scholarly journals Interspecific plastome recombination reflects ancient reticulate evolution in Picea (Pinaceae)

2016 ◽  
Author(s):  
Alexis R. Sullivan ◽  
Bastian Schiffthaler ◽  
Stacey Lee Thompson ◽  
Nathaniel R. Street ◽  
Xiao-Ru Wang
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Coniferous Forest ◽  
Forest Tree ◽  
Reticulate Evolution ◽  
Uniparental Inheritance ◽  
Plastid Inheritance ◽  
Plastome Evolution ◽  
Biparental Plastid Inheritance ◽  
Key Aspects

AbstractPlastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ~35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and ten other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

EVALUATION OF GENETIC FIDELITY FOLLOWING LONG TERM CRYOPRESERVATION OF CONIFEROUS FOREST TREE SPECIES OF THE FAMILY PINACEAE

2014 ◽  
pp. 121-126
Author(s):  
H. Häggman ◽  
S. Sutela ◽  
J. Edesi ◽  
J. Krajňáková ◽  
A. Bertolini ◽  
...  
Keyword(s):  
Tree Species ◽  
Coniferous Forest ◽  
Genetic Fidelity ◽  
Forest Tree ◽  
Forest Tree Species ◽  
The Family

scholarly journals Inferring species compositions of complex fungal communities from long- and short-read sequence data

2021 ◽  
Author(s):  
Yiheng Hu ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Tavish Eenjes ◽  
Abigail Graetz ◽  
...  
Keyword(s):  
Community Composition ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Composition Analysis ◽  
Sequencing Data ◽  
Species Classification ◽  
Shotgun Metagenomics ◽  
Query Coverage

Background: The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in culture. They can have complex genomes of over 1 Gb in size and are still underrepresented in whole genome sequence databases. Overall their description and analysis lags far behind other microbes such as bacteria. At the same time, classification of species via high throughput sequencing without prior purification is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. However, standardized procedures for characterizing unknown fungi from complex sequencing data have not yet been established. Results: We compared different metagenomics sequencing and analysis strategies for the identification of fungal species. Using two fungal mock communities of 44 phylogenetically diverse species, we compared species classification and community composition analysis pipelines using shotgun metagenomics and amplicon sequencing data generated from both short and long read sequencing technologies. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungi-specific database. During the assessment of classification algorithms, we found that applying cut-offs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without significant data loss. Conclusion: Overall, our study expands the toolkit for identifying fungi by improving sequence-based fungal classification, and provides a practical guide for the design of metagenomics analyses.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 29-44
Author(s):  
GUO-CHENG ZHANG ◽  
HUA-FENG HONG ◽  
GE-HONG CHEN ◽  
SHU-GANG LU ◽  
YAN-FEN CHANG
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reticulate Evolution ◽  
Southwestern China ◽  
Natural Classification ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Taxonomic Implications ◽  
Taxonomic Approach ◽  
Locus Classicus

The Hymenasplenium obliquissimum group contains the widespread H. obliquissimum and several geographically restricted species, including H. retusulum, H. wuliangshanense, H. latidens, H. changputungense, H. quercicola, H. szechuanense, H. furfuraceum, H. adiantifrons, and H. filipes. However, the taxonomy of this group is still unclear and needs to be revised because some entities were treated infraspecifically or as synonyms and the validation of some species still needs to be assessed. To formulate a natural classification and investigate the relationships in this group, we collected and studied specimens of species related to the H. obliquissimum group and obtained specimens of species described by Ching at their locus classicus in southwestern China. An integrative taxonomic approach was taken to delimit species in the group using cytological, morphological, and DNA sequence data. Specifically, in the phylogenetic analyses, the H. obliquissimum group was recovered as a monophyletic group, comprising five principal chloroplast lineages. Based on our inferences, we provided taxonomic implications of chloroplast lineages discovered in this study and suggested possible reticulate evolution in the H. obliquissimum group which was interpreted by the incongruence of chloroplast and nuclear phylogenies. Further studies to strengthen the taxonomic of taxa especially those with the co-existence of different ploidy levels are still warranted.

Phylogenomics of orchids and their mycorrhizal fungi : trees, diversity, and the pursuit of symbiosis

2019 ◽  
Author(s):  
◽  
Sarah Unruh
Keyword(s):  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mycorrhizal Symbiosis ◽  
Sequencing Data ◽  
Phylogenetic Structure ◽  
University Of Missouri ◽  
Fungal Symbiosis

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.

Influence of Nursery Cultural Practices on Cold Hardiness of Coniferous Forest Tree Seedlings

2001 ◽  
pp. 223-252 ◽  
Author(s):  
Stephen J. Colombo ◽  
Michael I. Menzies ◽  
Conor O’Reilly
Keyword(s):  
Cold Hardiness ◽  
Cultural Practices ◽  
Coniferous Forest ◽  
Forest Tree ◽  
Tree Seedlings

scholarly journals Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuka Torii ◽  
Kazuhiro Horiba ◽  
Satoshi Hayano ◽  
Taichi Kato ◽  
Takako Suzuki ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Early Stage ◽  
Rna Virus ◽  
Systemic Vasculitis ◽  
Human Herpesvirus ◽  
Acute Stage ◽  
Serum Samples

Abstract Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.

scholarly journals Quantifying evolutionary constraints on B-cell affinity maturation

2015 ◽  
Vol 370 (1676) ◽  
pp. 20140244 ◽  
Author(s):  
Connor O. McCoy ◽  
Trevor Bedford ◽  
Vladimir N. Minin ◽  
Philip Bradley ◽  
Harlan Robins ◽  
...  
Keyword(s):  
B Cell ◽  
Empirical Bayes ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Cell Receptor ◽  
Affinity Maturation ◽  
Variable Regions ◽  
Empirical Bayes Estimators ◽  
Stochastic Mapping

The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on BCRs using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.

scholarly journals The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology

2015 ◽  
Vol 9s1 ◽  
pp. BBI.S28988 ◽  
Author(s):  
Frank A. Feltus ◽  
Joseph R. Breen ◽  
Juan Deng ◽  
Ryan S. Izard ◽  
Christopher A. Konger ◽  
...  
Keyword(s):  
Big Data ◽  
Data Processing ◽  
Data Storage ◽  
Data Transfer ◽  
Sequence Data ◽  
Disruptive Technology ◽  
Data Generation ◽  
Key Aspects ◽  
Data Flow Control ◽  
Time Frames

In the last decade, high-throughput DNA sequencing has become a disruptive technology and pushed the life sciences into a distributed ecosystem of sequence data producers and consumers. Given the power of genomics and declining sequencing costs, biology is an emerging “Big Data” discipline that will soon enter the exabyte data range when all subdisciplines are combined. These datasets must be transferred across commercial and research networks in creative ways since sending data without thought can have serious consequences on data processing time frames. Thus, it is imperative that biologists, bioinformaticians, and information technology engineers recalibrate data processing paradigms to fit this emerging reality. This review attempts to provide a snapshot of Big Data transfer across networks, which is often overlooked by many biologists. Specifically, we discuss four key areas: 1) data transfer networks, protocols, and applications; 2) data transfer security including encryption, access, firewalls, and the Science DMZ; 3) data flow control with software-defined networking; and 4) data storage, staging, archiving and access. A primary intention of this article is to orient the biologist in key aspects of the data transfer process in order to frame their genomics-oriented needs to enterprise IT professionals.

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