scholarly journals Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast

2021 ◽  
Vol 7 (4) ◽  
pp. 287
Author(s):  
Carolina Santiago ◽  
Teresa Rito ◽  
Daniel Vieira ◽  
Ticiana Fernandes ◽  
Célia Pais ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Biological Significance ◽  
Fungal Species ◽  
Information Storage ◽  
Torulaspora Delbrueckii ◽  
Homologous Genes ◽  
Clusters Of Orthologous Groups ◽  
Cellular Processing ◽  
Intraspecies Variability ◽  
First Time

Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

scholarly journals Didymocyrtis epiphyscia, Lichenochora weillii, and Lichenoconium xanthoriae newly recorded from Turkey

Mycotaxon ◽  
2021 ◽  
Vol 136 (2) ◽  
pp. 523-528
Author(s):  
Mustafa Kocakaya
Keyword(s):  
Fungal Species ◽  
First Time

Three lichenicolous fungal species, Didymocyrtis epiphyscia, Lichenochora weillii, and Lichenoconium xanthoriae, are reported for the first time from Turkey. Comments on the taxonomy, ecology, and hosts and photographic illustrations are provided for each species.

scholarly journals Improvement in the diffraction efficiency of a polymer using an ionic liquid

2018 ◽  
Vol 83 (2) ◽  
pp. 213-220
Author(s):  
Sung Kim ◽  
Pankaj Attri ◽  
In Kim
Keyword(s):  
Diffraction Efficiency ◽  
Information Storage ◽  
Polymer Mixture ◽  
Dihydrogen Phosphate ◽  
Storage Devices ◽  
Dpss Laser ◽  
Photosensitive Polymer ◽  
Diode Pumped ◽  
First Time ◽  
532 Nm

In this paper, photosensitive materials for information storage devices are presented. The polymers were prepared using surface relief-grating (SRG) fabrication with a diode-pumped solid-state (DPSS) laser of 532 nm, and the diffraction efficiency (DE) of the polymers were assessed with a low-power DPSS laser at 633 nm. However, the diffraction efficiency of the azo-functionalized epoxy-based polymer was low, even after 15 min of exposure. To improve the efficiency and reduce the time it takes for the DE measurements of the photosensitive polymer, the polymer was combined ionic liquids (ILs). Various ILs, i.e., 1-methylimidazolium chloride ([Mim]Cl) from the imidazolium family of ILs and diethylammonium dihydrogen phosphate (DEAP), triethylammonium 4-aminotoluene-3-sulfonic acid (TASA) and tributylmethylammonium methyl sulphate (TBMS) from the ammonium family of ILs, were investigated. For the first time, it was observed that DE dramatically increased the DEAP?polymer mixture in 4 min compared to the polymer (alone) and other polymer?IL mixtures. Therefore, DEAP IL could help improve the efficiency of DE measurements in a shorter time.

scholarly journals Macrofungi from Siddababa Sacred Grove: West, Nepal

2014 ◽  
Vol 15 ◽  
pp. 107-116
Author(s):  
Hari P Aryal ◽  
Rajenda Poudel ◽  
U Budathoki
Keyword(s):  
Rainy Season ◽  
New Record ◽  
Fungal Species ◽  
Edible Mushrooms ◽  
Sacred Grove ◽  
Wild Edible Mushrooms ◽  
Riverine Forest ◽  
Taxonomic Description ◽  
First Time

During the survey of wild edible mushrooms in between tropical and temperate belt of Nepal in rainy season 2010 -2012, many macro fungal species were collected and identified. The paper highlights on new record of Volvorella taylorii (Berk and Broome) Sing. The species was reported and re-described for the first time from Nepal. Along with, taxonomic description of the two species of Volvorella found in the same studied area, have also been provided. Phytogeographycally, the sample collected area lies within a narrow limit of 9.75 hectare at the altitude between 335 and 400 masl in tropical deciduous riverine forest. The dried specimens are housed in the Tribhuvan University Central Herbarium (TUCH), Kirtipur Kathmandu, Nepal.  

Thermophilous fungi of decomposing sugarcane bagasse

1980 ◽  
Vol 58 (18) ◽  
pp. 2015-2016 ◽  
Author(s):  
D. K. Sandhu ◽  
Surinder Singh ◽  
M. K. Waraich
Keyword(s):  
Aspergillus Fumigatus ◽  
Sugarcane Bagasse ◽  
New Record ◽  
Fungal Species ◽  
Northern India ◽  
First Time ◽  
Temperature Responses

Twenty species of thermophilous fungi were identified from sugarcane bagasse at Batala in Northern India. Seven fungal species are reported from bagasse for the first time and Aspergillus caespitosns is a new record for India. Aspergillus fumigatus was the most common fungus followed by Mncor pusillus. The temperature responses of the fungi revealed 5 microthermophiles, 11 thermotolerant, and 4 true thermophiles. Three species of thermophilous fungi are reported in addition to those already recorded in the literature.

Veluticeps fasciculata sp. nov. (Gloeophyllaceae, Basidiomycota), a close relative to V. berkeleyi

Phytotaxa ◽  
2016 ◽  
Vol 243 (2) ◽  
pp. 163 ◽  
Author(s):  
Jiao Yang ◽  
Karen K. Nakasone ◽  
Shuang-Hui He
Keyword(s):  
Southern China ◽  
Brown Rot ◽  
Distinct Species ◽  
Fungal Species ◽  
Its Rdna ◽  
Close Relative ◽  
Rdna Sequences ◽  
First Time

A new brown-rot fungal species, Veluticeps fasciculata, is described from southern China. It is characterized by perennial effused basidiocarps with smooth or tuberculose hymenophore, nodose-septate generative hyphae, fasciculate cystidia (as hyphal pegs in hymenophore) and relatively small basidiospores. It occurs on wood of Cunninghamia and Cryptomeria. Although similar to Veluticeps berkeleyi, morphological and molecular (ITS rDNA sequences) data show that V. fasciculata is a distinct species. Complete description and illustrations are provided for the V. fasciculata. In addition, V. fimbriata is reported from China for the first time.

Iron-related transcriptomic variations in CaCo-2 cells, an in vitro model of intestinal absorptive cells

2006 ◽  
Vol 26 (1) ◽  
pp. 55-67 ◽  
Author(s):  
Céline Chicault ◽  
Bertrand Toutain ◽  
Annabelle Monnier ◽  
Marc Aubry ◽  
Patricia Fergelot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Annotation ◽  
In Vitro Model ◽  
Iron Absorption ◽  
Intracellular Iron ◽  
Absorptive Cells ◽  
Number Of Genes ◽  
Vitro Model ◽  
First Time

Regulation of iron absorption by duodenal enterocytes is essential for the maintenance of homeostasis by preventing iron deficiency or overload. Despite the identification of a number of genes implicated in iron absorption and its regulation, it is likely that further factors remain to be identified. For that purpose, we used a global transcriptomic approach, using the CaCo-2 cell line as an in vitro model of intestinal absorptive cells. Pangenomic screening for variations in gene expression correlating with intracellular iron content allowed us to identify 171 genes. One hundred nine of these genes are clustered into five types of expression profile. This is the first time that most of these genes have been associated with iron metabolism. Functional annotation of these five clusters indicates potential links between the immune response, proteolysis processes, and iron depletion. In contrast, iron overload is associated with cellular metabolism, especially that of lipids and glutathione involving redox function and electron transfer.

scholarly journals Description of Lepiotaceous Fungal Species of the Genera Chlorophyllum, Clarkeinda, Macrolepiota, Pseudolepiota, and Xanthagaricus, from Laos and Thailand

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 666
Author(s):  
Phongeun Sysouphanthong ◽  
Naritsada Thongklang ◽  
Jian-Kui Liu ◽  
Else C. Vellinga
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Fungal Species ◽  
Ongoing Research ◽  
Line Drawings ◽  
Dna And Rna ◽  
First Time

In our ongoing research on lepiotaceous taxa (Agaricaceae s.l.) in Laos and northern Thailand, we focus here on Chlorophyllum, Clarkeinda, Macrolepiota, Pseudolepiota, and Xanthagaricus. Collections were obtained from various habitats, including agricultural habitats, grasslands, and rainforests. A total of 12 taxa were examined and investigated. Of these 12, two are new for science; viz. Xanthagaricus purpureosquamulosus with brownish-grey to violet-brown squamules on a pale-violet to violet background; it shares the pileus color with X. caeruleus and X. ianthinus, but differs in other characters; and Macrolepiota excelsa, rather similar to M. procera but related toM. detersa. Two species, Pseudolepiota zangmui and Xanthagaricus necopinatus are recorded for the first time in Thailand. Four species of Chlorophyllum and a total of four species of Macrolepiota were found, viz., C. demangei and C. hortense with white basidiospores, C. molybdites and C. globosum with green basidiospores, M. detersa, M. dolichaula, the new M. excelsa, and M. velosa. Another rather common striking species is Clarkeinda trachodes, with yellow-green basidiospores. Each species is described in detail, with color photographs and line drawings. Phylogenetic analyses based on internal transcribed spacer (nrITS) region, the large subunit nuclear ribosomal (nrLSU) DNA and RNA polymerase II second largest subunit (rpb2) genes provide evidence for the placement of the species covered.

scholarly journals Effect of a novel alpha/beta hydrolase domain protein on tolerance of K. marxianus to lignocellulosic biomass derived inhibitors

2020 ◽  
Author(s):  
Dan Wu ◽  
Dongmei Wang ◽  
Jiong Hong
Keyword(s):  
Lignocellulosic Biomass ◽  
Resistance Mechanism ◽  
Cellulosic Biomass ◽  
Amino Acid Residues ◽  
Plasma Membrane Permeability ◽  
Industrial Fermentation ◽  
Homologous Genes ◽  
Ros Accumulation ◽  
Chain Acyl ◽  
First Time

Abstract Background: Lignocellulosic biomass is a promising renewable and sustainable resource for biofuels and chemicals. However, the inhibitors generated during lignocellulosic biomass pretreatment hinder microbial growth and interfere with fermentation. Studies on the tolerance to inhibitors, especially multiple inhibitors, are important in the construction of robust strains that can utilize lignocellulosic biomass. Results: The expression of an uncharted α/β hydrolase (ABHD) from Kluyveromyces marxianus was found to be up-regulated in the presence of single or multiple inhibitors; this enzyme was termed KmYME in this study. Disruption of KmYME made the yeast more susceptible to inhibitors, particularly to acetic acid, furfural and 5-hydroxymethylfurfural. KmYME was located in the mitoplast of mitochondria with targeting signals in the N-terminal 1-40 amino acid residues. Under inhibitor stress, the intracellular concentration of ATP, NAD(P) in the KmYME disrupted strain decreased. In addition, the KmYME disrupted strain lost more mitochondrial membrane potential, showed increased plasma membrane permeability, a more severe redox imbalance, and increased ROS accumulation, compared with those of the non-disrupted strain in the presence of the same inhibitors. The recombinant KmYME possessed esterase/thioesterase activity and preferred short-chain pNP aliphatic esters, long-chain acyl-CoA, and succinyl-CoA as substrates. The retro-complementation results indicated that the enzymatic activity of KmYME was necessary for the resistance to inhibitors. In addition, KmYME was also required for the resistance to other stresses including ethanol, temperature, and osmotic pressure. Disruption of two possible homologous genes in S. cerevisiae also reduced its tolerance to inhibitors. Conclusion: As an uncharted α/β hydrolase, KmYME which had esterase/thioesterase activity and located in mitochondrial matrix was identified for the first time. The esterase/thioesterase activity was necessary for the tolerance to lignocellulosic biomass derived inhibitors in K. marxianus. Disruption of KmYME reduced the tolerance to inhibitors by interfering with ATP, NAD and NADP synthesis. KmYME also correlated with tolerance to other stresses such as osmotic, ethanol, and temperature. This study may provide useful information for better understanding the resistance mechanism of multiple inhibitors, which is important in the creation of a robust strain for industrial fermentation that can use cellulosic biomass as substrate.

scholarly journals Distribution and diversity of Polyporaceae in Western India: An overview and addition to mycoflora of the Gujarat state

2018 ◽  
Vol 5 (1) ◽  
pp. 32-38 ◽  
Author(s):  
Ajit M Vasava ◽  
Ravi S Patel ◽  
Rina D Koyani ◽  
Kishore S. Rajput
Keyword(s):  
Single Species ◽  
Fungal Species ◽  
Western India ◽  
Gujarat State ◽  
Number Of Species ◽  
Dichomitus Squalens ◽  
Laetiporus Sulphureus ◽  
The Family ◽  
First Time ◽  
New Distribution

Extensive fieldwork in different climatic regimes of Gujarat state during last four years resulted in the collection of more than 349 fungal species. Out of these, 37 species from 20 genera were found to be from the family Polyporaceae. Among these, five species are being reported for the first time here as new distribution records. The highest number of species is represented by the genus Trametes while, Cerrena unicolo, Neolentinus kauffmanii, Dichomitus squalens, Panus conchatus and Laetiporus sulphureus possessed single species each.

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