High diversity of fungi associated with living parts of boreal forest bryophytes

Bryophytes are a dominant and functionally important component of the forest floor vegetation in boreal forests, yet little is known about the fungal diversity associated with these abundant plants. Using molecular identification, we document an ecologically and phylogenetically diverse array of fungi associated with the living parts of three widespread and abundant boreal forest bryophytes, i.e., Hylocomium splendens (Hedw.) Schimp. in B.S.G., Pleurozium schreberi (Brid.) Mitt., and Polytrichum commune Hedw. From 376 cloned ITS sequences, 158 operational taxonomic units (OTUs), roughly corresponding to the number of species, were defined based on sequence similarity searches (Fasta) and phylogenetic analyses. A main portion (62.8%) of the OTUs belonged to Ascomycota, 32.0% to Basidiomycota, 3.9% to Chytridiomycota, and 1.3% to Glomeromycota. The most common orders were Helotiales (18.6%), Agaricales (11.5%), Chaetothyriales (9.6%), and Tremellales (9.0%). Frequently detected OTUs of potentially high ecologic importance included two with high sequence similarity (>99%) to the agaric Entoloma conferendum (Britzelm.) Noordel and the endophyte Lophodermium piceae (Fckl.) Hoehn., and various OTUs with affinity to the Helotian genus Hyphodiscus. Several ectomycorrhiza-forming basidiomycetes were also detected. Most OTUs (77.2%) were only detected once and a very small overlap in composition of OTUs was observed among the three bryophytes, indicating the occurrence of an immense fungal diversity associated with boreal forest bryophytes that deserves further study.

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Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus

Viruses ◽

10.3390/v12121373 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1373

Author(s):

Sang Guen Kim ◽

Sung Bin Lee ◽

Sib Sankar Giri ◽

Hyoun Joong Kim ◽

Sang Wha Kim ◽

...

Keyword(s):

Genome Size ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Gc Content ◽

Genomic Analysis ◽

Open Reading Frames ◽

Comparative Genomic ◽

Limited Information ◽

High Sequence Similarity ◽

A Genome

Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.

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Filimonas effusa sp. nov., isolated from a freshwater river

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.003875 ◽

2020 ◽

Vol 70 (3) ◽

pp. 1508-1515 ◽

Cited By ~ 4

Author(s):

Wen-Ming Chen ◽

Tzu-Ying Chen ◽

Zhi-Hao Li ◽

Soon-Wo Kwon ◽

Shih-Yi Sheu

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

High Sequence Similarity ◽

Content Type ◽

Link Type ◽

Freshwater River

Strain TTM-71T, isolated from a freshwater river in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-71T is affiliated with species in the genus Filimonas . The 16S rRNA gene sequence similarity indicated that strain TTM-71T is closely related to species within the genus Filimonas (94.7–95.5 % sequence similarity) and had a high sequence similarity with Filimonas endophytica SR 2-06T (95.5 %). Strain TTM-71T showed 70.3 % average nucleotide identity and 24.9 % digital DNA–DNA hybridization identity with Filimonas lacunae YT21T. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed beige-colored colonies. Optimal growth occurred at 20 °C, pH 8, and in the presence of 0.5 % NaCl. The major fatty acids of strain TTM-71T were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The predominant hydroxy fatty acid was iso-C17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized aminolipid, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamine was homospermidine. The only isoprenoid quinone was MK-7. Genomic DNA G+C content was 45.6 mol%. On the basis of the polyphasic evidence presented, strain TTM-71T is considered to represent a novel species of the genus Filimonas , for which the name Filimonas effusa sp. nov. is proposed. The type strain is TTM-71T (=BCRC 81160T=LMG 31017T=KCTC 62871T).

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Bacterial genome chimaerism and the origin of mitochondria

Canadian Journal of Microbiology ◽

10.1139/w10-099 ◽

2011 ◽

Vol 57 (1) ◽

pp. 49-61 ◽

Cited By ~ 23

Author(s):

Ankur Abhishek ◽

Anish Bavishi ◽

Ashay Bavishi ◽

Madhusudan Choudhary

Keyword(s):

Rhodospirillum Rubrum ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Bacterial Genome ◽

Sister Group ◽

Rickettsia Prowazekii ◽

Origin And Evolution ◽

The Family ◽

Related Proteins ◽

Similarity Searches

Many studies have sought to determine the origin and evolution of mitochondria. Although the Alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. Some have argued that mitochondria originated from ancestors of the order Rickettsiales, or more specifically of the Rickettsiaceae family, while others believe that ancestors of the family Rhodospirillaceae are also equally likely the progenitors. To resolve some of these disputes, sequence similarity searches and phylogenetic analyses were performed against mitochondria-related proteins in Saccharomyces cerevisiae . The 86 common matches of 5 Alphaproteobacteria ( Rickettsia prowazekii , Rhodospirillum rubrum , R hodopseudomonas palustris , Rhodobacter sphaeroides , and Ochrobactrum anthropi ) to yeast mitochondrial proteins were distributed fairly evenly among the 5 species when sorted by highest identity or score. Moreover, exploratory phylogenetic analyses revealed that among these common matches, 44.19% (38) had branched most closely with O. anthropi, while only 34.88% (30) corresponded with Rickettsia prowazekii. More detailed phylogenetic analyses with additional Alphaproteobacteria and including genes from the mitochondria of Reclinomonas americana found matches of mitochondrial genes to those of members of the Rickettsiaceae, Anaplasmataceae, and Rhodospirillaceae families. The results support the idea that notable bacterial genome chimaerism has occurred en route to the formation of mitochondria.

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Structural organization and evolution of the marsupial zona pellucida

Reproduction ◽

10.1530/rep.0.1230013 ◽

2002 ◽

pp. 13-21 ◽

Cited By ~ 13

Author(s):

WG Breed ◽

RM Hope ◽

OW Wiebkin ◽

SC Spargo ◽

JA Chapman

Keyword(s):

Zona Pellucida ◽

Structural Organization ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Three Dimensional ◽

Reducing Agents ◽

Molecular Organization ◽

Dimensional Structure ◽

High Sequence Similarity ◽

Lectin Staining

In this review, the biochemical composition and structural organization of the marsupial and eutherian zonae pellucidae are compared. Differences between the zonae from these two groups of mammals are observed in their response to dilute proteases and reducing agents, in their potential glycosylation patterns, and in some of their functions. However, studies on the glycoconjugates and polypeptides of the three zona pellucida genes have not explained these different responses to the proteases and reducing agents. There is high sequence similarity between the zona polypeptides of marsupials and eutherians, as well as a similarity in the oligosaccharides present, as demonstrated by lectin staining. As the marsupial and eutherian lineages diverged from a common ancestor over 100 million years ago, these observations indicate that the three-dimensional structure of these glycoproteins is highly conserved throughout all mammals, although the complexity of its molecular organization has yet to be resolved. Phylogenetic analyses indicate that there are at least four groups of paralogous zona pellucida genes in vertebrates. The marsupial ZPA and ZPB genes have been named in accordance with their orthologues but the phylogenetic relationships of the marsupial ZPC gene require further investigation.

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Phylogenetic analyses and genomic variation of the 2019-nCoV

Journal of Pharmaceutical and Biopharmaceutical Research ◽

10.25082/jpbr.2020.01.004 ◽

2020 ◽

Vol 2 (1) ◽

pp. 126-130

Author(s):

Faiz Ul Haq ◽

◽

Sidrah Saleem ◽

Muhammad Imran ◽

Ayesha Ghazal ◽

...

Keyword(s):

Phylogenetic Tree ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Genomic Variation ◽

Molecular Characteristics ◽

Phylogenetic Tree Analysis ◽

High Sequence Similarity ◽

Human Environment ◽

Bat Coronavirus

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

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Flavobacterium dongtanense sp. nov., isolated from the rhizosphere of a wetland reed

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.022301-0 ◽

2011 ◽

Vol 61 (2) ◽

pp. 343-346 ◽

Cited By ~ 18

Author(s):

Yi-Ping Xiao ◽

Wei Hui ◽

Jung-Sook Lee ◽

Keun Chul Lee ◽

Zhe-Xue Quan

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Distinct Group ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Phenotypic Characteristics ◽

High Sequence Similarity ◽

Respiratory Quinone ◽

Optimum Ph ◽

Major Respiratory Quinone

Two strains of Gram-reaction-negative, rod-shaped, non-spore-forming, non-motile, aerobic bacteria, designated LW30T and LW29, were isolated from the rhizosphere of a wetland reed in Dongtan, Chongming Island, China. The strains formed pale-yellow colonies on R2A plates. Growth occurred at 4–37 °C (optimum 30 °C), at pH 6–9 (optimum pH 7–8) and in the presence of 0–3 % (w/v) NaCl (optimum 0–1 %). Oxidase and catalase activities and flexirubin-type pigments were absent. MK-6 was the major respiratory quinone. The major fatty acids were iso-C15 : 0, C15 : 0, iso-C15 : 1 G and iso-C17 : 1 ω9c. Strains LW30T and LW29 could be differentiated from related species by several phenotypic characteristics. Phylogenetic analyses based on 16S rRNA gene sequences placed strains LW30T and LW29 in the genus Flavobacterium with high sequence similarity to Flavobacterium cheniae NJ-26T (94.0 %) and Flavobacterium indicium GPTSA 100-9T (93.9 %). Together with F. indicium GPTSA 100-9T, strains LW30T and LW29 formed a distinct group in the phylogenetic tree. The DNA G+C content was 30 mol%. On the basis of the phylogenetic and phenotypic evidence, strains LW30T and LW29 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium dongtanense sp. nov. is proposed. The type strain is LW30T (=KCTC 22671T =CCTCC AB 209201T).

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Halorubrum Salipaludis Sp. Nov., Isolated From the Saline–Alkaline Soil

10.21203/rs.3.rs-868089/v1 ◽

2021 ◽

Author(s):

Qi Gong ◽

Pu Zhao ◽

Shaohua Miao ◽

Keke Yi ◽

Chunhong Ma ◽

...

Keyword(s):

Dna Hybridization ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Wetland Soil ◽

Rrna Gene ◽

Alkaline Soil ◽

High Sequence Similarity ◽

Respiratory Quinone ◽

Genomic Analyses ◽

Major Respiratory Quinone

Abstract Strain WN019T, an aerobic, motile, and pleomorphic rods bacterium, was isolated from the natural saline-alkali wetland soil of Binhai new district, Tianjin, China. Cells of strain WN019T were 0.5-0.8 µm in width and 2.0-2.5 µm in length, and the growth occurred optimally at 33-37 ℃, pH 7.5-8.0, and in the presence of 15.0-20.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate belonged to the genus Halorubrum and exhibited high sequence similarity of 97.8 % to Halorubrum saccharovorum JCM 8865T. The major respiratory quinone of strain WN019T were MK-8 and MK-8 (H2), and the major polar lipids were Glycolipid (GL), Phospholipid (PL), Phosphatidylglycerol-Sulfate (PGS), Phosphatidylglycerol (PG) and Phosphatidylglycerol-Phosphate-Methyl Ester (Me-PGP). The DNA G+C content of the strain was 67.3 mol%. The average nucleotide identity (ANI) based on whole genome sequences of strain WN019T and Halorubrum saccharovorum JCM 8865T was 87.5 %, and the digital DNA-DNA hybridization (dDDH) value between them was determined to be 35.4 %. Phenotypic, chemotaxonomic, phylogenetic, and genomic analyses suggested that strain WN019T represent a novel species of the genus Halorubrum, for which the name Halorubrum salipaludis sp. nov. is proposed. The type strain is WN019T (= KCTC 4269T = ACCC 19977T).

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Mutator-like Elements in Arabidopsis thaliana: Structure, Diversity and Evolution

Genetics ◽

10.1093/genetics/156.4.2019 ◽

2000 ◽

Vol 156 (4) ◽

pp. 2019-2031 ◽

Cited By ~ 2

Author(s):

Zhihui Yu ◽

Stephen I Wright ◽

Thomas E Bureau

Keyword(s):

Arabidopsis Thaliana ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Structural Diversity ◽

Structural Features ◽

Sequence Motifs ◽

Sequence Alignments ◽

High Sequence Similarity ◽

Related Sequence ◽

Size Heterogeneity

Abstract While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.

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Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

Plant Methods ◽

10.1186/s13007-021-00712-x ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Mohamed Ramadan ◽

Muna Alariqi ◽

Yizan Ma ◽

Yanlong Li ◽

Zhenping Liu ◽

...

Keyword(s):

Genetic Transformation ◽

Sequence Similarity ◽

High Specificity ◽

Transformation Method ◽

High Sequence Similarity ◽

Single Experiment ◽

Next Generation Sequencing Technology ◽

Cotton Transformation ◽

Assembly Method ◽

Multiple Genes

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

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