scholarly journals Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids

2016 ◽  
Vol 105 ◽  
pp. 166-176 ◽  
Author(s):  
Lei Zhao ◽  
Xia Li ◽  
Ning Zhang ◽  
Shu-Dong Zhang ◽  
Ting-Shuang Yi ◽  
...  
Keyword(s):  
Large Scale ◽  
Nuclear Genes ◽  
Evolutionary Relationships ◽  
Phylogenomic Analyses

scholarly journals New insights into Trypanosoma cruzi evolution and genotyping based on system-wide protein expression profiles (PhyloQuant)

2020 ◽  
Author(s):  
Simon Ngao Mule ◽  
Andrè Guillherme da Costa Martins ◽  
Livia Rosa-Fernandes ◽  
Gilberto Santos de Oliveira ◽  
Carla Monadeli Rodrigues ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Trypanosoma Cruzi ◽  
Protein Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Shotgun Proteomics ◽  
Close Correlation ◽  
Evolutionary Relationships ◽  
Trypanosome Species ◽  
Protein Expression Profiles

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is subdivided into seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution justifies the concerted efforts towards understanding the population structure of T. cruzi strains. In this study, we introduce a novel approach termed ‘phyloquant’ to infer the evolutionary relationships and assignment of T. cruzi strains to their DTUs based on differential protein expression profiles evidenced by bottom up large scale mass spectrometry-based quantitative proteomic features. Mass spectrometry features analyzed using parsimony (MS1, iBAQ and LFQ) showed a close correlation between protein expression and T. cruzi DTUs and closely related trypanosome species. Although alternative topologies with minor differences between the three MS features analyzed were demonstrated, we show congruence to well accepted evolutionary relationships of T. cruzi DTUs; in all analyses TcI and Tcbat were sister groups, and the parental nature of genotype TcII and the hybrid genotypes TcV/TcVI were corroborated. Character mapping of genetic distance matrices based on phylogenetics and phyloquant clustering showed statistically significant correlations. We propose the first quantitative shotgun proteomics approach as a complement strategy to the genetic-based assignment of T. cruzi strains to DTUs and evolutionary inferences. Moreover, this approach allows for the identification of differentially regulated and strain/DTU/species-specific proteins, with potential application in the identification of strain/DTU specific biomarkers and candidate therapeutic targets. In addition, the correlation between multi-gene protein expression and divergence of trypanosome species was evaluated, adding another level to understand the genetic subdivisions among T. cruzi DTUs.

scholarly journals Reference genome assemblies reveal the origin and evolution of allohexaploid oat

2021 ◽  
Author(s):  
Yuanying Peng ◽  
Honghai Yan ◽  
Laichun Guo ◽  
Cao Deng ◽  
Lipeng Kang ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Higher Plants ◽  
Cereal Crops ◽  
Origin And Evolution ◽  
Avena Species ◽  
Oxford Nanopore ◽  
Reference Quality ◽  
Phylogenomic Analyses ◽  
Reference Genomes

Abstract Common oat (Avena sativa) is one of the most important cereal crops serving as a valuable source of forage and human food. While reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich, polyploid genome. By using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated the first reference-quality genome assembly of hulless common oat with a contig N50 of 93 Mb. We also assembled the genomes of diploid and tetraploid Avena ancestors, which enabled us to identify oat subgenome, large-scale structural rearrangements, and preferential gene loss in the C subgenome after hexaploidization. Phylogenomic analyses of cereal crops indicated that the oat lineage descended before wheat, offering oat as a unique window into the early evolution of polyploid plants. The origin and evolution of hexaploid oat is deduced from whole-genome sequencing, plastid genome and transcriptomes assemblies of numerous Avena species. The high-quality reference genomes of Avena species with different ploidies and the studies of their polyploidization history will facilitate the full use of crop gene resources and provide a reference for the molecular mechanisms underlying the polyploidization of higher plants, helping us to overcome food security challenges.

scholarly journals Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Rei Kajitani ◽  
Dai Yoshimura ◽  
Yoshitoshi Ogura ◽  
Yasuhiro Gotoh ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
De Novo ◽  
Bacterial Genomes ◽  
Long Reads ◽  
Wide Range ◽  
Long Read ◽  
Phylogenomic Analyses ◽  
Error Removal ◽  
Iterative Error

Abstract De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

scholarly journals Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

2020 ◽  
Vol 107 (12) ◽  
pp. 1710-1735
Author(s):  
Erik J. M. Koenen ◽  
Catherine Kidner ◽  
Élvia R. Souza ◽  
Marcelo F. Simon ◽  
João R. Iganci ◽  
...  
Keyword(s):  
Nuclear Genes ◽  
Evolutionary Relationships ◽  
Hybrid Capture

Evolutionary Relationships among Mucoralean Fungi (Zygomycota): Evidence for Family Polyphyly on a Large Scale

Mycologia ◽  
2001 ◽  
Vol 93 (2) ◽  
pp. 286 ◽  
Author(s):  
Kerry O'Donnell ◽  
Francois M. Lutzoni ◽  
Todd J. Ward ◽  
Gerald L. Benny
Keyword(s):  
Large Scale ◽  
Evolutionary Relationships

scholarly journals Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

2009 ◽  
Vol 1 ◽  
pp. 231-238 ◽  
Author(s):  
Fabien Burki ◽  
Yuji Inagaki ◽  
Jon Bråte ◽  
John M. Archibald ◽  
Patrick J. Keeling ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenomic Analyses

scholarly journals Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mick Van Vlierberghe ◽  
Arnaud Di Franco ◽  
Hervé Philippe ◽  
Denis Baurain
Keyword(s):  
Transcriptome Sequencing ◽  
Large Scale ◽  
High Quality ◽  
Data Description ◽  
Sequencing Project ◽  
Microbial Eukaryote ◽  
Photosynthetic Organisms ◽  
Tree Inference ◽  
Context Tree ◽  
Phylogenomic Analyses

Abstract Objectives Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps. Data description We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.

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