scholarly journals High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida

2016 ◽  
Author(s):  
James Starrett ◽  
Shahan Derkarabetian ◽  
Marshal Hedin ◽  
Robert W. Bryson ◽  
John E. McCormack ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Tree Of Life ◽  
Animal Group ◽  
Species Discovery ◽  
Population Genomic ◽  
Phylogenetic Informativeness ◽  
Genomic Studies ◽  
Genomic Regions ◽  
Probe Set ◽  
Conserved Genomic Regions

AbstractArachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.

scholarly journals Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them

2016 ◽  
Author(s):  
Brant C. Faircloth
Keyword(s):  
Open Source ◽  
Sequence Data ◽  
Genomic Information ◽  
Genetic Studies ◽  
Software Code ◽  
Genomic Regions ◽  
Probe Set ◽  
Conserved Genomic Regions ◽  
Targeted Enrichment

AbstractTargeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic, and population genetic studies. Yet, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. These shortcomings limit the application of targeted enrichment methods to many organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. I demonstrate how this computational approach can be applied to diverse organismal groups by identifying sets of conserved loci and designing enrichment baits targeting thousands of these loci in the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera, or Lepidoptera. I then use in silico analyses to demonstrate that these conserved loci reconstruct the accepted relationships among genome sequences from the focal arthropod orders, and we perform in vitro validation of the Arachnid probe set as part of a separate manuscript (Starrett et al. Submitted). All of the documentation, design steps, software code, and probe sets developed here are available under an open-source license for restriction-free testing and use by any research group, and although the examples in this manuscript focus on understudied and exceptionally diverse arthropod groups, the software workflow is applicable to all organismal groups having some form of pre-existing genomic information.

scholarly journals Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Melina Campos ◽  
Luisa D. P. Rona ◽  
Katie Willis ◽  
George K. Christophides ◽  
Robert M. MacCallum
Keyword(s):  
Population Structure ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Mosquito Species ◽  
Gene Clusters ◽  
Selective Sweeps ◽  
Structure Heterogeneity ◽  
Genomic Studies ◽  
Time Required ◽  
Genomic Regions

Abstract Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes.

scholarly journals A target enrichment probe set for resolving the flagellate land plant tree of life

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jesse W. Breinholt ◽  
Sarah B. Carey ◽  
George P. Tiley ◽  
E. Christine Davis ◽  
Lorena Endara ◽  
...  
Keyword(s):  
Land Plant ◽  
Tree Of Life ◽  
Target Enrichment ◽  
Probe Set

scholarly journals Identification of RD5-EncodedMycobacterium tuberculosisProteins As B-Cell Antigens Used for Serodiagnosis of Tuberculosis

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Miao-Miao Zhang ◽  
Jun-Wei Zhao ◽  
Zhan-Qiang Sun ◽  
Jun Liu ◽  
Xiao-Kui Guo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Detection Sensitivity ◽  
Comparative Genomic ◽  
Healthy Controls ◽  
Specific Diagnosis ◽  
Pulmonary Tb ◽  
Genomic Studies ◽  
Immunodominant Antigens ◽  
Genomic Regions ◽  
Hiv Negative

Comparative genomic studies have identified severalMycobacterium tuberculosis-specific genomic regions of difference (RDs) which are absent in the vaccine strains ofMycobacterium bovisBCG and which may be useful in the specific diagnosis of tuberculosis (TB). In this study, all encoded proteins from DNA segment RD5 ofMycobacterium tuberculosis, that is, Rv3117–Rv3121, were recombined and evaluated by enzyme-linked immunosorbent assays for antibody reactivity with sera from HIV-negative pulmonary TB patients (n=60) and healthy controls (n=32). The results identified two immunodominant antigens, that is, Rv3117 and Rv3120, both of which revealed a statistically significant antigenic distinction between healthy controls and TB patients (P<0.05). In comparison with the well-known early-secreted antigen target 6 kDa (ESAT-6) (sensitivity 21.7%, specificity 90.6%), the higher detection sensitivity and higher specificity were achieved (Rv3117: sensitivity 25%, specificity 96.9%; Rv3120: sensitivity 31.7%, specificity 96.9%). Thus, the results highlight the immunosensitive and immunospecific nature of Rv3117 and Rv3120 and indicate promise for their use in the serodiagnosis of TB.

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

2020 ◽  
pp. PHYTO-08-20-035
Author(s):  
Pauline Hessenauer ◽  
Nicolas Feau ◽  
Upinder Gill ◽  
Benjamin Schwessinger ◽  
Gurcharn S. Brar ◽  
...  
Keyword(s):  
Population Genomics ◽  
Production Systems ◽  
Management Strategies ◽  
Forest Trees ◽  
Forest Production ◽  
Population Genomic ◽  
Genomic Studies ◽  
Pathogen Populations ◽  
Different Characteristics ◽  
Global Food

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

Molecular and morphological characterisation of Laimaphelenchus spiflatus n. sp. (Nematoda: Aphelenchoididae) from China

Nematology ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. 843-853
Author(s):  
Jianfeng Gu ◽  
Munawar Maria ◽  
Yiwu Fang ◽  
Xianfeng Chen ◽  
Lele Liu
Keyword(s):  
New Species ◽  
Body Size ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
The Other ◽  
Morphometric Data ◽  
Lateral Field ◽  
Chinese Pine ◽  
Lateral Lines ◽  
Genomic Regions

Summary Laimaphelenchus spiflatus n. sp. isolated from declining Chinese pine, Pinus tabuliformis, is described and illustrated. The new species can be characterised by its relatively long body size of 1150 ± 108 (976-1437) μm for females and 1092 ± 78.6 (905-1235) μm for males, lateral field with four lines, females with a long vulval flap, and tail conoid, slightly ventrally curved and ending in a stalk having 8-12 projections when observed with SEM. Males are common, with 27.3 (23.4-28.8) μm long spicules having blunt (not well-developed) condylus and rostrum and truncate simple distal tip, and four caudal papillae. By having a vulval flap, four lateral lines and tail end with a stalk (without four tubercles), the new species comes close to L. preissii, L. simlaensis, and L. unituberculus, but can be differentiated from them by morphological characters and morphometric data. In phylogenetic analyses using near full length 18S and D2-D3 expansion segments of 28S rDNA, Laimaphelenchus spiflatus n. sp. appeared as an independent lineage separated from the other Laimaphelenchus spp. that are currently sequenced for their aforementioned genomic regions.

scholarly journals Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation

2019 ◽  
Vol 59 (4) ◽  
pp. 925-937 ◽  
Author(s):  
Jessica L McKenzie ◽  
Dillon J Chung ◽  
Timothy M Healy ◽  
Reid S Brennan ◽  
Heather J Bryant ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Fundulus Heteroclitus ◽  
Secondary Contact ◽  
Mitochondrial Genomes ◽  
Evolutionary Forces ◽  
Population Genomic ◽  
Genomic Studies

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

scholarly journals Multiplex recombinase polymerase amplification (RPA) assay developed using unique genomic regions and coupled with a lateral flow device for rapid on-site detection of genus Clavibacter and C. nebraskensis

2020 ◽  
Author(s):  
Adriana Larrea-Sarmiento ◽  
James P. Stack ◽  
Anne M. Alvarez ◽  
Mohammad Arif
Keyword(s):  
Detection Limit ◽  
Abc Transporter ◽  
Bacterial Species ◽  
Lateral Flow ◽  
Recombinase Polymerase Amplification ◽  
Specific Primer ◽  
Lateral Flow Device ◽  
Flow Device ◽  
Genomic Regions ◽  
Probe Set

ABSTRACTClavibacter is an agriculturally important bacterial genus comprising nine host-specific species/subspecies including C. nebraskensis (Cn), which causes Goss’s wilt and blight of maize. A robust, simple, and field-deployable method is required to specifically detect Cn in infected plants and distinguish it from other Clavibacter species for quarantine purposes and timely disease management. A multiplex Recombinase Polymerase Amplification (RPA) coupled with a Lateral Flow Device (LFD) was developed for sensitive and rapid detection of Clavibacter and Cn directly from infected host. Unique and conserved genomic regions, the ABC transporter ATP-binding protein CDS/ABC-transporter permease and the MFS transporter gene, were used to design primers/probes for specific detection of genus Clavibacter and Cn, respectively. The assay was evaluated using 52 strains, representing all nine species/subspecies of Clavibacter, other closely related bacterial species, and naturally- and artificially-infected plant samples; no false positives or negatives were detected. The RPA reactions were also incubated in a closed hand at body temperature; results were again specific. The assay does not require DNA isolation and can be directly performed using host sap. The detection limit of 10 pg and 100 fg was determined for Clavibacter- and Cn-specific primers/probes, respectively. The detection limit for Cn-specific primer/probe set was decreased to 1,000 fg when 1 µL of host sap was added into the RPA reaction containing 10-fold serially diluted genomic DNA; though no effect was observed on Clavibacter-specific primer/probe set. The assay is accurate and has applications at point-of-need diagnostics. This is the first multiplex RPA for any plant pathogen.IMPORTANCEClavibacter species are prevalent worldwide as have the potential to result in systemic infection. In the past, detection attempts have relied on both molecular- and immunological-based assays; however, current detection methods are time consuming and laborious. Field-deployable tests are desirable to identify potential samples infected with Clavibacter species. This study demonstrates that the field-deployable isothermal multi-target recombinase polymerase amplification can be performed for the simultaneous detection of the genus Clavibacter in general (all species), and C. nebraskensis, in particular, without specialized equipment. Additionally, the multiplex RPA coupled with a LFD may confer the benefits of faster detection and discrimination of Clavibacter species that affect critical regions susceptible to infection. This user-friendly format offers a flexible assay to complement both nucleic acid amplification and novel diagnosis methods without the need for DNA purification; this assay may serve as a point-of-reference for developing multiplex RPA assay for other plant pathogens.

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