scholarly journals EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

2021 ◽  
Vol 6 (57) ◽  
pp. 2817
Author(s):  
Arianna Krinos ◽  
Sarah Hu ◽  
Natalie Cohen ◽  
Harriet Alexander
Keyword(s):  
Eukaryotic Microbes ◽  
Taxonomic Annotation

scholarly journals Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

2012 ◽  
Vol 11 (11) ◽  
pp. 1304-1312 ◽  
Author(s):  
Howard S. Judelson
Keyword(s):  
Protein Sequence ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Life Cycles ◽  
Aquatic Environments ◽  
Gene Fusions ◽  
Additional Species ◽  
Functional Studies ◽  
Eukaryotic Microbes ◽  
Genome Projects

ABSTRACT The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.

scholarly journals Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

2017 ◽  
Author(s):  
Marina Pais ◽  
Kentaro Yoshida ◽  
Artemis Giannakopoulou ◽  
Mathieu A. Pel ◽  
Liliana M. Cano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Natural Ecosystems ◽  
Asexual Lineage ◽  
Irish Famine ◽  
Eukaryotic Microbes ◽  
And Migration ◽  
Potato Famine

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

scholarly journals Improvement of eukaryotic proteins prediction from soil metagenomes

2021 ◽  
Author(s):  
Carole Belliardo ◽  
Georgios Koutsovoulos ◽  
Corinne Rancurel ◽  
Mathilde Clement ◽  
Justine Lipuma ◽  
...  
Keyword(s):  
Automated Analysis ◽  
Metagenomic Data ◽  
Analysis Pipeline ◽  
Shotgun Metagenomics ◽  
Assignment Method ◽  
Eukaryotic Proteins ◽  
Public Repositories ◽  
Soil Proteins ◽  
Taxonomic Annotation

Background | During the last decades, shotgun metagenomics and metabarcoding have highlighted the diversity of microorganisms from environmental or host-associated samples. Most assembled metagenome public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs and metagenome-assembled genomes (MAGs). Consequently, eukaryotic contigs and MAGs, with intrinsically different gene features, are not optimally annotated, resulting in an incorrect representation of the eukaryotic component of biodiversity, despite their biological relevance. Results | Using an automated analysis pipeline, we have filtered eukaryotic contigs from 6,873 soil metagenomes from the IMG/M database of the Joint Genome Institute. We have re-annotated genes using eukaryote-tailored methods, yielding 5,6 million eukaryotic proteins. Our pipeline improves eukaryotic proteins completeness, contiguity and quality. Moreover, the better quality of eukaryotic proteins combined with a more comprehensive assignment method improves the taxonomic annotation as well. Conclusions | Using public soil metagenomic data, we provide a dataset of eukaryotic soil proteins with improved completeness and quality as well as a more reliable taxonomic annotation. This unique resource is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates

2014 ◽  
Vol 6 (3) ◽  
pp. 293-306 ◽  
Author(s):  
Yuejian Mao ◽  
Xiangzhen Li ◽  
Eoghan M. Smyth ◽  
Anthony C. Yannarell ◽  
Roderick I. Mackie
Keyword(s):  
Root Exudates ◽  
Panicum Virgatum ◽  
Panicum Virgatum L ◽  
Eukaryotic Microbes

The Expansion of Life

2021 ◽  
pp. 99-118
Author(s):  
Franklin M. Harold
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Atmospheric Oxygen ◽  
Gene Level ◽  
Chance Events ◽  
Eukaryotic Microbes ◽  
Multicellular Organisms ◽  
And Behavior ◽  
New Phase ◽  
Recurrent Theme

The story of life tells of relentless expansion from obscure beginnings to smother the earth in organized biochemistry. First came the prokaryotes, Bacteria and Archaea, followed some two billion years later by eukaryotic microbes. The latter pattern of organization underpins the rise of multicellular organisms, and their spectacular proliferation over the past 600 million years. There have been no fundamentally new kinds of organisms since, but the rise of mind culminating in humanity may signal a new phase in life’s history. Life has expanded in both quantity and quality, a gyre of mounting size, complexity, and functional capacity; in some elusive sense evolution is progressive. Multicellularity, the key invention, is not singular but happened multiple times in several eukaryotic lineages. The proliferation of higher organisms was probably enabled by increased energy flow, and dependent on the increase in atmospheric oxygen. It is studded with innovations in structure, physiology, and behavior, whose origin is a recurrent theme in evolutionary biology. Novelty is rooted in mutational events at the gene level, supplemented by the acquisition of genes from the outside by both gene transfer and symbiosis, and possibly by other avenues. Chance events were scrutinized and culled by natural selection. There appears to be no intrinsic progressive drive, but natural selection generally favors the more functional and better organized.

scholarly journals Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis?

2014 ◽  
Vol 6 (1) ◽  
pp. 4-7 ◽  
Author(s):  
David M. Wilkinson ◽  
Angela L. Creevy ◽  
Chiamaka L. Kalu ◽  
David W. Schwartzman
Keyword(s):  
Lichen Symbiosis ◽  
Eukaryotic Microbes
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