scholarly journals Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States

2021 ◽  
Author(s):  
Carlos A Flores-Lopez ◽  
Elizabeth A Mitchell ◽  
Carolina E Reisenman ◽  
Sahotra Sarkar ◽  
Philip C Williamson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Copy ◽  
High Genetic Diversity ◽  
Genetic Lineages ◽  
Control Programs ◽  
The Usa

Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of T. cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T. indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using nucleotide sequences from four single-copy loci (COII-ND1, MSH2, DHFR-TS, TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those 4 genes collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi lineages should lead to an increased focus on understanding the epidemiological importance of this lineage, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.

scholarly journals Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Vessela Mavrodieva ◽  
Delano James ◽  
Karen Williams ◽  
Sarika Negi ◽  
Aniko Varga ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Common Source ◽  
Plum Pox Virus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
The Usa ◽  
Sequence Identities ◽  
Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

scholarly journals The Liver and the Hepatic Immune Response in Trypanosoma cruzi Infection, a Historical and Updated View

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1074
Author(s):  
Natalia Vacani-Martins ◽  
Marcelo Meuser-Batista ◽  
Carina de Lima Pereira dos Santos ◽  
Alejandro Marcel Hasslocher-Moreno ◽  
Andrea Henriques-Pons
Keyword(s):  
Immune Response ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Clinical Signs ◽  
Cell Types ◽  
Experimental Models ◽  
Chronic Patients ◽  
The Usa ◽  
Multiple Cell ◽  
Underlying Mechanisms

Chagas disease was described more than a century ago and, despite great efforts to understand the underlying mechanisms that lead to cardiac and digestive manifestations in chronic patients, much remains to be clarified. The disease is found beyond Latin America, including Japan, the USA, France, Spain, and Australia, and is caused by the protozoan Trypanosoma cruzi. Dr. Carlos Chagas described Chagas disease in 1909 in Brazil, and hepatomegaly was among the clinical signs observed. Currently, hepatomegaly is cited in most papers published which either study acutely infected patients or experimental models, and we know that the parasite can infect multiple cell types in the liver, especially Kupffer cells and dendritic cells. Moreover, liver damage is more pronounced in cases of oral infection, which is mainly found in the Amazon region. However, the importance of liver involvement, including the hepatic immune response, in disease progression does not receive much attention. In this review, we present the very first paper published approaching the liver’s participation in the infection, as well as subsequent papers published in the last century, up to and including our recently published results. We propose that, after infection, activated peripheral T lymphocytes reach the liver and induce a shift to a pro-inflammatory ambient environment. Thus, there is an immunological integration and cooperation between peripheral and hepatic immunity, contributing to disease control.

scholarly journals Rates of DNA evolution in Drosophila depend on function and developmental stage of expression.

Genetics ◽  
1993 ◽  
Vol 133 (2) ◽  
pp. 291-298
Author(s):  
J R Powell ◽  
A Caccone ◽  
J M Gleason ◽  
L Nigro
Keyword(s):  
Dna Hybridization ◽  
Developmental Stages ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Copy ◽  
Evolutionary Divergence ◽  
Cdna Sequences ◽  
Copy Dna ◽  
Dna 2 ◽  
Single Copy Dna

Abstract DNA-sequence divergence of genes expressed in the embryonic stage was compared with the divergence of genes expressed in adults for 13 species of Drosophila representing various degrees of relatedness. DNA-DNA hybridization experiments were conducted using as tracers complementary DNA (cDNA) reversed transcribed from poly(A)+ mRNA isolated from different developmental stages. The results indicate: (1) cDNA is less diverged than total single-copy DNA; (2) cDNA sequences are not in the rapidly evolving fraction of the single-copy genome of Drosophila; (3) early in evolutionary divergence embryonic messages are about half as diverged as adult messages; sequence data from some of the species compared indicate this is likely due to differences in rates of silent substitutions in genes expressed at different stages of development; and (4) at greater evolutionary distance, the differences in embryonic and adult messages disappear; this could be due to lineage-specific shifts in codon usage.

scholarly journals Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

2018 ◽  
Author(s):  
Siyue Xiao ◽  
Yunheng Ji ◽  
Jian Liu ◽  
Xun Gong
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Extinction Risk ◽  
Demographic History ◽  
Single Copy ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Natural Reserve ◽  
Endangered Status

Background Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic in the dry-hot valley of Jinsha River basin from southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected, other known populations that fall outside the natural reserve may preserve specific genetic resources while face with larger extinction risk because of lacking essential monitoring. Methods In this study, we analyzed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far by sequencing three chloroplastic DNA regions (psbA-trnH, psbM-trnD, and trnS-trnG), four single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, and eleven microsatellite loci (SSR) from 102 individuals. Results and Discussion We found relative high genetic diversity within populations and high genetic differentiation among the populations of C. panzhihuaensis, which is similar with the other Asian inland cycads. Despite no significant phylogeographical structure was detected, small and unprotected populations possess higher genetic diversity and more unique haplotypes, which deserve due attention. Results of demographic dynamics suggest that human activity is the key factor that leads C. panzhihuaensis to endangered status. Basing on the genetic characterization of C. panzhihuaensis, we proposed several practical guidelines for the conservation of this species, especially for its small populations.

scholarly journals Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

2021 ◽  
Vol 8 ◽  
Author(s):  
Carlos Flores ◽  
Naomi Ariyama ◽  
Benjamín Bennett ◽  
Juan Mena ◽  
Claudio Verdugo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Swine Industry ◽  
High Genetic Diversity ◽  
Monophyletic Cluster ◽  
Genetic Lineages ◽  
Young Pigs ◽  
Human Astroviruses ◽  
Porcine Astrovirus

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.

scholarly journals A Trypanosoma cruzi Small Surface Molecule Provides the First Immunological Evidence that Chagas' Disease Is Due to a Single Parasite Lineage

2002 ◽  
Vol 195 (4) ◽  
pp. 401-413 ◽  
Author(s):  
Javier M. Di Noia ◽  
Carlos A. Buscaglia ◽  
Claudia R. De Marchi ◽  
Igor C. Almeida ◽  
Alberto C.C. Frasch
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Cross Reactivity ◽  
Economic Problem ◽  
Future Research ◽  
Biological Traits ◽  
Small Surface ◽  
Genetic Lineages ◽  
Human Infections ◽  
Glycosylphosphatidyl Inositol

Chagas' disease is a major health and economic problem caused by the protozoan Trypanosoma cruzi. Multiple independently evolving clones define a complex parasite population that can be arranged into two broad genetic lineages termed T. cruzi I and II. These lineages have different evolutionary origin and display distinct ecological and biological traits. Here we describe a novel molecule termed TSSA for trypomastigote small surface antigen that provides the first immunological marker allowing discrimination between lineages. TSSA is a surface, glycosylphosphatidyl inositol (GPI)-anchored mucin-like protein, highly antigenic during the infection. TSSA sequences from different parasite isolates reveal a population dimorphism that perfectly matches with the two T. cruzi lineages. Interestingly, this dimorphism is restricted to the central region of the molecule, which comprises the immunodominant B cell epitopes. This sequence variability has a major impact on TSSA antigenicity, leading to no immunological cross-reactivity between both isoforms for antibodies present either in immunization or infection sera. Furthermore, the absolute seroprevalence for TSSA in confirmed Chagasic patients is restricted to T. cruzi II isoform, strongly suggesting that human infections are due to this particular subgroup. Even though association of T. cruzi II with Chagas' disease has been proposed based on molecular markers, this is the first immunological evidence supporting this hypothesis. The implications of these results for the future research on Chagas' disease could be envisaged.

scholarly journals Genome survey sequencing of common vetch (Vicia sativa L.) and genetic diversity analysis of Chinese germplasm with genomic SSR markers

2021 ◽  
Author(s):  
Lin Ma ◽  
Xiao Wang ◽  
Min Yan ◽  
Fang Liu ◽  
Shuxing Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Gc Content ◽  
Vicia Sativa ◽  
Whole Genome ◽  
Common Vetch ◽  
High Genetic Diversity ◽  
Genome Survey ◽  
Genome Features ◽  
High Quality Sequence

Abstract Background Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. Methods and results In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1568 Mbp, 0.4345 and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. Conclusion This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

scholarly journals Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1196
Author(s):  
Alfonso Herreros-Cabello ◽  
Francisco Callejas-Hernández ◽  
Núria Gironès ◽  
Manuel Fresno
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Genomic Structure ◽  
Gene Families ◽  
Infection Process ◽  
Surface Proteins ◽  
Genome Plasticity ◽  
The Core ◽  
Parasite Survival

Chagas disease caused by the parasite Trypanosoma cruzi affects millions of people. Although its first genome dates from 2005, its complexity hindered a complete assembly and annotation. However, the new sequencing methods have improved genome annotation of some strains elucidating the broad genetic diversity and complexity of this parasite. Here, we reviewed the genomic structure and regulation, the genetic diversity, and the analysis of the principal multi-gene families of the recent genomes for several strains. The telomeric and sub-telomeric regions are sites with high recombination events, the genome displays two different compartments, the core and the disruptive, and the genome plasticity seems to play a key role in the survival and the infection process. Trypanosoma cruzi (T. cruzi) genome is composed mainly of multi-gene families as the trans-sialidases, mucins, and mucin-associated surface proteins. Trans-sialidases are the most abundant genes in the genome and show an important role in the effectiveness of the infection and the parasite survival. Mucins and MASPs are also important glycosylated proteins of the surface of the parasite that play a major biological role in both insect and mammal-dwelling stages. Altogether, these studies confirm the complexity of T. cruzi genome revealing relevant concepts to better understand Chagas disease.

Genetic Characterization of Exotic Commercial Honey Bee (Hymenoptera: Apidae) Populations in Thailand Reveals High Genetic Diversity and Low Population Substructure

2019 ◽  
Vol 113 (1) ◽  
pp. 34-42 ◽  
Author(s):  
Atsalek Rattanawannee ◽  
Orawan Duangphakdee ◽  
Chanpen Chanchao ◽  
Chinachote Teerapakpinyo ◽  
Nattapot Warrit ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Honey Bee ◽  
Sequence Data ◽  
Middle Eastern ◽  
Population Substructure ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Mitochondrial Coi ◽  
Hardy Weinberg Equilibrium ◽  
Wax Production

Abstract Domestication of animal species is often associated with a reduction in genetic diversity. The honey bee, Apis mellifera Linnaeus, 1758, has been managed by beekeepers for millennia for both honey and wax production and for crop pollination. Here we use both microsatellite markers and sequence data from the mitochondrial COI gene to evaluate genetic variation of managed A. mellifera in Thailand, where the species is introduced. Microsatellite analysis revealed high average genetic diversity with expected heterozygosities ranging from 0.620 ± 0.184 to 0.734 ± 0.071 per locus per province. Observed heterozygosities were generally lower than those expected under Hardy–Weinberg equilibrium, both locally and across the population as a whole. Mitochondrial sequencing revealed that the frequency of two evolutionary linages (C—Eastern European and O—Middle Eastern) are similar to those observed in a previous survey 10 yr ago. Our results suggest that Thai beekeepers are managing their A. mellifera in ways that retain overall genetic diversity, but reduce genetic diversity between apiaries.

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