scholarly journals Genetics of adaptation of the ascomycetous fungus Podospora anserina to submerged cultivation

2018 ◽  
Author(s):  
Olga A. Kudryavtseva ◽  
Ksenia R. Safina ◽  
Olga A. Vakhrusheva ◽  
Maria D. Logacheva ◽  
Aleksey A. Penin ◽  
...  
Keyword(s):  
Positive Selection ◽  
Sequence Data ◽  
Podospora Anserina ◽  
Data Availability ◽  
Submerged Cultivation ◽  
Sequencing Data ◽  
Russian Science ◽  
Nucleotide Substitutions ◽  
Ascomycetous Fungus

AbstractPodospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first four years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, the G-protein alpha subunit FadA evolved in seven out of eight experimental populations. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed allele replacements were adaptive and driven by positive selection.Author summaryLiving beings adapt to novel conditions that are far from their original environments in different ways. Studying mechanisms of adaptation is crucial for our understanding of evolution. The object of our interest is a multicellular fungus Podospora anserina. This fungus is known for its pronounced senescence and a definite lifespan, but it demonstrates an unlimited lifespan and no signs of senescence when grown under submerged conditions. Soon after transition to submerged cultivation, the rate of growth of P. anserina increases and its pigmentation changes. We wanted to find out whether there are any genetic changes that contribute to adaptation of P. anserina to these novel conditions and initiated a long-term evolutionary experiment on eight independent populations. Over the first four years of the experiment, 148 mutations were fixed in these populations. Many of these mutations lead to inactivation of the part of the developmental pathway in P. anserina, probably reallocating resources to vegetative proliferation in liquid medium. Our observations imply that strong positive selection drives changes in at least some of the affected protein-coding genes.Data AvailabilityGenome sequence data have been deposited at DDBJ/ENA/GenBank under accessions QHKV00000000 (founder genotype A; version QHKV01000000) and QHKU00000000 (founder genotype B; version QHKU01000000), with the respective BioSample accessions SAMN09270751 and SAMN09270757, under BioProject PRJNA473312. Sequencing data have been deposited at the SRA with accession numbers SRR7233712-SRR7233727, under the same BioProject.FundingExperimental work and sequencing were supported by the Russian Foundation for Basic Research (grants no. 16-04-01845a and 18-04-01349a). Bioinformatic analysis was supported by the Russian Science Foundation (grant no. 16-14-10173). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

scholarly journals Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation

2019 ◽  
Vol 11 (10) ◽  
pp. 2807-2817
Author(s):  
Olga A Kudryavtseva ◽  
Ksenia R Safina ◽  
Olga A Vakhrusheva ◽  
Maria D Logacheva ◽  
Aleksey A Penin ◽  
...  
Keyword(s):  
Parallel Evolution ◽  
Fungal Growth ◽  
Acid Sites ◽  
Podospora Anserina ◽  
Submerged Cultivation ◽  
Nucleotide Substitutions ◽  
Evolution Experiment ◽  
G Protein Alpha Subunit ◽  
Ascomycetous Fungus

Abstract Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.

scholarly journals A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’untranslated Region (3’UTR)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

Genetic instability of the short-living ascomycetous fungus Podospora anserina induced by prolonged submerged cultivation

Microbiology ◽  
2011 ◽  
Vol 80 (6) ◽  
pp. 784-796 ◽  
Author(s):  
O. A. Kudryavtseva ◽  
I. S. Mazheika ◽  
A. E. Solovchenko ◽  
O. V. Kamzolkina
Keyword(s):  
Genetic Instability ◽  
Podospora Anserina ◽  
Submerged Cultivation ◽  
Ascomycetous Fungus

scholarly journals A novel distinct genetic variant of tomato torrado virus with substantially shorter RNA1-specific 3'untranslated region (3'UTR)

2021 ◽  
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek ◽  
Aleksandra Obrępalska-Stęplowska
Keyword(s):  
Amino Acid ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide ◽  
Plant Sequence

Abstract Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal'17 collected in the 2017 year, derived from the ToTV-Wal'03 after long-term passages in plant. Sequence analyses of the ToTV-Wal`17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3'UTR of ToTV-Wal'17 RNA1 was 394 nts shorter in comparison to Wal'03. The performed sequence analyses pointed that 3'UTR of RNA1of ToTV-Wal'17 is the most divergent across all previously described European isolates.

Thoughts on the Long-Term Strategy, Science and Democracy

2006 ◽  
pp. 4-19 ◽  
Author(s):  
L. Abalkin
Keyword(s):  
Strategy Development ◽  
Russian Science ◽  
Global Trends ◽  
The World ◽  
World Development ◽  
Crucial Condition

The article covers unified issues of the long-term strategy development, the role of science as well as democracy development in present-day Russia. The problems of budget proficit, the Stabilization Fund issues, implementation of the adopted national projects, an increasing role of regions in strengthening the integrity and prosperity of the country are analyzed. The author reveals that the protection of businessmen and citizens from the all-embracing power of bureaucrats is the crucial condition of democratization of the society. Global trends of the world development and expert functions of the Russian science are presented as well.

Positive selection signatures in Anqing six‐end‐white pig population based on reduced‐representation genome sequencing data

2021 ◽  
Author(s):  
L. Guo ◽  
H. Sun ◽  
Q. Zhao ◽  
Z. Xu ◽  
Z. Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Genome Sequencing ◽  
Population Based ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Reduced Representation

scholarly journals OP0271 REAL-WORLD CLINICAL BURDEN AND GLUCOCORTICOID USE IN PATIENTS WITH POLYMYALGIA RHEUMATICA

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 169.1-169
Author(s):  
R. Punekar ◽  
P. Lafontaine ◽  
J. H. Stone
Keyword(s):  
Cardiovascular Disease ◽  
Health Plan ◽  
Polymyalgia Rheumatica ◽  
Data Availability ◽  
Categorical Variables ◽  
Continuous Variables ◽  
Rank Tests ◽  
Medical Claim ◽  
Diagnosis Codes

Background:Polymyalgia rheumatica (PMR) is a chronic inflammatory condition characterized by aching and morning stiffness in the neck, shoulders and pelvic girdle. It is a common inflammatory rheumatic disease in patients age >50 years, particularly women. While giant cell arteritis (GCA) is present in 9–21% of PMR cases, many PMR patients have symptoms independent of GCA. Current treatment options are limited to long-term glucocorticoid (GC), however, with risks of GC-related complications, including cardiovascular disease, osteoporosis, and diabetes mellitus.Objectives:To compare GC use and subsequent GC-related complications in patients with PMR vs a general population (GnP) cohort.Methods:This retrospective, observational cohort study was based on Optum’s de-identified Clinformatics®Data Mart Database (study period 01Jan2006-30June2018). The PMR cohort included patients with ≥1 inpatient or ≥2 outpatient claims ≥30 days apart with PMR related diagnosis codes (ICD-9: 725.xx or ICD-10: M35.3x) between 01Jan2006–30June2017 (patient identification period) during which first occurrence of a PMR-related medical claim was set as the index date (ID). Patients with ≥1 medical claim related to rheumatoid arthritis (RA) or GCA during the study period were excluded. The GnP cohort included patients without any RA, GCA or PMR diagnosis codes during the study period, with their ID set as 12 months from the start of continuous health plan enrollment. Patients in both cohorts were required to be age ≥50 years (on ID) with continuous health plan enrollment ≥12 months pre- and post-ID. Cohorts were 1:1 propensity score matched. GC use and incidence of GC-related complications were assessed from GC initiation, starting from the baseline period (12-months pre-ID) through to the end of GC use during the post-index period (i.e. the end of data availability, end of the study period or death [whichever occurred first]). Mean, standard deviation (SD) and median values for continuous variables, and frequency (n and %) for categorical variables were compared between the matched cohorts. Wilcoxon sum rank tests andt-tests on continuous variables and Chi-square tests or Fisher’s exact tests on categorical variables between matched cohorts were conducted. Duration of GC use was analyzed using the Kaplan-Meier method and compared between matched cohorts using log-rank tests.Results:In each of the PMR and GnP cohorts, 16,865 patients were included. In both matched cohorts, median age was 76 years, median Elixhauser comorbidity index score was 2.0, and the majority (~65%) were women. The median follow-up duration was 45 months and 51 months in the PMR and GnP cohorts, respectively. A higher proportion of patients in the PMR cohort than the matched GnP cohort (90.4% vs 62.8%;p<0.001) used GC. The mean (SD) duration of GC therapy was significantly longer in the PMR cohort than in the matched GnP cohort (242.1 [±317.2] days vs 35.5 [±124.6] days;p<0.001). Although patients in the PMR cohort had a lower average daily dose of GC (prednisone equivalent) vs the GnP cohort (mean [SD] mg 16.3 [± 21.9] vs 27.8 [±24.5], respectively [p<0.0001)], the cumulative GC dose was significantly higher in the PMR cohort than the GnP cohort (2125.4 [±3689.5] mg vs 476.6 [±1450.9] mg;p<0.001). This indicates PMR patients used chronic low dose GC while the GnP patients utilized higher dose GC burst therapy less frequently. The number of incident complications associated with GC use were significantly greater in the PMR cohort, and included hypertension, diabetes, skin toxicity, infections, neuropsychiatric effects, endocrine abnormalities, renal dysfunction/ failure, ocular effects, and cardiovascular disease (p<0.05).Conclusion:The overall GC burden in patients with PMR is high. With a higher incidence of GC-related comorbidities among PMR patients, early onset of these complications may be a significant contributor to long-term healthcare costs in these patients.Acknowledgments:This study was funded by Sanofi, Inc. Medical writing, under the direction of authors, was provided by Gauri Saal, MA Economics, Prime, Knutsford, UK, and funded by Sanofi.Disclosure of Interests:Rajeshwari Punekar Shareholder of: Sanofi, Employee of: Sanofi, Patrick LaFontaine Shareholder of: Sanofi, Employee of: Sanofi, John H. Stone Grant/research support from: Roche, Consultant of: Roche

scholarly journals REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data

2020 ◽  
Author(s):  
Russell Lewis McLaughlin
Keyword(s):  
Structural Variation ◽  
Sequence Data ◽  
Neurological Diseases ◽  
Repeat Expansion ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing ◽  
Repeat Expansions ◽  
Paired End Sequencing

Abstract Motivation Repeat expansions are an important class of genetic variation in neurological diseases. However, the identification of novel repeat expansions using conventional sequencing methods is a challenge due to their typical lengths relative to short sequence reads and difficulty in producing accurate and unique alignments for repetitive sequence. However, this latter property can be harnessed in paired-end sequencing data to infer the possible locations of repeat expansions and other structural variation. Results This article presents REscan, a command-line utility that infers repeat expansion loci from paired-end short read sequencing data by reporting the proportion of reads orientated towards a locus that do not have an adequately mapped mate. A high REscan statistic relative to a population of data suggests a repeat expansion locus for experimental follow-up. This approach is validated using genome sequence data for 259 cases of amyotrophic lateral sclerosis, of which 24 are positive for a large repeat expansion in C9orf72, showing that REscan statistics readily discriminate repeat expansion carriers from non-carriers. Availabilityand implementation C source code at https://github.com/rlmcl/rescan (GNU General Public Licence v3).

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 732-741 ◽  
Author(s):  
Wolfgang Staiber
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Sequence Data ◽  
Structural Evolution ◽  
5S Rdna ◽  
Oligonucleotide Primer ◽  
Homologous Gene ◽  
Gene Sequences ◽  
Nucleotide Substitutions ◽  
Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%–100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

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