Segitiga Terumbu Karang; Filogenetika; Polymerase Chain Reaction (PCR)

scholarly journals Balancing selection and high genetic diversity of Plasmodium vivax circumsporozoite central region in parasites from Brazilian Amazon and Rio de Janeiro Atlantic Forest

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241426
Author(s):  
Natália Ketrin Almeida-de-Oliveira ◽  
Rebecca de Abreu-Fernandes ◽  
Lidiane Lima-Cury ◽  
Aline Rosa de Lavigne ◽  
Anielle de Pina-Costa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Atlantic Forest ◽  
Rio De Janeiro ◽  
Balancing Selection ◽  
Cell Epitope ◽  
Haplotype Network ◽  
Brazilian Amazon ◽  
Variable Number ◽  
Terminal Region ◽  
High Genetic Diversity

Circumsporozoite protein (CSP) is the primary pre-erythrocytic vaccine target in Plasmodium species. Knowledge about their genetic diversity can help predict vaccine efficacy and the spread of novel parasite variants. Thus, we investigated pvcsp gene polymorphisms in 219 isolates (136 from Brazilian Amazon [BA], 71 from Rio de Janeiro Atlantic Forest [AF], and 12 from non-Brazilian countries [NB]). Forty-eight polymorphic sites were detected, 46 in the central repeat region (CR), and two in the C-terminal region. Also, the CR presents InDels and a variable number of repeats. All samples correspond to the VK210 variant, and 24 VK210 subtypes based on CR. Nucleotide diversity (π = 0.0135) generated a significant number of haplotypes (168) with low genetic differentiation between the Brazilian regions (Fst = 0.208). The haplotype network revealed similar distances among the BA and AF regions. The linkage disequilibrium indicates that recombination does not seem to be acting in diversity, reinforcing natural selection’s role in accelerating adaptive evolution. The high diversity (low Fst) and polymorphism frequencies could be indicators of balancing selection. Although malaria in BA and AF have distinct vector species and different host immune pressures, consistent genetic signature was found in two regions. The immunodominant B-cell epitope mapped in the CR varies from seven to 19 repeats. The CR T-cell epitope is conserved only in 39 samples. Concerning to C-terminal region, the Th2R epitope presented nonsynonymous SNP only in 6% of Brazilian samples, and the Th3R epitope remained conserved in all studied regions. We conclude that, although the uneven distribution of alleles may jeopardize the deployment of vaccines directed to a specific variable locus, a unique vaccine formulation could protect populations in all Brazilian regions.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

scholarly journals Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ming Sun ◽  
Zhixiao Dong ◽  
Jian Yang ◽  
Wendan Wu ◽  
Chenglin Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Large Scale ◽  
Genetic Research ◽  
High Yield ◽  
Yield Strain ◽  
Tissue Samples ◽  
Prairie Grass ◽  
The Future ◽  
Genomic Resource

Abstract Background Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. Results Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. Conclusion A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.

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