5,562 results match your criteria analyses inferred

Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005).

Syst Appl Microbiol 2021 Mar 26;44(3):126199. Epub 2021 Mar 26.

Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy. Electronic address:

The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hördt et al. Read More

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Taxonomy and Phylogeny of the Complex With Descriptions of Six New Species From East Asia.

Front Microbiol 2021 26;12:644979. Epub 2021 Mar 26.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.

is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. Read More

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The endemic Chamaecytisus albidus is nodulated by symbiovar genistearum of Bradyrhizobium in the Moroccan Maamora Forest.

Syst Appl Microbiol 2021 Mar 26;44(3):126197. Epub 2021 Mar 26.

Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco. Electronic address:

Out of 54 isolates from root nodules of the Moroccan-endemic Chamaecytisus albidus plants growing in soils from the Maamora cork oak forest, 44 isolates formed nodules when used to infect their original host plant. A phenotypic analysis showed the metabolic diversity of the strains that used different carbohydrates and amino acids as sole carbon and nitrogen sources. The isolates grew on media with pH values ranging from 6 to 8. Read More

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Population genomics of the maize pathogen Ustilago maydis: demographic history and role of virulence clusters in adaptation.

Genome Biol Evol 2021 Apr 10. Epub 2021 Apr 10.

Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.

The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. Read More

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Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms.

Front Genet 2021 22;12:617282. Epub 2021 Mar 22.

Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, Paris, France.

Networks are powerful tools to represent and investigate biological systems. The development of algorithms inferring regulatory interactions from functional genomics data has been an active area of research. With the advent of single-cell RNA-seq data (scRNA-seq), numerous methods specifically designed to take advantage of single-cell datasets have been proposed. Read More

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Microbiomes of willow-galling sawflies: effects of host plant, gall type, and phylogeny on community structure and function.

Genome 2021 Apr 7:1-12. Epub 2021 Apr 7.

Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway.

While free-living herbivorous insects are thought to harbor microbial communities composed of transient bacteria derived from their diet, recent studies indicate that insects that induce galls on plants may be involved in more intimate host-microbe relationships. We used 16S rDNA metabarcoding to survey larval microbiomes of 20 nematine sawfly species that induce bud or leaf galls on 13 species. The 391 amplicon sequence variants (ASVs) detected represented 69 bacterial genera in six phyla. Read More

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New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline.

BMC Ecol Evol 2021 Apr 6;21(1):51. Epub 2021 Apr 6.

SNSB-Zoologische Staatssammlung München, Munich, Germany.

Background: The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea's location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated. Read More

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Voxel-wise functional connectivity of the default mode network in epilepsies: a systematic review and meta-analysis.

Curr Neuropharmacol 2021 Mar 25. Epub 2021 Mar 25.

The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731. China.

Background: Default mode network (DMN) is recognized to be involved in generation and propagation of epileptic activities in various epilepsies. Converging evidence has suggested disturbed functional connectivity (FC) in epilepsies, which was inferred to be related to underlying pathological mechanisms. However, abnormal changes of FC in DMN revealed by different studies are controversial, which obscures the role of DMN in distinct epilepsies. Read More

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Pitfalls and challenges in genetic test interpretation: An exploration of genetic professionals experience with interpretation of results.

Clin Genet 2021 May;99(5):638-649

Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.

The interpretation of genetic testing results is subject to error. This observational study illustrates examples of pitfalls and challenges in interpretation of genetic testing results as reported by genetics professionals. We surveyed genetics professionals to describe interpretation challenges, the types of variants that were involved, and the reported clinical impact of misconception of a test result. Read More

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The Phylogenetic Relationship Revealed Three New Wood-Inhabiting Fungal Species From Genus .

Front Microbiol 2021 17;12:650195. Epub 2021 Mar 17.

Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China.

Wood-inhabiting fungi play a significant role in wood degradation and the cycle of matter in the ecological system. In the present study, three new wood-inhabiting fungal species, , , and spp. nov. Read More

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Inference of DNA methylation patterns in molluscs.

Philos Trans R Soc Lond B Biol Sci 2021 May 5;376(1825):20200166. Epub 2021 Apr 5.

LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.

Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Read More

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Phylogeny, Global Biogeography and Pleomorphism of .

Microorganisms 2021 Mar 29;9(4). Epub 2021 Mar 29.

Westerdijk Fungal Biodiversity Institute, 3508 AD Utrecht, The Netherlands.

() is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Read More

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Phylogenetic and Haplotype Network Analyses of Species in China Based on Sequences of Multiple Loci.

Biology (Basel) 2021 Mar 1;10(3). Epub 2021 Mar 1.

Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.

is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (), beta-tubulin gene (), calmodulin gene (), and histone-3 gene () were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of with closely related species. Read More

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Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network.

Microorganisms 2021 Mar 6;9(3). Epub 2021 Mar 6.

Department of Ecology, University of Kaiserslautern, D-67633 Kaiserslautern, Germany.

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Read More

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First report of the mitogenome of (Diptera, Tachinidae) from Beijing, China.

Mitochondrial DNA B Resour 2021 Mar 17;6(3):862-864. Epub 2021 Mar 17.

School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.

(Mesnil, 1967) (Diptera, Tachinidae) is a parasitic fly species and of great ecological importance in natural systems as parasitoids of herbivorous insects. The mitogenome of . was sequenced and analyzed here for the first time. Read More

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The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling.

Evol Bioinform Online 2021 15;17:11769343211003079. Epub 2021 Mar 15.

Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.

is a highly variable genomic region of SARS-CoV-2. Although non-essential and the precise functions are unknown, it has been suggested that this protein assists in SARS-CoV-2 replication in the early secretory pathway and in immune evasion. We utilized the binding partners of SARS-CoV-2 proteins in human HEK293T cells and performed genome-wide phylogenetic profiling and clustering analyses in 446 eukaryotic species to predict and discover ORF8 binding partners that share associated functional mechanisms based on co-evolution. Read More

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A novel reference dated phylogeny for the genus Spodoptera Guenée (Lepidoptera: Noctuidae: Noctuinae): new insights into the evolution of a pest-rich genus.

Mol Phylogenet Evol 2021 Mar 29:107161. Epub 2021 Mar 29.

DGIMI, Univ Montpellier, INRAE, Montpellier, France. Electronic address:

The noctuid genus Spodoptera currently consists of 31 species with varied host plant breadths, ranging from monophagous and oligophagous non-pest species to polyphagous pests of economic importance. Several of these pest species have become major invaders, colonizing multiple continents outside their native range. Such is the case of the infamous fall armyworm, Spodoptera frugiperda (J. Read More

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An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk.

Sci Rep 2021 Mar 31;11(1):7272. Epub 2021 Mar 31.

Inserm U1194, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.

Modular response analysis (MRA) is a widely used inference technique developed to uncover directions and strengths of connections in molecular networks under a steady-state condition by means of perturbation experiments. We devised several extensions of this methodology to search genomic data for new associations with a biological network inferred by MRA, to improve the predictive accuracy of MRA-inferred networks, and to estimate confidence intervals of MRA parameters from datasets with low numbers of replicates. The classical MRA computations and their extensions were implemented in a freely available R package called aiMeRA ( https://github. Read More

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Elucidation of the complicated scenario of primate gene evolution.

J Virol 2021 Mar 31. Epub 2021 Mar 31.

Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo 1088639, Japan

APOBEC3 proteins play pivotal roles in defenses against retroviruses, including HIV-1, as well as retrotransposons. Presumably due to the evolutionary arms race between the hosts and retroelements, APOBEC3 genes have rapidly evolved in primate lineages through sequence diversification, gene amplification and loss, and gene fusion. Consequently, modern primates possess a unique set or "repertoire" of APOBEC3 genes. Read More

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Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae).

Syst Biol 2021 Mar 31. Epub 2021 Mar 31.

Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main group of genera (i. Read More

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OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.

Bioinformatics 2021 Mar 31. Epub 2021 Mar 31.

Department of Computational Biology, University of Lausanne, Switzerland.

Motivation: Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. Read More

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Large-scale labeling and assessment of sex bias in publicly available expression data.

BMC Bioinformatics 2021 Mar 30;22(1):168. Epub 2021 Mar 30.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

Background: Women are at more than 1.5-fold higher risk for clinically relevant adverse drug events. While this higher prevalence is partially due to gender-related effects, biological sex differences likely also impact drug response. Read More

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Microarthropod contributions to fitness variation in the common moss .

Proc Biol Sci 2021 Mar 31;288(1947):20210119. Epub 2021 Mar 31.

Department of Biology, Portland State University, PO Box 751, Portland, OR 97202-0751, USA.

The evolution of sustained plant-animal interactions depends critically upon genetic variation in the fitness benefits from the interaction. Genetic analyses of such interactions are limited to a few model systems, in part because genetic variation may be absent or the interacting species may be experimentally intractable. Here, we examine the role of sperm-dispersing microarthropods in shaping reproduction and genetic variation in mosses. Read More

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Factors Controlling the Lower Radioactivity and Its Relation with Higher Organic Matter Content for Middle Jurassic Oil Shale in Yuqia Depression, Northern Qaidam Basin, China: Evidence from Organic and Inorganic Geochemistry.

ACS Omega 2021 Mar 8;6(11):7360-7373. Epub 2021 Mar 8.

Qinghai Geological Survey, Xining 810012, China.

Organic-rich oil shale with unusual lower radioactivity (expressed by GR) was found in Member 7 of Dameigou Formation, middle Jurassic (Jd) in Yuqia depression of northern Qaidam Basin, China. In order to systematically and contrastively investigate the factors controlling the lower GR and its relation with higher organic matter (OM) content (expressed by total organic carbon, abbr. TOC), organic and inorganic geochemical analyses were performed on samples consisting of oil shale and the underlying conformable contact dark shale from Well YQ-1Y. Read More

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Plastome phylogenomics of the East Asian endemic genus .

Plant Divers 2021 Feb 29;43(1):35-42. Epub 2020 May 29.

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.

is a dioecious genus endemic to East Asia that consists of two extant species: and . Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between and related taxa by sequencing the whole plastome DNA sequences for both extant species of and comparing them to published plastomes within Sapindales. Read More

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February 2021

Molecular phylogeny, biogeography and character evolution of the montane genus Juss. (Bignoniaceae).

Plant Divers 2021 Feb 22;43(1):1-14. Epub 2020 Sep 22.

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.

The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau (QTP) fosters habitat fragmentation that drives morphological differentiation of mountain plant species. Consequently, determining phylogenetic relationships between plant subgenera using morphological characters is unreliable. Therefore, we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus . Read More

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February 2021