Biology subjects

Gelfand, M. S.

Publications and source records attributed to Gelfand, M. S..

3 recordsLinked to original sources

bioRxiv2018

Comparative analysis of Streptococcus genomes

BackgroundGenome sequencing of multiple strains demonstrated high variability in gene content even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome, that is, the complete set of genes observed in a given species or a higher level taxon. Here we analysed the pan-genome structure and the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\n\nResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\n\nAbout 7% of single-copy periphery genes have been found in different syntenic regions. More than a half of these genes are rare in all Streptococcus species; others are rare in at least one species. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are candidates for horizontal transfer between species.\n\nAn inversion of length 15 kB found in four independent branches of S. pneumoniae has breakpoints formed by genes encoding a surface antigen protein (PhtD). The observed parallelism may indicate the action of an antigen variation mechanism.\n\nConclusionsMembers of the genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, understanding of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

genomics↗

bioRxiv2018

Far beyond common leeching: insights into an ancient medical device through integrated omics data

Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today. We annotated the Hirudo medicinalis genome and performed RNA-seq on salivary cells isolated from three closely related leech species, H. medicinalis, Hirudo orientalis, and Hirudo verbana. Differential expression analysis verified by proteomics identified salivary cell-specific genes, many of which encode previously unknown salivary components. However, the genes encoding known anticoagulants were not differentially expressed in the salivary cells. The function-related analysis of the unique salivary cell genes enabled an update of the concept of interactions between salivary proteins and components of haemostasis. Thus, our study provides one of the most comprehensive knowledge of the genetic fundamentals of the blood-sucking lifestyle in leeches.

systems biology↗

bioRxiv2018

Genome evolution in Burkholderia spp

BackgroundThe genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization.\n\nResultsWe performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\n\nConclusionsThis study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.

genomics↗