Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom Amauroderma rugosum, a traditional medicinal species in the family Ganodermataceae

Mycologia ◽  
2021 ◽  
Vol 113 (2) ◽  
pp. 268-277
Author(s):  
Weiping Lin ◽  
Yanhua Shi ◽  
Guangtao Jia ◽  
Hengyi Sun ◽  
Tongyi Sun ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Phylogenomic Analysis ◽  
Medicinal Mushroom ◽  
Medicinal Species ◽  
The Family

scholarly journals Inuit plant use in the eastern Subarctic: comparative ethnobotany in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 271-282
Author(s):  
Alain Cuerrier ◽  
Courtenay Clark ◽  
Christian H. Norton
Keyword(s):  
Lifestyle Changes ◽  
Ethnobotanical Knowledge ◽  
Structured Interviews ◽  
Medicinal Species ◽  
Medicinal Uses ◽  
Plant Uses ◽  
The Family ◽  
Plant Names ◽  
Family Level ◽  
Comparative Ethnobotany

Plants are important in traditional Inuit life. They are used for food, tea, medicine, etc. Based on semi-structured interviews with 35 informants, we documented and compared plant names and uses in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut. Plant names and uses were expected to be similar between communities owing to common boreal–subarctic environments and cultural ties. Both communities reported the same number of taxa, with equivalent proportions of vascular and nonvascular plants, growth forms, use categories, and medicinal uses. Forty-three species were used in each community, for a total of 78 species from 39 families. Despite a high overlap in species distributions, only 35% of nonvascular and 56% of vascular species were used in both communities. Correspondence was higher at the family level (64% of nonvascular and 75% of vascular families shared). The Ericaceae family was the most used, followed by Rosaceae. Thirteen of 30 medicinal species were shared between communities. There was a low correspondence regarding the conditions for which the medicinal species were used. Edible taxa were shared the most (52%). Plant uses unique to either Nain or Kangiqsualujjuaq may reveal separate bodies of traditional knowledge, or may reflect an overall loss of ethnobotanical knowledge in the Subarctic due to recent lifestyle changes.

scholarly journals Pareuzebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae, isolated from a tidal flat sediment

2020 ◽  
Author(s):  
Zhaobin Huang ◽  
Xiaomei Wei ◽  
Qiliang Lai ◽  
Shiyong Chen ◽  
Jianjun Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae , sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae . Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).

scholarly journals Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

2020 ◽  
Vol 70 (3) ◽  
pp. 1785-1792 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Phylogenomic Analyses ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

Acerihabitans arboris gen. nov., sp. nov., a new member of the family Pectobacteriaceae isolated from sap drawn from Acer pictum

2021 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Hanna Choe ◽  
Ji-Sun Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family Pectobacteriaceae and formed a distinct clade between members of the genera Sodalis and Biostraticola with gene support index of 89. The closest phylogenetic neighbours were Biostraticola tofi DSM 19580T (97.3% 16S rRNA gene sequence similarity) and Sodalis praecaptivus HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family Pectobacteriaceae , for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.

Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Yajun Ge ◽  
Bin Wang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Gui Zhang ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Major Fatty Acid ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family

Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051T and Pragia fontium DSM 5563T, while strain CF-1111T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273T and Pectobacterium punjabense SS95T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458T and CF-917) and group Ⅱ (CF-1111T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia . Summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c, 23.9 and 17.2 %, respectively), C16 : 0 (21.8 and 22.1 %, respectively) and C14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c, 12.3 %) was also a major fatty acid for strain CF-458T while cyclo-C17 : 0 (13.1%) was for strain CF-1111T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458T and CF-1111T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458T=CGMCC 1.16483T=GDMCC 1.1586T=JCM 33489T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111T=CGMCC 1.16786T=GDMCC 1.1587T=JCM 33490T), respectively.

scholarly journals Draft Genome Sequences of Itaconate-Producing Ustilaginaceae

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Elena Geiser ◽  
Florian Ludwig ◽  
Thiemo Zambanini ◽  
Nick Wierckx ◽  
Lars M. Blank
Keyword(s):  
Metabolic Engineering ◽  
Genome Sequencing ◽  
De Novo ◽  
Draft Genome ◽  
Essential Genes ◽  
Smut Fungi ◽  
Genome Sequences ◽  
The Family

Some smut fungi of the family Ustilaginaceae produce itaconate from glucose. De novo genome sequencing of nine itaconate-producing Ustilaginaceae revealed genome sizes between 19 and 25 Mbp. Comparison to the itaconate cluster of U. maydis MB215 revealed all essential genes for itaconate production contributing to metabolic engineering for improving itaconate production.

scholarly journals Physiological indexese macro- and micronutrients in plant tissue and essential oil of Mentha piperita L. grown in nutrient solution with variation in N, P, K and Mg levels

2014 ◽  
Vol 16 (1) ◽  
pp. 97-106 ◽  
Author(s):  
E.F.S. David ◽  
M.M. Mischan ◽  
M.O.M. Marques ◽  
C.S.F. Boaro
Keyword(s):  
Essential Oil ◽  
Nutrient Solution ◽  
Dry Mass ◽  
Oil Yield ◽  
Mentha Piperita ◽  
Medicinal Species ◽  
The Family ◽  
Physiological Indexes ◽  
Macro And Micronutrients ◽  
Essential Oil Yield

Mentha piperita L. is an aromatic and medicinal species of the family Lamiaceae, known as mint or peppermint, and its leaves and branches produce essential oil rich in menthol. This study aimed to evaluate physiological indexes, macro- and micronutrients inthe shootsand essential oil of Mentha piperita L. grown in nutrient solution number 2 of Hoagland and Arnon (1950) with different N, P, K and Mg levels. Shoot length, dry mass of the different organs, total dry mass, leaf area, essential oil yield and composition, and macronutrient (N, P, K, Mg, Ca, S) and micronutrient (Mn, Cu, Fe, Zn) contents in the shoot were evaluated. Plants treated with 65%N/50%P/25%K/100%Mg had a tendency towards longer shoot, greaterroot and leaf blade dry masses, higher essential oil yield, higher menthol levels and lower menthone levels. The results showed that Mentha can be grown in nutrient solution by reducing 65% N, 50% P, 25% K and 100% Mg. This solution had better development compared to the other tested treatments. Therefore,we recommendMentha piperita L. to be grown with such nutrient levels.

scholarly journals Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2637
Author(s):  
Jolien D’aes ◽  
Marie-Alice Fraiture ◽  
Bert Bogaerts ◽  
Sigrid C. J. De Keersmaecker ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetically Modified ◽  
Added Value ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

Sign in / Sign up

Export Citation Format

Share Document