The biosynthetic gene cluster of porothramycin, a sequence-selective DNA alkylating compound, was identified in the genome of producing strain Streptomyces albus subsp. albus (ATCC 39897) and sequentially characterized. A 39.7 kb long DNA region contains 27 putative genes, 18 of them revealing high similarity with homologous genes from biosynthetic gene cluster of closely related pyrrolobenzodiazepine (PBD) compound anthramycin. However, considering the structures of both compounds, the number of differences in the gene composition of compared biosynthetic gene clusters was unexpectedly high, indicating participation of alternative enzymes in biosynthesis of both porothramycin precursors, anthranilate, and branched L-proline derivative. Based on the sequence analysis of putative NRPS modules Por20 and Por21, we suppose that in porothramycin biosynthesis, the methylation of anthranilate unit occurs prior to the condensation reaction, while modifications of branched proline derivative, oxidation, and dimethylation of the side chain occur on already condensed PBD core. Corresponding two specific methyltransferase encoding genes por26 and por25 were identified in the porothramycin gene cluster. Surprisingly, also methyltransferase gene por18 homologous to orf19 from anthramycin biosynthesis was detected in porothramycin gene cluster even though the appropriate biosynthetic step is missing, as suggested by ultra high-performance liquid chromatography-diode array detection-mass spectrometry (UHPLC-DAD-MS) analysis of the product in the S. albus culture broth.

• MeSH
• anthramycin analogy a deriváty   biosyntéza   chemie   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• molekulární struktura MeSH
• multigenová rodina * MeSH
• sekvenční analýza MeSH
• Streptomyces chemie   genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• anthramycin MeSH
• bakteriální proteiny MeSH
• porothramycin A MeSH Prohlížeč

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more vrn-A1 copies.

• Klíčová slova
• CNV, VRN1, allelic variation, alternative splice variants, next generation sequencing, wheat,
• MeSH
• alely * MeSH
• alternativní sestřih MeSH
• chléb MeSH
• genetická variace * MeSH
• genová dávka * MeSH
• inzerční mutageneze MeSH
• polyploidie * MeSH
• pšenice genetika   MeSH
• represorové proteiny genetika   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• represorové proteiny MeSH

RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for script execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz .

• MeSH
• DNA sondy chemie   genetika   MeSH
• DNA chemie   genetika   MeSH
• genomika metody   MeSH
• lidé MeSH
• repetitivní sekvence nukleových kyselin MeSH
• sekvenční analýza DNA metody   MeSH
• shluková analýza MeSH
• software MeSH
• transpozibilní elementy DNA MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA sondy MeSH
• DNA MeSH
• transpozibilní elementy DNA MeSH

Bacillus thuringiensis (Bt) is efficient, strongly specific, and avirulent to humans, making it one of the most popular biopesticides in the world. Bt LLP29 is a mosquitocidal strain that was first isolated from Magnolia denudata. To understand its molecular mechanism against mosquitoes, the genome of Bt LLP29 was sequenced and annotated in this study. The LLP29 genome was found to have a total length of 5.99 Mb, with an average G + C content of 35.21%. A total of 6107 coding sequences were also detected, together with 42 rRNAs and 124 tRNAs and 135 other RNAs. With the help of annotation databases, including GO, COG, KEGG, Nr and Swiss-Prot, most unigene functions were identified. At the same time, a collinear analysis was performed on the genome of LLP29. There were also some virulence genes detected, including cry, chitinase, zwittermicin and vip.

• Klíčová slova
• Bacillus thuringiensis, Genome sequencing, LLP29, Mosquito, Toxicity,
• MeSH
• anotace sekvence MeSH
• Bacillus thuringiensis genetika   MeSH
• bakteriální proteiny genetika   MeSH
• faktory virulence genetika   MeSH
• genom bakteriální genetika   MeSH
• sekvenční analýza MeSH
• sekvenování celého genomu * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• faktory virulence MeSH

The entire nucleotide sequence for the coding regions of a Danish PMTV isolate 54-15 was determined and compared to other known and sequenced isolates of PMTV. Many nucleotide and amino acid changes were found in parts of RNA coding for the triple gene block (TGB) proteins and in the part of the RNA coding for the read-through region of the coat protein (CP). These regions for two other isolates, the mild one 54-10 and the severe one 54-19, were sequenced. Only two amino acid changes were found to correlate with the subdivision of isolates according to symptom development into mild and severe subgroups. In addition, the phylogenetic tree was obtained suggesting the closest relationship between isolates 54-15 and 54-10. Although the sequence comparisons indicate a high genetic stability of PMTV populations, a surprising change was found in the newly sequenced isolates--the replacement of the AUG start codon of the fourth gene of the TGB encoding RNA, coding for a cystein-rich protein, by the less efficient GUG start codon.

• MeSH
• fylogeneze MeSH
• genom virový MeSH
• molekulární sekvence - údaje MeSH
• nemoci rostlin virologie   MeSH
• RNA-viry genetika   izolace a purifikace   MeSH
• rostlinné viry genetika   izolace a purifikace   MeSH
• sekvenční analýza DNA * MeSH
• Solanum tuberosum virologie   MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Geografické názvy
• Dánsko MeSH

The aim of the present study was to characterize bacteria of the genus Streptococcus isolated from the oral cavity of the guinea pig as well as to assess the significance of these microorganisms as potential veterinary and human pathogens. Sixty-two streptococcal isolates recovered from 27 clinically healthy guinea pigs were examined genotypically by sequencing the 16S rRNA and groEL genes. Among these isolates, only 13 could be assigned to a species described previously (mainly Streptococcus parasanguinis, S. mitis and S. suis), and the majority of the remaining ones differed considerably from the streptococcal species known to date (16S rRNA and groEL sequence similarities were < 97% and < 87%, respectively). Based on 16S rRNA sequences, these unidentified isolates were divided into seven groups (clades), of which clades I through III comprised most of the isolates examined and had also the widest distribution among guinea pig colonies. Upon groEL gene sequence analysis, however, members of the three clades grouped together without forming such distinct clusters. The remaining clades distinguished by 16S rRNA sequencing could also be discerned by the second gene, and they contained only a few isolates often restricted to one or a few animal colonies. The present work reveals that the guinea pig mouth is inhabited by a vast number of phylogenetically diverse, so far unrecognized populations of streptococci, most of them being apparently host-specific genomospecies. On the contrary, S. parasanguinis and S. mitis are also common human commensals and S. suis is a well-recognized zoonotic pathogen.

• MeSH
• fylogeneze MeSH
• genetická variace * MeSH
• morčata MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• sekvenční analýza MeSH
• Streptococcus * genetika   MeSH
• zvířata MeSH
• Check Tag
• morčata MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.

• Klíčová slova
• CenH3, Cereba, ChIP-seq, PacBio HiFi reads, flow cytometry, nanopore, ribosomal DNA, satellite, telomeric repeats,
• MeSH
• chromozomy rostlin genetika   MeSH
• genom rostlinný genetika   MeSH
• ječmen (rod) * genetika   MeSH
• ribozomální DNA genetika   MeSH
• sekvenční analýza DNA MeSH
• telomery genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ribozomální DNA MeSH

Hantavirus carried by the European common vole Microtus arvalis from Moravia (Czech Republic) was analyzed by RT-PCR-sequencing and by reactivity with a panel of monoclonal antibodies (MAbs). Sequencing of the full-length S segment and the proximal part of the M segment showed that the virus belonged to genotype Tula (TUL) we discovered earlier in Microtus arvalis from Central Russia. This finding supported the concept of host dependence of hantaviruses. Phylogenetic analyses suggested a similar evolutionary history for S and M genes of TUL strains; thus far there is no evidence for reassortment in TUL. Geographic clustering of TUL genetic variants was observed and different levels of the genetic variability were revealed resembling those estimated for another hantavirus, Puumala (PUU). Comparison of the deduced N protein sequence from Russia and from Moravia showed that genetic drift in TUL occurred not only by accumulation of point mutations but also by the deletion of a nucleotide triplet. It encoded Ser252 which was located within a highly variable hydrophilic part of the N protein carrying B-cell epitopes and presumably forming a loop. Analysis of naturally expressed TUL N-antigen derived from lung tissue of infected voles with MAbs indicated antigenic heterogeneity among TUL strains.

• MeSH
• antigeny virové imunologie   MeSH
• Arvicolinae virologie   MeSH
• DNA virů MeSH
• fylogeneze MeSH
• genetická variace MeSH
• Hantavirus klasifikace   genetika   imunologie   MeSH
• králíci MeSH
• molekulární sekvence - údaje MeSH
• monoklonální protilátky imunologie   MeSH
• nukleokapsida imunologie   MeSH
• protilátky virové imunologie   MeSH
• RNA virová * MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza MeSH
• virové proteiny MeSH
• zvířata MeSH
• Check Tag
• králíci MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• antigeny virové MeSH
• DNA virů MeSH
• monoklonální protilátky MeSH
• protilátky virové MeSH
• RNA virová * MeSH
• virové proteiny MeSH

The nucleotide sequence was determined for Czech potato mop-top virus (PMTV) isolate Korneta-Nemilkov, found in the potato field situated in South Bohemia. The nucleotide and amino acid sequences were compared with other PMTV isolates available in databases. The sequence identity was always >99% when Czech isolate RNA 2 and RNA 3 sequences were compared with each of the 3 Danish isolates and with Sw isolate, and slightly lower when compared to Scottish isolates. Similarity of deduced proteins was 100% for 5 out of 6 proteins used in comparison of Czech isolate with Danish isolate 54-15. The only difference between 2 isolates was found in coat protein (CP) gene. Interestingly, the CP of the Czech isolate seems to be 100% identical to the one of Sw, while many changes were found in the region encoding TGBp2, TGBp3 and cysteine-rich protein (CRP) for these 2 isolates. The lowest similarity scores were found when comparing the Czech isolate CRP with CRP of Scottish isolates.

• MeSH
• molekulární sekvence - údaje MeSH
• nemoci rostlin virologie   MeSH
• RNA-viry klasifikace   genetika   izolace a purifikace   MeSH
• rostlinné viry klasifikace   genetika   izolace a purifikace   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA * MeSH
• Solanum tuberosum virologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

MOTIVATION: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. RESULTS: k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats.

• MeSH
• centromera genetika   MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• molekulární sekvence - údaje MeSH
• rýže (rod) genetika   MeSH
• satelitní DNA genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• DNA rostlinná MeSH
• satelitní DNA MeSH