Comparative analysis of the genomic diversity of SARS-COV-2 circulating in the territories of the Rostov region and the republic of Crimea in the period from March to June 2021

Objective: To compare the genomic diversity of SARS-CoV-2 strains that were spread in the Rostov region and the Republic of Crimea in the period from March to June 2021.Materials and Methods: A total of 194 samples were sequenced and 186 genovariants were recognized among them using the Pangolin program. Multiple alignment was performed and dendrograms were constructed for the samples belonging to the alpha and delta genovariants.Results: Changes of the predominant genovariants were revealed for territories of the Rostov Region and the Republic of Crimea from March to June. An increasing percent of the alpha variant was observed in both regions during the spring followed by the rapid emergence of the delta variant, which became predominant in June.Conclusion: It was shown that alpha variant samples from the Rostov region share a pool of common mutations, while in contrast, alpha variant samples from the Republic of Crimea are closer to those sampled from Moscow and Moscow region. At the end of May, the delta gene variant begins to be revealed, which is rapidly replacing other lines in all the territories considered in this study.

MARS: a tool for haplotype-resolved population-based structural variation detection

Motivation: Linked-reads enables genome-wide phased diploid assemblies. These haplotype-resolved assemblies allow us to genotype structural variants (SVs) with a high sensitivity and be able to further phase them. Yet, existing SV callers are designed for haploid genome assemblies only, and there is no tool to call SV from a large population of diploid assemblies which can define and refine SVs from a global view. Results: We introduce MARS (Multiple Alignment-based Refinement of Svs) in linked-reads for the detection of the most common SV types - indels from diploid genome assemblies of a large population. We evaluated SVs from MARS based on Mendelian law of inheritance and PacBio HiFi reads and it achieved a high validation rate around 73%-87% for indels that we have selected from 34 assembled samples.

TITANIA: Model Free Interpretation of Residual Dipolar Couplings in the context of Organic Compounds

The direct use of RDCs as restraint to construct structures based on RDCs is proposed for organic compounds. It uses the vector and dynamics information available in multi alignment data sets directly for the joint determination of conformation and configuration of organic compounds. We show that employing these data even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. <br>

TITANIA: Model Free Interpretation of Residual Dipolar Couplings in the context of Organic Compounds

The direct use of RDCs as restraint to construct structures based on RDCs is proposed for organic compounds. It uses the vector and dynamics information available in multi alignment data sets directly for the joint determination of conformation and configuration of organic compounds. We show that employing these data even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. <br>

Genome-wide identification of HSF family in peach and functional analysis of PpHSF5 involvement in root and aerial organ development

Background Heat shock factors (HSFs) play important roles during normal plant growth and development and when plants respond to diverse stressors. Although most studies have focused on the involvement of HSFs in the response to abiotic stresses, especially in model plants, there is little research on their participation in plant growth and development or on the HSF (PpHSF) gene family in peach (Prunus persica). Methods DBD (PF00447), the HSF characteristic domain, was used to search the peach genome and identify PpHSFs. Phylogenetic, multiple alignment and motif analyses were conducted using MEGA 6.0, ClustalW and MEME, respectively. The function of PpHSF5 was confirmed by overexpression of PpHSF5 into Arabidopsis. Results Eighteen PpHSF genes were identified within the peach genome. The PpHSF genes were nonuniformly distributed on the peach chromosomes. Seventeen of the PpHSFs (94.4%) contained one or two introns, except PpHSF18, which contained three introns. The in silico-translated PpHSFs were classified into three classes (PpHSFA, PpHSFB and PpHSFC) based on multiple alignment, motif analysis and phylogenetic comparison with HSFs from Arabidopsis thaliana and Oryza sativa. Dispersed gene duplication (DSD at 67%) mainly contributed to HSF gene family expansion in peach. Promoter analysis showed that the most common cis-elements were the MYB (abiotic stress response), ABRE (ABA-responsive) and MYC (dehydration-responsive) elements. Transcript profiling of 18 PpHSFs showed that the expression trend of PpHSF5 was consistent with shoot length changes in the cultivar ‘Zhongyoutao 14’. Further analysis of the PpHSF5 was conducted in 5-year-old peach trees, Nicotiana benthamiana and Arabidopsis thaliana, respectively. Tissue-specific expression analysis showed that PpHSF5 was expressed predominantly in young vegetative organs (leaf and apex). Subcellular localization revealed that PpHSF5 was located in the nucleus in N. benthamiana cells. Two transgenic Arabidopsis lines were obtained that overexpressed PpHSF5. The root length and the number of lateral roots in the transgenic seedlings were significantly less than in WT seedlings and after cultivation for three weeks. The transgenic rosettes were smaller than those of the WT at 2–3 weeks. The two transgenic lines exhibited a dwarf phenotype three weeks after transplanting, although there was no significant difference in the number of internodes. Moreover, the PpHSF5-OE lines exhibited enhanced thermotolerance. These results indicated that PpHSF5 might be act as a suppresser of growth and development of root and aerial organs.

The Potential of the SP System in Machine Learning and Data Analysis for Image Processing

This paper aims to describe how pattern recognition and scene analysis may with advantage be viewed from the perspective of the SP system (meaning the SP theory of intelligence and its realisation in the SP computer model (SPCM), both described in an appendix), and the strengths and potential of the system in those areas. In keeping with evidence for the importance of information compression (IC) in human learning, perception, and cognition, IC is central in the structure and workings of the SPCM. Most of that IC is achieved via the powerful concept of SP-multiple-alignment, which is largely responsible for the AI-related versatility of the system. With examples from the SPCM, the paper describes: how syntactic parsing and pattern recognition may be achieved, with corresponding potential for visual parsing and scene analysis; how those processes are robust in the face of errors in input data; how in keeping with what people do, the SP system can “see” things in its data that are not objectively present; the system can recognise things at multiple levels of abstraction and via part-whole hierarchies, and via an integration of the two; the system also has potential for the creation of a 3D construct from pictures of a 3D object from different viewpoints, and for the recognition of 3D entities.

Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome

In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS could operate on sequences with x = 4.4. We also used MAHDS to analyze a set of promoter sequences from the Arabidopsis thaliana genome and discovered many conserved regions upstream of the transcription initiation site (from −499 to +1 bp); a part of the downstream region (from +1 to +70 bp) also significantly contributed to the obtained alignments. The possibilities of applying the newly developed method for the identification of promoter sequences in any genome are discussed. A server for multiple alignment of nucleotide sequences has been created.

Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

We tested the functionality of ITS-based DNA barcoding in lichen fungi using Colombian samples of the genus Usnea as an example. New ITS sequences were generated for 15 samples from five localities in two different ecoregions, representing varying morphologies and medullary chemistries. We employed five strategies to identify the samples: (1) BLASTn on the NCBI BLAST site with the original identifications of the best matching reference sequences; (2) as previous, but with revised identifications of the reference sequences based on a separately published revision of ITS sequences published for the genus; (3) local BLASTn in BioEdit using a separately published, revised and curated set of ITS reference sequences for the genus; (4) multiple alignment based phylogenetic analysis within the framework of all available ITS sequences for Usnea s.str.; and (5) integrative taxonomy, combining molecular phylogeny and comparative analysis of phenotype and chemical data. Using the latter approach as reference, we found that NCBI BLASTn with original identifications performed poorly, resulting in an identification success rate of only 7% (a single sample). NCBI BLASTn with revised identifications more than tripled identification success (23%), but was still unsatisfactory. Local BLASTn in BioEdit using the revised, curated reference data further doubled identification success (47%), but remained inadequate. Multiple alignment-based phylogenetic analysis achieved an identification success rate of 80% compared to the result from integrative taxonomy. Based on these results, we conclude that ITS-based DNA barcoding of the genus Usnea under the current circumstances performs poorly, but can be substantially improved using three strategies: (1) update identifications of reference sequences in primary repositories such as GenBank or alternatively use a curated reference data set; (2) perform local BLAST with a curated reference data set focusing on the target genus only, combined with multiple alignment-based phylogenetic analysis as a verification step; and (3) close substantial geographic and taxonomic gaps in the existing reference data. Our analyses suggest that if a near-complete reference data set with correct identifications existed for the genus, then standard BLAST approaches could achieve high levels of identification success close to 100%. As part of our DNA barcoding exercise, which generated the first 15 ITS sequences for Colombian samples of the genus Usnea, we confirm the presence of U. aranea and U. wasmuthii in Colombia and we report for the first time U. tenuicorticata for the country.