Brevilactibacter Soli Sp. Nov., a Novel Member of the Genus Brevilactibacter Isolated from Soil in China

A Gram-stain-positive, cocci-shaped, facultatively anaerobic, non-motile bacterial strain, designated YIM S02567T, was isolated from a forest soil sample collected from Gejiu City, Yunnan Province, south-west PR China. Growth was observed at 10–45°C, at pH 6.0-9.5, in the presence of up to 4.0 % (w/v) NaCl on R2A medium. Through the results of 16S rRNA gene sequence similarity analysis showed that strain YIM S02567T was most closely related to the type strain of Brevilactibacter sinopodophylli (95.38 %) and Propioniciclava tarda (94.67%), phylogenetic analysis based on genome data showed that strain YIM S02567T should be assigned to the genus Brevilactibacter. The cell-wall diamino acid was meso-diaminopimelic acid. The major cellular fatty acids were identified as anteiso-C15:0 and C16:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and two unidentified glycolipids. The predominant menaquinone was MK-9(H4). The genomic DNA G + C content was 71.20 mol%. Based on the polyphasic taxonomic evidence, strain YIM S02567T is assigned to a novel member of the genus Brevilactibacter, for which the name Brevilactibacter soli sp. nov., (type strain YIM S02567T = CCTCC AB 2020128T = CGMCC 1.18504T = KCTC 49478T) is proposed.

Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.

Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework

As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm; some computing errors may occur. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. A star alignment algorithm is designed and generated to demonstrate the development process.

Genetic Similarity Analysis Based on Positive and Negative Sequence Patterns of DNA

Similarity analysis of DNA sequences can clarify the homology between sequences and predict the structure of, and relationship between, them. At the same time, the frequent patterns of biological sequences explain not only the genetic characteristics of the organism, but they also serve as relevant markers for certain events of biological sequences. However, most of the aforementioned biological sequence similarity analysis methods are targeted at the entire sequential pattern, which ignores the missing gene fragment that may induce potential disease. The similarity analysis of such sequences containing a missing gene item is a blank. Consequently, some sequences with missing bases are ignored or not effectively analyzed. Thus, this paper presents a new method for DNA sequence similarity analysis. Using this method, we first mined not only positive sequential patterns, but also sequential patterns that were missing some of the base terms (collectively referred to as negative sequential patterns). Subsequently, we used these frequent patterns for similarity analysis on a two-dimensional plane. Several experiments were conducted in order to verify the effectiveness of this algorithm. The experimental results demonstrated that the algorithm can obtain various results through the selection of frequent sequential patterns and that accuracy and time efficiency was improved.

Fungus-originated genes in the genomes of cereal and pasture grasses acquired through ancient lateral transfer

Evidence for ancestral gene transfer between Epichloë fungal endophyte ancestors and their host grass species is described. From genomes of cool-season grasses (the Poeae tribe), two Epichloë-originated genes were identified through DNA sequence similarity analysis. The two genes showed 96% and 85% DNA sequence identities between the corresponding Epichloë genes. One of the genes was specific to the Loliinae sub-tribe. The other gene was more widely conserved in the Poeae and Triticeae tribes, including wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). The genes were independently transferred during the last 39 million years. The transferred genes were expressed in plant tissues, presumably retaining molecular functions. Multiple gene transfer events between the specific plant and fungal lineages are unique. A range of cereal crops is included in the Poeae and Triticeae tribes, and the Loliinae sub-tribe is consisted of economically important pasture and forage crops. Identification and characterisation of the 'natural' adaptation transgenes in the genomes of cereals, and pasture and forage grasses, that worldwide underpin the production of major foods, such as bread, meat, and milk, may change the ‘unnatural’ perception status of transgenic and gene-edited plants.

Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave

A Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain 5.0403-2T, was isolated from a cave soil sample collected from Tiandong Cave, Guizhou Province, south-west PR China. Cells showed positive oxidase and catalase reactions. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3OH and summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl). The cellular polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, three unidentified phosphoglycolipids and four unidentified lipids. The genomic DNA G+C content was 36.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5.0403-2T should be assigned to the genus Sphingobacterium . Results of 16S rRNA gene sequence similarity analysis showed that strain 5.0403-2T was most similar to Sphingobacterium bovisgrunnientis KCTC 52685T (98.7 %), Sphingobacterium composti KCTC 12578T (98.0 %) and Sphingobacterium alimentarium DSM 22362T (97.3 %) and less than 95.0 % similar to other species of the genus Sphingobacterium . The average nucleotide identity values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 94.2, 82.3 and 77.2 % respectively. The digitalDNA–DNA hybridization values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 68.4, 25.6 and 20.7 %. These results indicated that the isolate represented a novel genomic species. The polyphasic taxonomic characteristics indicated that strain 5.0304-2T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium cavernae sp. nov. (type strain 5.0403–2T=KCTC 62981T=CCTCC AB 2019257T) is proposed.