scholarly journals What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

2021 ◽  
Vol 9 (2) ◽  
pp. 299
Author(s):  
Angela Conti ◽  
Laura Corte ◽  
Debora Casagrande Pierantoni ◽  
Vincent Robert ◽  
Gianluigi Cardinali
Keyword(s):  
Single Copy ◽  
Sensu Stricto ◽  
Fungal Species ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Protein Encoding ◽  
The Many ◽  
Next Generation Sequencing Ngs ◽  
Encoding Genes

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

scholarly journals The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

2020 ◽  
Author(s):  
Thomas Taetzsch ◽  
Dillon Shapiro ◽  
Randa Eldosougi ◽  
Tracey Myers ◽  
Robert Settlage ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Skeletal Muscles ◽  
Tibialis Anterior Muscle ◽  
Muscle Fibers ◽  
Progressive Degeneration ◽  
Protein Encoding ◽  
Small Muscle ◽  
Encoding Genes

AbstractDuchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

scholarly journals Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bruno Silvestre Lira ◽  
Maria José Oliveira ◽  
Lumi Shiose ◽  
Raquel Tsu Ay Wu ◽  
Daniele Rosado ◽  
...  
Keyword(s):  
Tomato Fruit ◽  
Protein Family ◽  
Tomato Genome ◽  
Physiological Processes ◽  
Fruit Development And Ripening ◽  
Protein Encoding ◽  
Ripening Inhibitor ◽  
Encoding Genes ◽  
Signalling Cascade

Abstract Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

scholarly journals What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 599 ◽  
Author(s):  
Catarina Pinho ◽  
Bárbara Santos ◽  
Vanessa Mata ◽  
Mariana Seguro ◽  
Maria Romeiras ◽  
...  
Keyword(s):  
Diet Composition ◽  
Taxonomic Resolution ◽  
Faecal Pellets ◽  
Cabo Verde ◽  
Reserve Management ◽  
Conservation Actions ◽  
Conservation Plans ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.

scholarly journals Comparative Sequence Analysis of Mycobacterium leprae and the New Leprosy-Causing Mycobacterium lepromatosis

2009 ◽  
Vol 191 (19) ◽  
pp. 6067-6074 ◽  
Author(s):  
Xiang Y. Han ◽  
Kurt C. Sizer ◽  
Erika J. Thompson ◽  
Juma Kabanja ◽  
Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Mycobacterium Leprae ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Neutral Evolution ◽  
Rrna Gene ◽  
Protein Encoding ◽  
Mycobacterium Lepromatosis ◽  
Encoding Genes

ABSTRACT Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged ∼10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.

scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Reference Genome ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Pathogen Control ◽  
Genome Assemblies ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

scholarly journals Mixed-Species Genomic Microarray Analysis of Fecal Samples Reveals Differential Transcriptional Responses of Bifidobacteria in Breast- and Formula-Fed Infants

2009 ◽  
Vol 75 (9) ◽  
pp. 2668-2676 ◽  
Author(s):  
Eline S. Klaassens ◽  
Rolf J. Boesten ◽  
Monique Haarman ◽  
Jan Knol ◽  
Frank H. Schuren ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Genes ◽  
Transcriptional Responses ◽  
Fecal Samples ◽  
Young Infants ◽  
Exact Function ◽  
Wide Range ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Although their exact function remains enigmatic, bifidobacteria are among the first colonizers of the newborn infant gut and further develop into abundant communities, notably in response to diet. Therefore, the transcriptional responses of bifidobacteria in rapidly processed fecal samples from young infants that were fed either breast milk or a formula containing a mixture of galacto- and fructo-oligosaccharides were studied. The presence and diversity of the bifidobacterial fecal communities were determined using PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR for specific species. Changes in the total number of bifidobacteria as well as in species diversity were observed, indicating the metabolic activities of the bifidobacteria within the infant gut. In addition, total RNAs isolated from infant feces were labeled and hybridized to a bifidobacterium-specific microarray comprising approximately 6,000 clones of the major bifidobacterial species of the human gut. Approximately 270 clones that showed the most prominent hybridization with the samples were sequenced. Fewer than 10% of the hybridizing clones contained rRNA genes, whereas the vast majority of the inserts showed matches with protein-encoding genes predicted to originate from bifidobacteria. Although a wide range of functional groups was covered by the obtained sequences, the largest fraction (14%) of the transcribed genes assigned to a functional category were predicted to be involved in carbohydrate metabolism, while some were also implicated in exopolysaccharide production or folate production. A total of three of the above-described protein-encoding genes were selected for quantitative PCR and sequence analyses, which confirmed the expression of the corresponding genes and the expected nucleotide sequences. In conclusion, the results of this study show the feasibility of obtaining insight into the transcriptional responses of intestinal bifidobacteria by analyzing fecal RNA and highlight the in vivo expression of bifidobacterial genes implicated in host-related functions.

scholarly journals The role of miRNA in regulation of AXL, DAPK1, NFIB gene expression in breast cancer

2018 ◽  
pp. 130-133
Author(s):  
И.В. Пронина ◽  
Е.А. Филиппова ◽  
С.С. Лукина ◽  
А.М. Бурденный ◽  
Т.П. Казубская ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Epithelial Mesenchymal Transition ◽  
Negative Regulator ◽  
Protein Coding ◽  
Mesenchymal Transition ◽  
Protein Encoding ◽  
Apoptotic Pathways ◽  
Encoding Genes

Рак молочной железы (РМЖ) характеризуется эпигенетическими нарушениями, которые приводят к нарушению регуляции экспрессии опухоль ассоциированных белок-кодирующих генов, что влияет на развитие опухоли. Цель исследования - поиск новых микроРНК, потенциально вовлеченных в регуляцию экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB), связанных с регуляцией апоптоза и эпителиально-мезенхимального перехода при РМЖ. Методом количественной ПЦР определены изменения экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB) и 3 микроРНК (miR-127-5p, -132-3р, -9-5p), предсказанных с помощью алгоритмов miRWalk 2.0 как регуляторные. Определены статистически значимые отрицательные корреляции между изменениями уровней экспрессии микроРНК и мРНК для следующих пар: miR-127-5p - DAPK1 (Rs = -0,503, p = 0,001) и miR-9-5p - DAPK1 (Rs = -0,335, p = 0,040). Таким образом, установлена потенциальная роль двух микроРНК в регуляции экспрессии гена DAPK1, активатора различных путей апоптоза и негативного регулятора ЭМП, что имеет фундаментальное значение и может найти применение для разработки таргетной терапии РМЖ. Breast cancer (BC) is characterized by epigenetic disorders, which lead to dysregulation of protein-coding gene expression; together these result in development of a tumor. The goal of the study was to search for new miRNAs that are potentially involved in regulation of the expression of three protein-encoding genes (AXL, DAPK1, NFIB) associated with regulation of apoptosis and the epithelial-mesenchymal transition in breast cancer. Quantitative PCR was used to determine changes in the expression of three protein-coding genes (AXL, DAPK1, NFIB) and three miRNAs (miR-127-5p, -132-3p, -9-5p) that had been predicted to be regulators by miRWalk 2.0 algorithms. Statistically significant negative correlations between changes in miRNA and mRNA expression were determined for the following pairs: miR-127-5p - DAPK1 (Rs = -0.503, p = 0.001) and miR-9-5p - DAPK1 (Rs = -0.335, p = 0.040). Therefore, the study showed a potential role of two miRNAs in regulation of the DAPK1 gene expression, an activator of various apoptotic pathways and a negative regulator of EMT. This result is fundamentally important and can be used to develop targeted therapies for breast cancer.

Mitochondrial genome of Rhabdosynochus viridisi (Monogenea: Diplectanidae), a parasite of Pacific white snook Centropomus viridis

2021 ◽  
Vol 95 ◽  
Author(s):  
V. Caña-Bozada ◽  
R. Llera-Herrera ◽  
E.J. Fajer-Ávila ◽  
F.N. Morales-Serna
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Cdna Libraries ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Genomic Information ◽  
Coding Regions ◽  
Protein Encoding ◽  
Encoding Genes

Abstract We report the nearly complete mitochondrial genome of Rhabdosynochus viridisi – the first for this genus – achieved by combining shotgun sequencing of genomic and cDNA libraries prepared using low-input protocols. This integration of genomic information leads us to correct the annotation of the gene features. The mitochondrial genome consists of 13,863 bp. Annotation resulted in the identification of 12 protein-encoding genes, 22 tRNA genes and two rRNA genes. Three non-coding regions, delimited by three tRNAs, were found between the genes nad5 and cox3. A phylogenetic analysis grouped R. viridisi with three other species of diplectanid monogeneans for which mitochondrial genomes are available.

Expression study of soybean germin-like gene family reveals a role of GLP7 gene in various abiotic stress tolerances

2016 ◽  
Vol 96 (2) ◽  
pp. 296-304 ◽  
Author(s):  
Yongguang Li ◽  
Dayong Zhang ◽  
Weina Li ◽  
Ali Inayat Mallano ◽  
Yuhang Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Primary Root ◽  
Plant Glycoproteins ◽  
Protein Encoding ◽  
Oxidative Tolerance ◽  
Abiotic Stress Treatment ◽  
Encoding Genes ◽  
Soybean Leave

Germin-like proteins (GLPs) are ubiquitous plant glycoproteins (belonging to the cupin super family) that play diverse roles, including abiotic stress resistance in many plant species. To identify the molecular functions underlying abiotic stress responses, the expression of germin-like protein encoding genes of soybean GmGLPs was analyzed. qRT-PCR analyses of 21 GmGLPs transcripts abundances were conducted in soybean leave tissues. The results showed that GmGLPs transcripts were highly abundant upon treatments with high salinity, PEG6000, abscisic acid (ABA) and methyl viologen (MV). The peaks of transcript copiousness induced by PEG6000 and NaCl were mostly observed after 18 h, while some genes expressed earlier than 4 h after abiotic stress treatment. A specific GmGLP7 gene, that was highly abundant under salinity, drought, ABA and MV conditions, was further characterized. The ectopic overexpression of GmGLP7 (Glyma.08G226800.1) in transgenic Arabidopsis enhanced drought, salt, and oxidative tolerance and resulted in hypersensitive phenotypes toward ABA-mediated seed germination and primary root elongation, compared to the wild-type. Taken together, these results suggest that GmGLP7 positively confers abiotic tolerance in plants.

scholarly journals RNA Arbitrarily Primed PCR Survey of Genes Regulated by ToxR in the Deep-Sea Bacterium Photobacterium profundum Strain SS9

2001 ◽  
Vol 183 (5) ◽  
pp. 1688-1693 ◽  
Author(s):  
Kelly A. Bidle ◽  
Douglas H. Bartlett
Keyword(s):  
Gene Expression ◽  
Virulence Gene ◽  
Environmental Signals ◽  
Virulence Gene Expression ◽  
New Genes ◽  
Protein Encoding ◽  
Arbitrarily Primed Pcr ◽  
Photobacterium Profundum ◽  
Encoding Genes

ABSTRACT We are currently investigating the role of ToxR-mediated gene regulation in Photobacterium profundum strain SS9. SS9 is a moderately piezophilic (“pressure loving”) psychrotolerant marine bacterium belonging to the family Vibrionaceae. InVibrio cholerae, ToxR is a transmembrane DNA binding protein involved in mediating virulence gene expression in response to various environmental signals. A homolog to V. choleraeToxR that is necessary for pressure-responsive gene expression of two outer membrane protein-encoding genes was previously found in SS9. To search for additional genes regulated by ToxR in SS9, we have used RNA arbitrarily primed PCR (RAP-PCR) with wild-type and toxRmutant strains of SS9. Seven ToxR-activated transcripts and one ToxR-repressed transcript were identified in this analysis. The cDNAs corresponding to these partial transcripts were cloned and sequenced, and ToxR regulation of their genes was verified. The products of these genes are all predicted to fall into one or both of two functional categories, those whose products alter membrane structure and/or those that are part of a starvation response. The transcript levels of all eight newly identified genes were also characterized as a function of hydrostatic pressure. Various patterns of pressure regulation were observed, indicating that ToxR activation or repression cannot be used to predict the influence of pressure on gene expression in SS9. These results provide further information on the nature of the ToxR regulon in SS9 and indicate that RAP-PCR is a useful approach for the discovery of new genes under the control of global regulatory transcription factors.

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