High-throughput sequencing reveals dietary segregation in Malaysian babblers

Abstract The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the four genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and less than 35% were shared simultaneously by three or more babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.

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Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

Nucleic Acids Research ◽

10.1093/nar/gkw471 ◽

2016 ◽

Vol 44 (14) ◽

pp. e123-e123 ◽

Cited By ~ 24

Author(s):

Yun Zheng ◽

Bo Ji ◽

Renhua Song ◽

Shengpeng Wang ◽

Ting Li ◽

...

Keyword(s):

High Throughput ◽

Small Rna ◽

High Throughput Sequencing ◽

Accurate Detection ◽

Wide Range

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Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks

mSphere ◽

10.1128/msphere.00614-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 35

Author(s):

Rafal Tokarz ◽

Stephen Sameroff ◽

Teresa Tagliafierro ◽

Komal Jain ◽

Simon H. Williams ◽

...

Keyword(s):

New York ◽

High Throughput ◽

High Throughput Sequencing ◽

Ixodes Scapularis ◽

The United States ◽

Dermacentor Variabilis ◽

Amblyomma Americanum ◽

Animal Pathogens ◽

Wide Range ◽

Sequencing Platforms

ABSTRACT Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis ( n = 1,138), Amblyomma americanum ( n = 720), and Dermacentor variabilis ( n = 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species. The most frequently detected viruses were phylogenetically related to members of the Bunyaviridae and Rhabdoviridae families, as well as the recently proposed Chuviridae . Our work expands our understanding of tick viromes and underscores the high viral diversity that is present in ticks. IMPORTANCE The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.

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jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

10.1101/650747 ◽

2019 ◽

Author(s):

Lucas A. Nell

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Population Genomics ◽

R Package ◽

Gene Trees ◽

Sequencing Platform ◽

Genomic Variants ◽

Pacific Biosciences ◽

Wide Range ◽

Reference Genomes

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.

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Learning Sparse Log-Ratios for High-Throughput Sequencing Data

10.1101/2021.02.11.430695 ◽

2021 ◽

Author(s):

Elliott Gordon-Rodriguez ◽

Thomas P. Quinn ◽

John P. Cunningham

Keyword(s):

High Throughput ◽

Latent Variables ◽

High Throughput Sequencing ◽

Compositional Data ◽

Predictive Accuracy ◽

Learning Algorithm ◽

Sequencing Data ◽

Genetic Sequencing ◽

Wide Range ◽

Benchmark Datasets

AbstractThe automatic discovery of interpretable features that are associated to an outcome of interest is a central goal of bioinformatics. In the context of high-throughput genetic sequencing data, and Compositional Data more generally, an important class of features are the log-ratios between subsets of the input variables. However, the space of these log-ratios grows combinatorially with the dimension of the input, and as a result, existing learning algorithms do not scale to increasingly common high-dimensional datasets. Building on recent literature on continuous relaxations of discrete latent variables, we design a novel learning algorithm that identifies sparse log-ratios several orders of magnitude faster than competing methods. As well as dramatically reducing runtime, our method outperforms its competitors in terms of sparsity and predictive accuracy, as measured across a wide range of benchmark datasets.

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Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

10.1101/2021.02.10.430568 ◽

2021 ◽

Author(s):

Rosie Drinkwater ◽

Elizabeth L. Clare ◽

Arthur Y. C. Chung ◽

Stephen J. Rossiter ◽

Eleanor M. Slade

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Dung Beetle ◽

Blood Feeding ◽

Preliminary Evidence ◽

Dung Beetles ◽

High Throughput Analysis ◽

Humid Forest ◽

Terrestrial Vertebrates ◽

Wide Range

AbstractThe application of environmental DNA (eDNA) sampling in biodiversity surveys has gained widespread acceptance, especially in aquatic systems where free eDNA can be readily collected by filtering water. In terrestrial systems, eDNA-based approaches for assaying vertebrate biodiversity have tended to rely on blood-feeding invertebrates, including leeches and mosquitoes (termed invertebrate-derived DNA or iDNA). However, a key limitation of using blood-feeding taxa as samplers is that they are difficult to trap, and, in the case of leeches, are highly restricted to humid forest ecosystems. Dung beetles (superfamily Scarabaeoidea) feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps; are globally distributed; and also occur in a wide range of biomes, allowing mammal diversity to be compared across habitats. In this exploratory study, we test the potential utility of dung beetles as vertebrate samplers by sequencing the mammal DNA contained within their guts. First, using a controlled feeding experiment, we show that mammalian DNA can be retrieved from the guts of large dung beetles (Catharsius renaudpauliani) for up to 10 hours after feeding. Second, by combining high-throughput sequencing of a multi-species assemblage of dung beetles with PCR replicates, we show that multiple mammal taxa can be identified with high confidence. By providing preliminary evidence that dung beetles can be used as a source of mammal DNA, our study highlights the potential for this widespread group to be used in future biodiversity monitoring surveys.

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High throughput sequencing unravels tomato-pathogen interactions towards a sustainable plant breeding

Horticulture Research ◽

10.1038/s41438-021-00607-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Maria Doroteia Campos ◽

Maria do Rosário Félix ◽

Mariana Patanita ◽

Patrick Materatski ◽

Carla Varanda

Keyword(s):

Plant Breeding ◽

High Throughput ◽

Plant Pathogen ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Molecular Networks ◽

Sequencing Data ◽

Sources Of Resistance ◽

Tomato Plants ◽

Wide Range

AbstractTomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Next-generation sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant–pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant’s innate immune mechanisms in view of plant breeding.

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In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

10.1101/027235 ◽

2015 ◽

Cited By ~ 1

Author(s):

M.V. Cannon ◽

J. Hester ◽

A. Shalkhauser ◽

E.R. Chan ◽

K. Logue ◽

...

Keyword(s):

High Throughput ◽

Dna Sequences ◽

Water Samples ◽

High Throughput Sequencing ◽

Biological Diversity ◽

Pcr Amplification ◽

Environmental Dna ◽

Asian Carp ◽

Broad Perspective ◽

Wide Range

Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semiaquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.

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Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

Journal of Virology ◽

10.1128/jvi.00723-16 ◽

2016 ◽

Vol 90 (18) ◽

pp. 8169-8180 ◽

Cited By ~ 15

Author(s):

Niccolò Alfano ◽

Johan Michaux ◽

Serge Morand ◽

Ken Aplin ◽

Kyriakos Tsangaras ◽

...

Keyword(s):

Southeast Asia ◽

High Throughput ◽

High Throughput Sequencing ◽

Leukemia Virus ◽

Southeast Asian ◽

Content Type ◽

Hybridization Capture ◽

Wide Range ◽

Gibbon Ape Leukemia Virus ◽

Koala Retrovirus

ABSTRACTGibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies ofMelomysburtonifrom Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the IndonesianM. burtonisubsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV inM. burtoniprovides further evidence thatM. burtoni, and potentially other lineages within the widespread subfamilyMurinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution ofM. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents.IMPORTANCEGibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only aMelomysburtonisubspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize thatMelomysburtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

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Genetic structure of the American ginseng (Panax quinquefolius L.) in Eastern Canada using reduced-representation high-throughput sequencing

Botany ◽

10.1139/cjb-2016-0144 ◽

2017 ◽

Vol 95 (4) ◽

pp. 429-434 ◽

Cited By ~ 3

Author(s):

Simon Joly ◽

Annie Archambault ◽

Stéphanie Pellerin ◽

Andrée Nault

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

High Throughput ◽

High Throughput Sequencing ◽

Natural Populations ◽

American Ginseng ◽

Panax Quinquefolius ◽

Eastern Canada ◽

Reduced Representation ◽

Wide Range

The American ginseng (Panax quinquefolius L.) has been used for a wide range of medicinal purposes for more than 300 years, and is at risk in most of its range because of harvesting in natural populations, herbivory, and habitat loss. Its genetic structure is largely unknown in the previously glaciated areas of Eastern Canada, although such information could provide useful information for restoration strategies. We generated and analysed data from a reduced-representation high-throughput sequencing approach with a BAMOVA population model to partition the genetic variation within and among six natural populations of American ginseng in Eastern Canada. We found that an important and significant fraction of the genetic variation was structured among populations ([Formula: see text] = 42%; FST = 34%) at the geographical scale of the study (<250 km). No clear evidence of isolation-by-distance was observed. This important genetic structure observed among American ginseng populations from a region that was covered by ice during the last glaciations is similar to what had been found in previous studies on southern populations or throughout the species range.

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seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data

F1000Research ◽

10.12688/f1000research.16083.1 ◽

2018 ◽

Vol 7 ◽

pp. 1466 ◽

Cited By ~ 2

Author(s):

Erik Fasterius ◽

Cristina Al-Khalili Szigyarto

Keyword(s):

Genetic Variation ◽

Liver Cancer ◽

High Throughput ◽

High Throughput Sequencing ◽

R Package ◽

Ease Of Use ◽

Sequencing Data ◽

Dna And Rna ◽

High Throughput Sequencing Data ◽

Wide Range

High throughput sequencing technologies are flourishing in the biological sciences, enabling unprecedented insights into e.g. genetic variation, but require extensive bioinformatic expertise for the analysis. There is thus a need for simple yet effective software that can analyse both existing and novel data, providing interpretable biological results with little bioinformatic prowess. We present seqCAT, a Bioconductor toolkit for analysing genetic variation in high throughput sequencing data. It is a highly accessible, easy-to-use and well-documented R-package that enables a wide range of researchers to analyse their own and publicly available data, providing biologically relevant conclusions and publication-ready figures. SeqCAT can provide information regarding genetic similarities between an arbitrary number of samples, validate specific variants as well as define functionally similar variant groups for further downstream analyses. Its ease of use, installation, complete data-to-conclusions functionality and the inherent flexibility of the R programming language make seqCAT a powerful tool for variant analyses compared to already existing solutions. A publicly available dataset of liver cancer-derived organoids is analysed herein using the seqCAT package, demonstrating that the organoids are genetically stable. A previously known liver cancer-related mutation is additionally shown to be present in a sample though it was not listed in the original publication. Differences between DNA- and RNA-based variant calls in this dataset are also analysed revealing a high median concordance of 97.5%.

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