scholarly journals Soil eukaryote community shift but not composition is consistently recovered by different OTU inference methods applied to long read metabarcoding data

2021 ◽  
Author(s):  
Shadi Eshghi Sahraei ◽  
Brendan Furneaux ◽  
Kerri Kluting ◽  
Mustafa Zahieh ◽  
Håkan Rydin ◽  
...  
Keyword(s):  
Plant Community ◽  
Large Fraction ◽  
Operational Taxonomic Units ◽  
Community Shift ◽  
Long Read ◽  
Ecological Patterns ◽  
Phylogenetic Resolution ◽  
Community Transition ◽  
Carex Acuta ◽  
Inference Methods

Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communites of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing and evaluated the performance of three different methods for generation of operational taxonomic units (OTUs). The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus’s time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigare how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.

scholarly journals Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

2022 ◽  
Author(s):  
Claire M&eacuterot ◽  
Kristina S R Stenl&oslashkk ◽  
Clare Venney ◽  
Martin Laporte ◽  
Michel Moser ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genetic Architecture ◽  
Large Fraction ◽  
Sympatric Species ◽  
Secondary Contact ◽  
Species Differentiation ◽  
Lake Whitefish ◽  
Structural Variants ◽  
Species Pairs ◽  
Long Read

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

scholarly journals Avian MHC Evolution in the Era of Genomics: Phase 1.0

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1152 ◽  
Author(s):  
Emily A. O’Connor ◽  
Helena Westerdahl ◽  
Reto Burri ◽  
Scott V. Edwards
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Structural Evolution ◽  
Great Depth ◽  
Long Read ◽  
Ecological Patterns ◽  
In The Wild ◽  
The Many ◽  
Avian Mhc

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

scholarly journals Hybrid genome assembly and annotation of Danionella translucida, a transparent fish with the smallest known vertebrate brain

2019 ◽  
Author(s):  
Mykola Kadobianskyi ◽  
Lisanne Schulze ◽  
Markus Schuelke ◽  
Benjamin Judkewitz
Keyword(s):  
Large Scale ◽  
Genetic Manipulation ◽  
Large Fraction ◽  
Model Organism ◽  
Close Relative ◽  
Vertebrate Brain ◽  
Hybrid Genome ◽  
Long Read ◽  
Optical Turbidity ◽  
Low Coverage

Studying the activity of distributed neuronal circuits at a cellular resolution in vertebrates is very challenging due to the size and optical turbidity of their brains. We recently presented Danionella translucida, a close relative of zebrafish, as a model organism suited for studying large-scale neural network interactions in adult individuals. Danionella remains transparent throughout its life, has the smallest known vertebrate brain and possesses a rich repertoire of complex behaviours. Here we sequenced, assembled and annotated the Danionella translucida genome employing a hybrid Illumina/Nanopore read library as well as RNA-seq of embryonic, larval and adult mRNA. We achieved high assembly continuity using low-coverage long-read data and annotated a large fraction of the transcriptome. This dataset will pave the way for molecular research and targeted genetic manipulation of the smallest known vertebrate brain.

Plant Community Effects and Genetic Diversity of Post-fire Princess Tree (Paulownia tomentosa) Invasions

2017 ◽  
Vol 10 (2) ◽  
pp. 125-135 ◽  
Author(s):  
Joseph B. Lovenshimer ◽  
Michael D. Madritch
Keyword(s):  
Genetic Diversity ◽  
Plant Community ◽  
Large Scale ◽  
Tree Age ◽  
Native Plant ◽  
Tree Invasions ◽  
Community Shift ◽  
Low Genetic Diversity ◽  
Before And After ◽  
Invasive Tree

Many naturalized populations of the invasive tree princess tree exist in North America, yet little research has quantified its effect on native plant communities. A series of recent wildfires in the Linville Gorge Wilderness Area (LGWA) promoted multiple large-scale princess tree invasions in this ecologically important area. To measure community shifts caused by these princess tree invasions across burn areas, we sampled vegetation in paired invaded and noninvaded plots in mature and immature invasions within two burn areas of the LGWA. Plant community composition shifted in response to princess tree invasion across all invasion stages and burn areas. Species richness and Shannon diversity values decreased in invaded plots. Overall community structure also differed in invaded plots within immature invasions (P=0.004). The distribution of princess tree age classes in both burn areas indicates that fire promotes invasion but is not necessary for subsequent recruitment. Additionally, preliminary genetic analyses among distinct princess tree populations revealed very low genetic diversity, suggesting that a single introduction may have occurred in the LGWA. This information regarding community shift and strong post-fire recruitment by princess tree may inform management decisions by prioritizing princess tree control immediately after wildfires and immediately before and after prescribed burns.

scholarly journals Ecological patterns are robust to use of exact sequence variants versus operational taxonomic units

2018 ◽  
Author(s):  
Sydney I. Glassman ◽  
Jennifer B.H. Martiny
Keyword(s):  
Exact Sequence ◽  
Beta Diversity ◽  
Marker Gene ◽  
Large Field ◽  
Sequence Variants ◽  
Abiotic Conditions ◽  
Alpha And Beta Diversity ◽  
Operational Taxonomic Units ◽  
Statistical Inferences ◽  
Ecological Patterns

AbstractRecent controversy focuses on the best method for delineating microbial taxa, based on either traditional operational taxonomic units (OTUs) or exact sequence variants (ESVs) of marker gene sequences. We sought to test if the binning approach (ESVs versus OTUs) affected the ecological conclusions of a large field study. The dataset included sequences of both bacteria (16S) and fungi (ITS), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all alpha- and beta-diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Thus, we conclude that for typical alpha- and beta-diversity analyses, OTU or ESV methods will likely reveal similar ecological results and determining which method to employ will depend on the question at hand.

scholarly journals An Integrated Sequencing Approach for Updating of Pseudorabies Virus Transcriptome

2020 ◽  
Author(s):  
Gábor Torma ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Dániel Göbhardter ◽  
Zoltán Deim ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Large Fraction ◽  
Viral Gene Expression ◽  
Transcriptome Profiling ◽  
Current Data ◽  
Viral Gene ◽  
Systematic Analysis ◽  
Rna Molecules ◽  
Oxford Nanopore ◽  
Long Read

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencings with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5’-truncated putative mRNAs embedded into larger host mRNAs. A large fraction of these RNA molecules contain in-frame ORFs, which may encode N-terminally truncated polypeptides. These study demonstrates that the PRV transcriptome is much more complex than previously appreciated.

scholarly journals An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 242
Author(s):  
Gábor Torma ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Dániel Göbhardter ◽  
Zoltán Deim ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Large Fraction ◽  
Viral Gene Expression ◽  
Transcriptome Profiling ◽  
Current Data ◽  
Viral Gene ◽  
Systematic Analysis ◽  
Rna Molecules ◽  
Long Read ◽  
High Level

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5′-truncations of larger putative mRNAs being 3′-co-terminal with canonical mRNAs of PRV. A large fraction of these putative RNAs contain in-frame ATGs, which might initiate translation of N-terminally truncated polypeptides. Our analyses indicate that CTO-S, a replication origin-associated RNA molecule is expressed at an extremely high level. This study demonstrates that the PRV transcriptome is much more complex than previously appreciated.

scholarly journals Host plant associations in Western Palaearctic Longitarsus flea beetles (Chrysomelidae, Galerucinae, Alticini): a preliminary phylogenetic assessment

ZooKeys ◽  
2019 ◽  
Vol 856 ◽  
pp. 101-114 ◽  
Author(s):  
Daniele Salvi ◽  
Paola D’Alessandro ◽  
Maurizio Biondi
Keyword(s):  
Host Plant ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Plant Associations ◽  
Large Genus ◽  
Phylogenetic Resolution ◽  
Related Plant ◽  
Plant Families ◽  
Western Palaearctic ◽  
Inference Methods

Longitarsus Latreille (Chrysomelidae, Galerucinae, Alticini) is a very large genus of phytophagous insects, with more than 700 species distributed in all zoogeographical regions. Patterns of host use have been a central topic in phytophagous insect research. In this study a first assessment is provided to test the hypothesis that host-plant association is phylogenetically conserved in Western Palaearctic Longitarsus species. Maximum Likelihood and Bayesian Inference methods were used to infer a phylogeny based on DNA sequence data from two mitochondrial genes from 52 Longitarsus species from the Western Palaearctic. In agreement with the host phylogenetic conservatism hypothesis, a strict association between most of the recovered clades and specific plant families was found, except for species associated with Boraginaceae. Low phylogenetic resolution at deep nodes limited the evaluation of whether closely related Longitarsus clades are associated with the same plant family or to closely related plant families.

scholarly journals Meta-aligner: Long-read alignment based on genome statistics

2016 ◽  
Author(s):  
Damoun Nashta-ali ◽  
Ali Aliyari ◽  
Mohammad Amin Edrisi ◽  
Ahmad Ahmadian Moghadam ◽  
Seyed Abolfazl Motahari ◽  
...  
Keyword(s):  
Performance Improvement ◽  
Time Complexity ◽  
Reference Genome ◽  
Large Fraction ◽  
Decision Making Process ◽  
Second Phase ◽  
Improve Performance ◽  
Long Reads ◽  
Long Read ◽  
Significant Performance

AbstractFast and accurate alignment of long-reads plays an important role in reducing the overall cost of long-read sequencing. In this paper, we propose Meta-aligner, an efficient and accurate long-read aligner that exploits the statistics of reference genome to improve performance in terms of reducing time complexity and achieving significantly higher recall for very noisy and long reads. The first step of algorithm adopts well-known short-read aligners in order to rapidly align a large fraction of reads through a progressive process of aligning read fragments to the reference genome. In the second phase, the remaining reads are handled by simultaneous alignment of all read fragments and a decision making process which exploits the overall information provided by the corresponding mapped fragments. By using this procedure, significant performance improvement is attained in comparison with traditional schemes in the case of PacBio long-reads.

scholarly journals Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11721
Author(s):  
Taylor Priest ◽  
Luis H. Orellana ◽  
Bruno Huettel ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann
Keyword(s):  
North Atlantic ◽  
The Arctic ◽  
Fram Strait ◽  
Water Column Stability ◽  
Exchange Processes ◽  
Sea Ice Decline ◽  
Long Read ◽  
Ecological Patterns ◽  
Sequencing Platforms ◽  
Impacts Of Climate Change

The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2–3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.

Sign in / Sign up

Export Citation Format

Share Document