scholarly journals Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution

2018 ◽  
Author(s):  
Lisa N. Barrow ◽  
Julie M. Allen ◽  
Xi Huang ◽  
Staffan Bensch ◽  
Christopher C. Witt
Keyword(s):  
Evolutionary Dynamics ◽  
Nuclear Dna ◽  
Genomic Sequence ◽  
Cost Effective ◽  
Substantial Improvement ◽  
Bioinformatics Pipeline ◽  
Sequence Capture ◽  
Open Access Database ◽  
Pooling Strategies ◽  
Nuclear Loci

AbstractAvian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently-developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences, and pooling strategies. Our method was successful for samples with parasitemia as low as ∼0.03% (3 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoon sample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe kit sequences, and describe our bioinformatics pipeline using aTRAM 2.0, PHYLUCE, and custom Perl and Python scripts. This approach can be applied to the tens of thousands of avian samples that have already been screened for haemosporidians, and greatly improve our understanding of parasite speciation, biogeography, and evolutionary dynamics.

scholarly journals Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands

2020 ◽  
Author(s):  
Matej Dolinay ◽  
Tadeáš Nečas ◽  
Breda M. Zimkus ◽  
Andreas Schmitz ◽  
Eric B. Fokam ◽  
...  
Keyword(s):  
Species Complex ◽  
Nuclear Dna ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Central Africa ◽  
Reticulate Evolution ◽  
Early Pleistocene ◽  
Population Declines ◽  
Sequence Capture ◽  
Mtdna Lineages

ABSTRACTPuddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Highlands (Cameroon Volcanic Line) in western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, with only two of them distinguished at the species level – southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages with a pooled identification as ‘P. steindachneri’. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses to delimit species (together with morphology) and to study biogeography. Nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the splitting pattern and depths of divergences supported only four main clades—besides P. jimzimkusi and P. njiomock, only two from the four ‘P. steindachneri’ mtDNA lineages. One is here described as a new species, P. sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a phylogenetic artefact – a ladder-like tree pattern. The presence of hybrids is undesirable in standard phylogenetic analyses, but is essential and beneficial in the network multispecies coalescent. This latter approach allowed us an insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (warm interglacials) of montane forests. The genomic phylogeographic pattern supports the earliest division between southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). Mount Oku harboring three species is of particular conservation importance. This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. We therefore urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.

scholarly journals Transforming biorefinery designs with ‘Plug-In Processes of Lignin’ to enable economic waste valorization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhi-Hua Liu ◽  
Naijia Hao ◽  
Yun-Yan Wang ◽  
Chang Dou ◽  
Furong Lin ◽  
...  
Keyword(s):  
Cellulosic Ethanol ◽  
Cost Effective ◽  
Substantial Improvement ◽  
Selling Price ◽  
Waste Valorization ◽  
Lignin Valorization ◽  
Capital Costs ◽  
Carbon Efficiency ◽  
Synergistic Enhancement ◽  
Total Capital

AbstractBiological lignin valorization has emerged as a major solution for sustainable and cost-effective biorefineries. However, current biorefineries yield lignin with inadequate fractionation for bioconversion, yet substantial changes of these biorefinery designs to focus on lignin could jeopardize carbohydrate efficiency and increase capital costs. We resolve the dilemma by designing ‘plug-in processes of lignin’ with the integration of leading pretreatment technologies. Substantial improvement of lignin bioconversion and synergistic enhancement of carbohydrate processing are achieved by solubilizing lignin via lowering molecular weight and increasing hydrophilic groups, addressing the dilemma of lignin- or carbohydrate-first scenarios. The plug-in processes of lignin could enable minimum polyhydroxyalkanoate selling price at as low as $6.18/kg. The results highlight the potential to achieve commercial production of polyhydroxyalkanoates as a co-product of cellulosic ethanol. Here, we show that the plug-in processes of lignin could transform biorefinery design toward sustainability by promoting carbon efficiency and optimizing the total capital cost.

scholarly journals Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method

2018 ◽  
Vol 6 (6) ◽  
pp. 1188-1198 ◽  
Author(s):  
Angela Abicht ◽  
Florentine Scharf ◽  
Stephanie Kleinle ◽  
Ulrike Schön ◽  
Elke Holinski-Feder ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Cost Effective

scholarly journals LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

2021 ◽  
Author(s):  
Eszter Lakatos ◽  
Helen Hockings ◽  
Maximilian Mossner ◽  
Michelle Lockley ◽  
Trevor A. Graham
Keyword(s):  
Copy Number ◽  
Evolutionary Dynamics ◽  
Cost Effective ◽  
Copy Number Alterations ◽  
Liquid Biopsies ◽  
Metastatic Lung ◽  
Low Pass ◽  
Somatic Copy Number Alterations

AbstractCell-free DNA (cfDNA) measured via liquid biopsies provides a way for minimally-invasive monitoring of tumour evolutionary dynamics during therapy. Here we present liquidCNA, a method to track subclonal evolution from longitudinally collected cfDNA samples based on somatic copy number alterations (SCNAs). LiquidCNA utilises SCNA profiles derived through cost-effective low-pass whole genome sequencing to automatically and simultaneously genotype and quantify the size of the dominant subclone without requiring prior knowledge of the genetic identity of the emerging clone. We demonstrate the accuracy of liquidCNA in synthetically generated sample sets and in vitro and in silico mixtures of cancer cell lines. Application in vivo in patients with metastatic lung cancer reveals the progressive emergence of a novel tumour sub-population. LiquidCNA is straightforward to use, computationally inexpensive and enables continuous monitoring of subclonal evolution to understand and control therapy-induced resistance.

scholarly journals NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2577
Author(s):  
Imogen A. Wright ◽  
Kayla E. Delaney ◽  
Mary Grace K. Katusiime ◽  
Johannes C. Botha ◽  
Susan Engelbrecht ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Cost Effective ◽  
Full Length ◽  
Sequencing Error ◽  
Consensus Building ◽  
Genome Sequences ◽  
Bioinformatics Pipeline ◽  
Oxford Nanopore ◽  
Single Genome ◽  
Hiv 1

HIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviruses may rebound if ART is interrupted and are the barrier to an HIV cure. Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. NanoHIV is a new tool that uses an iterative consensus generation approach to construct accurate, near full-length HIV-1 proviral single-genome sequences from ONT data. To validate the approach, single-genome sequences generated using NanoHIV consensus building were compared to Illumina® consensus building of the same nine single-genome near full-length amplicons and an average agreement of 99.4% was found between the two sequencing approaches.

scholarly journals More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

2012 ◽  
Vol 8 (5) ◽  
pp. 783-786 ◽  
Author(s):  
Nicholas G. Crawford ◽  
Brant C. Faircloth ◽  
John E. McCormack ◽  
Robb T. Brumfield ◽  
Kevin Winker ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Common Ancestor ◽  
Sister Group ◽  
Single Copy ◽  
Recent Analysis ◽  
Phylogenetic Position ◽  
Ultraconserved Elements ◽  
Sequence Capture ◽  
Genomic Scale ◽  
Nuclear Loci

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.

scholarly journals The BPP program for species tree estimation and species delimitation

2015 ◽  
Vol 61 (5) ◽  
pp. 854-865 ◽  
Author(s):  
Ziheng Yang
Keyword(s):  
Species Delimitation ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Species Tree ◽  
Joint Analysis ◽  
Coalescent Model ◽  
Species Phylogeny ◽  
Multispecies Coalescent ◽  
Tree Estimation ◽  
Nuclear Loci

Abstract This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.

DNA-DNA Hybridization, Phylogenetic Reconstruction and the Fossil Record

1988 ◽  
Vol 1 ◽  
pp. 75-88 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Dna Hybridization ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Cost Effective ◽  
Single Copy ◽  
Molecular Techniques ◽  
Phylogenetic Information ◽  
Molecular Approaches ◽  
Molecular Characters ◽  
Rates Of Molecular Evolution

In 1962 Zuckerkandl & Pauling suggested that the amino acid sequence of proteins might evolve in a clock-like fashion and thus may be useful for phylogenetic reconstruction. Since then, many different molecular approaches to phylogenetic reconstruction have been proposed (Wilson et al., 1977). Enthusiasm for the clock hypothesis was dampened by the discovery that rates of molecular evolution for many macromolecules have been highly variable through time (Romero-Herrera et al., 1979). However, the contribution of molecular characters to the study of phylogeny is not necessarily dependent on the notion of a molecular clock and molecular approaches continue to be an important source of phylogenetic information. One of the more powerful and cost-effective molecular techniques for phylogenetic purposes is DNA-DNA hybridization, which measures the single-copy nuclear DNA sequence divergences between species.

Synthesis and Properties of Al-Based Amorphous and Microcrystalline Thin Films

2001 ◽  
Vol 672 ◽  
Author(s):  
Christoph Ettl ◽  
Lothar Berger ◽  
Joachim W. Mrosk ◽  
Hans-Jörg Fecht
Keyword(s):  
Aluminum Alloys ◽  
High Vacuum ◽  
High Strength ◽  
Cost Effective ◽  
Electron Beam Evaporation ◽  
Substantial Improvement ◽  
Ultra High Vacuum ◽  
Metal Alloys ◽  
Alloy Thin Film ◽  
Polycrystalline Aluminum

ABSTRACTAmorphous metal alloys are ideally suited for interconnects in micro-electromechanical sys- tems (MEMS) because of their resistance against stress- and electromigration, and their stability in chemically aggressive environments, which should both lead to a substantial improvement of lifetime and reliability of robust sensors. While amorphous refractory metal alloys and amor- phous silicides are excellent interconnect materials for devices operating at elevated tempera- tures, these systems lack the cost-effective and easy interconnect processing of the prevalent polycrystalline aluminum alloy metallizations. Amorphous aluminum alloys are applicable to devices operating at up to 200°C, and their stressmigration resistance and chemical stability is far superior to conventional polycrystalline aluminum alloys. These new metallizations are very promising for processing interconnects, in particular because of their high strength and ductility, though having low density, and their relatively low electrical resistivity compared to other amor- phous metal alloys. Therefore these metallizations are especially suited for surface acoustic wave (SAW) sensors, where the interconnects are exposed to considerable mechanical strains. In this work amorphous Aluminum Yttrium alloy thin film metallizations deposited on appropriate sub- strates at room temperature (R.T.) by ultra-high vacuum (UHV) electron beam evaporation will be presented, and their mechanical and electronic properties together with their temperature sta- bility will be investigated.

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