scholarly journals Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets

2021 ◽  
Author(s):  
Lei Han ◽  
Tianming Lan ◽  
Desheng Li ◽  
Haimeng Li ◽  
Linhua Deng ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Population Genetic ◽  
Drug Targets ◽  
Giant Panda ◽  
Host Population ◽  
Potential Drug ◽  
Chitin Synthesis ◽  
Population Genetic Analysis ◽  
A Genome ◽  
The Impact

Helminth diseases have long been a threat to the health of humans and animals. Roundworms are important organisms for studying parasitic mechanisms, disease transmission and prevention. The study of parasites in the giant panda is of importance for understanding how roundworms adapt to the host. Here, we report a high-quality chromosome-scale genome of Baylisascaris schroederi with a genome size of 253.60 Mb and 19,262 predicted protein-coding genes. We found that gene families related to epidermal chitin synthesis and environmental information processes in the roundworm genome have expanded significantly. Furthermore, we demonstrated unique genes involved in essential amino acid metabolism in the B. schroederi genome, inferred to be essential for the adaptation to the giant panda-specific diet. In addition, under different deworming pressures, we found that four resistance-related genes (glc-1, nrf-6, bre-4 and ced-7) were under strong positive selection in a captive population. Finally, 23 known drug targets and 47 potential drug target proteins (essential homologues linked to lethal phenotypes) were identified. The genome provides a unique reference for inferring the early evolution of roundworms and their adaptation to the host. Population genetic analysis and drug sensitivity prediction provide insights revealing the impact of deworming history on population genetic structure of importance for disease prevention.

scholarly journals Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets

2021 ◽  
Author(s):  
Lei Han ◽  
Tianming Lan ◽  
Desheng Li ◽  
Haimeng Li ◽  
Linhua Deng ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Population Genetic ◽  
Drug Targets ◽  
Giant Panda ◽  
Chitin Synthesis ◽  
Population Genetic Analysis ◽  
Adaptation Mechanism ◽  
Living Fossil ◽  
A Genome ◽  
The Impact

Helminth diseases have long been a threat to the health of humans and animals. Roundworms are important organisms for studying parasitic mechanisms, disease transmission and prevention. The study of parasites in the living fossil giant panda is of great significance for understanding the adaptation mechanism of roundworms to the host. Here, we report a high-quality chromosome-scale genome of Baylisascaris schroederi with a genome size of 262 Mb and 19,291 predicted protein-coding genes. We found a significant expansion of genes related to epidermal chitin synthesis and environmental information processing in roundworms genome. Furthermore, we demonstrated unique genes involved in essential amino acid metabolism in the B. schroederi genome, inferred to be essential for the adaptation to the giant panda-specific diet. In addition, under different deworming pressures, we found that four resistance-related genes (glc-1, nrf-6, bre-4 and ced-7) were under strong positive selection in captive population. Finally, 23 known drug targets and 47 potential target proteins were identified. The genome provides a unique reference for inferring the early evolution of roundworms and the mechanisms underlying adaptive. Population genetic analysis and drug prediction provide insights for revealing the impact of deworming history on population genetic structure and prevention.

scholarly journals SINE jumping contributes to large-scale polymorphisms in the pig genomes

2021 ◽  
Author(s):  
Cai Chen ◽  
Enrico D'Alessandro ◽  
Eduard Murani ◽  
Yao Zheng ◽  
Domenico Giosa ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Population Genetic ◽  
Large Scale ◽  
Structural Variations ◽  
Population Genetic Analysis ◽  
Protein Coding ◽  
Pig Breeds ◽  
A Genome ◽  
Trait Locus ◽  
And Cluster Analysis

Abstract Background: Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results: Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5% intragenic and 26.5% intergenic), followed by SINEA2 (10.5% intragenic and 9% intergenic) and SINEA3 (12.5% intragenic and 5.0% intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80% accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34% of SINE RIPs generated by SINEA1 element. Over 65% of pig SINE RIPs overlap with genes, with significant enrichment in the first and second introns of protein-coding and long non-coding RNA genes. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions: Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35, 000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

scholarly journals PANOPLY: A cloud-based platform for automated and reproducible proteogenomic data analysis

2020 ◽  
Author(s):  
D. R. Mani ◽  
Myranda Maynard ◽  
Ramani Kothadia ◽  
Karsten Krug ◽  
Karen E. Christianson ◽  
...  
Keyword(s):  
Data Analysis ◽  
Drug Targets ◽  
Complex Data ◽  
Potential Drug ◽  
Post Translational Modification ◽  
Simple Interface ◽  
The Impact ◽  
Potential Drug Targets ◽  
Insight Into ◽  
Generation Sequencing

ABSTRACTProteogenomics involves the integrative analysis of genomic, transcriptomic, proteomic and post-translational modification data produced by next-generation sequencing and mass spectrometry-based proteomics. Several publications by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and others have highlighted the impact of proteogenomics in enabling deeper insight into the biology of cancer and identification of potential drug targets. In order to encapsulate the complex data processing required for proteogenomics, and provide a simple interface to deploy a range of algorithms developed for data analysis, we have developed PANOPLY—a cloud-based platform for automated and reproducible proteogenomic data analysis. A wide array of algorithms have been implemented, and we highlight the application of PANOPLY to the analysis of cancer proteogenomic data.

scholarly journals Swayne's hartebeest in Ethiopia: population estimate, genetic variability and competition with livestock

Oryx ◽  
2021 ◽  
pp. 1-9
Author(s):  
Misganaw Tamrat ◽  
Anagaw Atickem ◽  
Øystein Flagstad ◽  
Martha Fischer ◽  
Christian Roos ◽  
...  
Keyword(s):  
Protected Areas ◽  
Disease Transmission ◽  
Population Genetic ◽  
National Park ◽  
Resource Competition ◽  
Population Decline ◽  
Iucn Red List ◽  
Ethiopian Rift ◽  
Population Genetic Analysis ◽  
D Loop

Abstract Swayne's hartebeest Alcelaphus buselaphus swaynei was once widely distributed in the Horn of Africa. By the early 20th century, however, it was extirpated across most of its range and is now limited to two relict populations in the Ethiopian Rift Valley and categorized as Endangered on the IUCN Red List. In this study, we estimated the size and genetic diversity of these two remaining populations, with a particular focus on competition with livestock. We used a total block count method for both Swayne's hartebeest and livestock population counts, and faecal samples for a population genetic analysis. We estimated the total population of Swayne's hartebeest to be 1,528, with 518 individuals in Senkele Swayne's Hartebeest Sanctuary and 1,010 individuals in Maze National Park. Livestock densities were 212 and 153 times those of Swayne's hartebeest in Senkele Swayne's Hartebeest Sanctuary and Maze National Park, respectively. Among 73 mitochondrial D-loop sequences (34 from Senkele Swayne's Hartebeest Sanctuary and 39 from Maze National Park), we found 22 haplotypes (Senkele 12, Maze 16, shared 6). Population genetic parameters suggest only weak sub-structuring between the two populations (FST = 0.164). Despite the positive population trends in both protected areas, the spatial overlap with livestock may lead to future population decline as a result of resource competition and disease transmission. We therefore recommend further translocation to other protected areas within the species’ former range.

scholarly journals A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency

2014 ◽  
Vol 23 (19) ◽  
pp. 5123-5132 ◽  
Author(s):  
Linda P. O'Reilly ◽  
Olivia S. Long ◽  
Murat C. Cobanoglu ◽  
Joshua A. Benson ◽  
Cliff J. Luke ◽  
...  
Keyword(s):  
Drug Targets ◽  
Rnai Screen ◽  
Potential Drug ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Antitrypsin Deficiency ◽  
Potential Drug Targets

scholarly journals Effects of Coinfection on the Dynamics of Two Pathogens in a Tick-Host Infection Model

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Bei Sun ◽  
Xue Zhang ◽  
Marco Tosato
Keyword(s):  
Disease Transmission ◽  
Host Population ◽  
Infection Model ◽  
Uniform Persistence ◽  
Reproduction Numbers ◽  
Boundary Equilibrium ◽  
Tick Borne Disease ◽  
Host Infection ◽  
The Impact ◽  
Disease Free

As both ticks and hosts may carry one or more pathogens, the phenomenon of coinfection of multiple tick-borne diseases becomes highly relevant and plays a key role in tick-borne disease transmission. In this paper, we propose a coinfection model involving two tick-borne diseases in a tick-host population and calculate the basic reproduction numbers at the disease-free equilibrium and two boundary equilibria. To explore the impact of coinfection, we also derive the invasion reproduction numbers which indicate the potential of a pathogen to persist when another pathogen already exists in tick and host populations. Then, we obtain the global stability of the system at the disease-free equilibrium and the boundary equilibrium, respectively, and further demonstrate the existence conditions for uniform persistence of the two diseases. The final numerical simulations mainly verify the theoretical results of coinfection.

scholarly journals Microparasite dispersal in metapopulations: a boon or bane to the host population?

2018 ◽  
Vol 285 (1885) ◽  
pp. 20181519 ◽  
Author(s):  
Christina P. Tadiri ◽  
Marilyn E. Scott ◽  
Gregor F. Fussmann
Keyword(s):  
Disease Transmission ◽  
Species Conservation ◽  
Host Population ◽  
Isolated Populations ◽  
Parasite Abundance ◽  
Low Level ◽  
Parasite Distribution ◽  
High Level ◽  
Host Parasite ◽  
The Impact

Although connectivity can promote host species persistence in a metapopulation, dispersal may also enable disease transmission, an effect further complicated by the impact that parasite distribution may have on host–parasite population dynamics. We investigated the effects of connectivity and initial parasite distribution (clustered or dispersed) on microparasite–host dynamics in experimental metapopulations, using guppies and Gyrodactylus turnbulli . We created metapopulations of guppies divided into four subpopulations and introduced either a low level of parasites to all subpopulations (dispersed) or a high level of parasites to one subpopulation (clustered). Controlled migration among subpopulations occurred every 10 days. In additional trials, we introduced low or high levels of parasites to isolated populations. Parasites persisted longer in metapopulations than in isolated populations. Mortality was lowest in isolated populations with low-level introductions. The interaction of connectivity and initial parasite distribution influenced parasite abundance. With low-level introductions, connectivity helped the parasite persist longer but had little effect on the hosts. With high levels, connectivity also benefited the hosts, lowering parasite burdens. These findings have implications for disease management and species conservation.

scholarly journals SINE jumping contributes to large-scale polymorphisms in the pig genomes

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Cai Chen ◽  
Enrico D’Alessandro ◽  
Eduard Murani ◽  
Yao Zheng ◽  
Domenico Giosa ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Population Genetic ◽  
Large Scale ◽  
Structural Variations ◽  
Population Genetic Analysis ◽  
Protein Coding ◽  
Pig Breeds ◽  
A Genome ◽  
Trait Locus ◽  
And Cluster Analysis

Abstract Background Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5 % intragenic and 26.5 % intergenic), followed by SINEA2 (10.5 % intragenic and 9 % intergenic) and SINEA3 (12.5 % intragenic and 5.0 % intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80 % accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34 % of SINE RIPs generated by SINEA1 element. Over 65 % of pig SINE RIPs overlap with genes, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35,000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

scholarly journals Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date

2021 ◽  
Author(s):  
F. J. Canales ◽  
G. Montilla-Bascón ◽  
W. A. Bekele ◽  
C. J. Howarth ◽  
T. Langdon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Large Scale ◽  
Population Genomics ◽  
Heading Date ◽  
Population Genetic Analysis ◽  
High Genetic Diversity ◽  
A Genome ◽  
Interactive Map

Key messageGenomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement.AbstractDuring the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

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