scholarly journals Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

2021 ◽  
Author(s):  
Kumar Gaurav ◽  
Sanu Arora ◽  
Paula Silva ◽  
Javier Sánchez-Martín ◽  
Richard Horsnell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Wild Progenitor ◽  
Population Genomic ◽  
Wheat Improvement ◽  
Genomic Regions

AbstractAegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

scholarly journals Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

2021 ◽  
Author(s):  
Kumar Gaurav ◽  
Sanu Arora ◽  
Paula Silva ◽  
Javier Sánchez-Martín ◽  
Richard Horsnell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Candidate Genes ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Pest Resistance ◽  
Wild Progenitor ◽  
Genomic Regions ◽  
Synthetic Hexaploids ◽  
Diploid Ancestor

AbstractAegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.

scholarly journals Clonal diversity of Haemophilus influenzae carriage isolated from under the age of 6 years children

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Fahimeh Shooraj ◽  
Bahman Mirzaei ◽  
Seyed Fazlollah Mousavi ◽  
Farzaneh Hosseini
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Genomic Analysis ◽  
Clonal Diversity ◽  
Invasive Disease ◽  
Pulsed Field Gel Electrophoresis ◽  
Genomic Diversity ◽  
Biochemical Tests ◽  
Genetic Origin ◽  
Susceptibility Tests

Abstract Objectives Pharyngeal carriers such as H. influenzae seem to constitute the only reservoir and probably the only transmission vehicle of the invasive disease. The aims of this study were to estimate the prevalence of H. influenzae carriage, to characterize antibiotic susceptibility, and to explore genetic diversity of H. influenzae isolates. Sampling was carried out as nasopharynx swabs among children less than 6 years old volunteers. After traditional biochemical tests, isolates were confirmed by targeting omp6 sequence. Following the susceptibility tests, genomic diversity of strains was analyzed by Pulsed-Field Gel Electrophoresis procedure. Results Out of 328 nasopharynx swabs, 73 strains were identified as H. influenzae. Among H. influenzae isolates, resistance to chloramphenicol (42%) and ampicillin (43%) was observed. Levofloxacin is the most effective antibiotic and the least effect belonged to tetracycline. By genomic analysis of selected H. influenza, 28 PFGE patterns were achieved among which 11 patterns included at least 2 strains. All strains clustered into 25 different clones. The dendrogram analysis of the isolated H. influenzae strains showed that some of these strains had a clonal relationship and common genetic origin. According to our results, antibiotic resistance didn’t show any significant correlation with the clonality of strains.

scholarly journals Clonal diversity of Haemophilus influenzae carriage isolated from under the age of 6 years children

2019 ◽  
Author(s):  
Fahimeh Shooraj ◽  
Bahman Mirzaei(Former Corresponding Author) ◽  
Seyed Fazlollah Mousavi(New Corresponding Author) ◽  
Farzaneh Hosseini
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Genomic Analysis ◽  
Clonal Diversity ◽  
Invasive Disease ◽  
Pulsed Field Gel Electrophoresis ◽  
Genomic Diversity ◽  
Biochemical Tests ◽  
Genetic Origin ◽  
Susceptibility Tests

Abstract Objectives: Pharyngeal carriers such as H. influenzae seem to constitute the only reservoir and probably the only transmission vehicle of the invasive disease. The aims of this study were to estimate the prevalence of H. influenzae carriage, to characterize antibiotic susceptibility, and to explore genetic diversity of H. influenzae isolates. Sampling was carried out as nasopharynx swabs among children less than 6 years old volunteers. After traditional biochemical tests, isolates were confirmed by targeting omp6 sequence. Following the susceptibility tests, genomic diversity of strains was analyzed by Pulsed-Field Gel Electrophoresis procedure. Results: Out of 328 nasopharynx swabs,73 strains were identified as H. influenzae. Among H. influenzae isolates, resistance to chloramphenicol (42%) and ampicillin (43%) was observed. Levofloxacin is the most effective antibiotic and the least effect belonged to tetracycline. By genomic analysis of selected H. influenza, 28 PFGE patterns were achieved among which 11 patterns included at least 2 strains. All strains clustered into 25 different clones. The dendrogram analysis of the isolated H. influenzae strains showed that some of these strains had a clonal relationship and common genetic origin. According to our results, antibiotic resistance didn’t show any significant correlation with the clonality of strains.

scholarly journals Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

2021 ◽  
Author(s):  
Kyle D Gustafson ◽  
Roderick B Gagne ◽  
Michael R Buchalski ◽  
T Winston Vickers ◽  
Seth PD Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Puma Concolor ◽  
Genomic Diversity ◽  
Strong Linkage Disequilibrium ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Genome Wide ◽  
Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

scholarly journals Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Diercles Francisco Cardoso ◽  
Gerardo Alves Fernandes Júnior ◽  
Daiane Cristina Becker Scalez ◽  
Anderson Antonio Carvalho Alves ◽  
Ana Fabrícia Braga Magalhães ◽  
...  
Keyword(s):  
Growth Traits ◽  
Genomic Analysis ◽  
Principal Component ◽  
Divergent Selection ◽  
Genomic Diversity ◽  
Population Subdivision ◽  
Selection Signatures ◽  
Inbreeding Coefficients ◽  
Angus Cattle ◽  
Genomic Regions

Abstract Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77–65.25 Mb) and 14 (22.81–23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.

scholarly journals Biogeography and Microscale Diversity Shape the Biosynthetic Potential of Fungus-growing Ant-associated Pseudonocardia

2019 ◽  
Author(s):  
Bradon R. McDonald ◽  
Marc G. Chevrette ◽  
Jonathan L. Klassen ◽  
Heidi A. Horn ◽  
Eric J. Caldera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Genome ◽  
Genomic Analysis ◽  
Barro Colorado Island ◽  
Bacterial Populations ◽  
Ant Colonies ◽  
Geographic Patterns ◽  
Population Genomic ◽  
Close Proximity ◽  
Fungus Growing Ants

AbstractThe geographic and phylogenetic scale of ecologically relevant microbial diversity is still poorly understood. Using a model mutualism, fungus-growing ants and their defensive bacterial associate Pseudonocardia, we analyzed genetic diversity and biosynthetic potential in 46 strains isolated from ant colonies in a 20km transect near Barro Colorado Island in Panama. Despite an average pairwise core genome similarity of greater than 99%, population genomic analysis revealed several distinct bacterial populations matching ant host geographic distribution. We identified both genetic diversity signatures and divergent genes distinct to each lineage. We also identify natural product biosynthesis clusters specific to isolation locations. These geographic patterns were observable despite the populations living in close proximity to each other and provides evidence of ongoing genetic exchange. Our results add to the growing body of literature suggesting that variation in traits of interest can be found at extremely fine phylogenetic scales.

scholarly journals Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs

2019 ◽  
Author(s):  
Rachel C. Williams ◽  
Marina B. Blanco ◽  
Jelmer W. Poelstra ◽  
Kelsie E. Hunnicutt ◽  
Aaron A. Comeault ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Analysis ◽  
Population Level ◽  
Comparative Genomic ◽  
Effective Population ◽  
High Coverage ◽  
Genome Wide ◽  
Conservation Concern ◽  
Genomic Regions ◽  
Dwarf Lemur

AbstractMadagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genus Cheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur, Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genome sequences for wild-caught individuals representing species: C. sp. cf. medius, C. major, C. crossleyi and C. sibreei. This study represents the largest contribution to date of novel genomic resources for Madagascar’s lemurs. We find concordant phylogenetic relationships among the four lineages of Cheirogaleus across most of the genome, and yet detect a number of discordant genomic regions consistent with ancient admixture. We hypothesized that these regions could have resulted from adaptive introgression related to hibernation, indeed finding that genes associated with hibernation are present, though most significantly, that gene ontology categories relating to transcription are over-represented. We estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population of C. medius that we refer to as C. sp. cf. medius. Results are consistent with a recent decline in effective population size, which is evident across species. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution.

scholarly journals A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation

2010 ◽  
Vol 79 (2) ◽  
pp. 950-960 ◽  
Author(s):  
Jason W. Sahl ◽  
Hans Steinsland ◽  
Julia C. Redman ◽  
Samuel V. Angiuoli ◽  
James P. Nataro ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Middle Income ◽  
E Coli ◽  
Colonization Factor ◽  
Genomic Core ◽  
Genomic Regions

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

scholarly journals Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yoshitaka Tateishi ◽  
Yuriko Ozeki ◽  
Akihito Nishiyama ◽  
Mari Miki ◽  
Ryoji Maekura ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Mycobacterium Intracellulare ◽  
Clinical Strains ◽  
Genetic Components ◽  
Genomic Regions ◽  
Insight Into

Abstract Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

scholarly journals Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 211
Author(s):  
Mazin Mahjoob Mohamed Mahjoob ◽  
Yasir Serag Alnor Gorafi ◽  
Nasrein Mohamed Kamal ◽  
Yuji Yamasaki ◽  
Izzat Sidahmed Ali Tahir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Association Studies ◽  
Aegilops Tauschii ◽  
Genome Wide Association ◽  
Physiological Traits ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Wide Range ◽  
Or Genes

Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker–trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.

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