Background Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria , the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time. Results Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica , A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes. Conclusions Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara . We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.

Bioluminescent solid‐phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer–target complexes during design and development of the specific aptamers. The assay involves Ca2+‐regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.

The paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (Larix sibirica Ledeb.) transcriptome sequences was investigated in the presented study. It was found that the larch transcriptome demonstrates a number of unexpected symmetries in the statistical and combinatorial properties.Keywords: nucleotide sequence complexity, frequency dictionary, order, Larix sibirica, Siberian larch, symmetry, transcriptome, triplet. DOI: 10.17516/1997-1389-2015 . For our further analysis we also assumed that neither other symbols, nor blan spaces are supposed to be found in a sequence; a sequence under consideration is also suppose to be coherent (i. e. consisting of a single piece).. For our further analysis we also assumed that neither other symbols, nor blank spaces are supposed to be found in a sequence; a sequence under consideration is also supposed to be coherent (i. e. consisting of a single piece).We studied an order and structuredness over a set of sequences from finite alphabet Key idea in our search for a structure and order in a set of symbol sequences (transcriptome nucleotide sequences) is to translate sequences into their frequency dictionary (Bugaenko et al., 1996(Bugaenko et al., , 1997(Bugaenko et al., , 1998Hu and Wang, 2001). There could be a number of various definitions of a frequency dictionary, but we will use the basic one that is a list of all the strings of a given length accompanied with a frequency of each string (a detailed description is given below). It is crucial that the transformation of a symbol sequence into a frequency dictionary allows us to map a set of sequences into a metric space. The latter provided us with powerful and extended tools for analysis.We will briefly outline the concept of our study and then demonstrate the main results obtained. First, we changed each symbol sequence (that is a nucleotide sequence in the Siberian larch transcriptome set) into a frequency dictionary. Then, we studied distribution of those dictionaries in a multidimensional space trying to infer any regularities and clusters.Second, for each clustering we checked for stability of clustering. This clustering was carried out using the K-means technique.Third, we compared the statistical properties of the clusters identified by K-means and found that these clusters demonstrated a very strong symmetry in terms of the statistical properties.In brief, the clusters showed extremely low level of discrepancy in the Chargaff's second parity rule. This low discrepancy is the most intriguing fact concerning the properties of the studied transcriptome sequence set. Materials and Methods Transcriptome nucleotide sequence dataThe transcriptome Surely, this part of the transcriptome requires special studies. Frequency DictionaryPreviously (Bugaenko et al., 1996(Bugaenko et al., , 1997(Bugaenko et al., , 1998Hu and Wang, 2001), a frequency dictionary was proposed to be a fun...

No abstract