Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

The information capacity of nucleotide sequences is defined through the specific entropy of frequency dictionary of a sequence determined with respect to another one containing the most probable continuations of shorter strings. This measure distinguishes a sequence both from a random one, and from ordered entity. A comparison of sequences based on their information capacity is studied. An order within the genetic entities is found at the length scale ranged from 3 to 8. Some other applications of the developed methodology to genetics, bioinformatics, and molecular biology are discussed.

Information capacity of nucleotide sequences measures the unexpectedness of a continuation of a given string of nucleotides, thus having a sound relation to a variety of biological issues. A continuation is defined in a way maximizing the entropy of the ensemble of such continuations. The capacity is defined as a mutual entropy of real frequency dictionary of a sequence with respect to the one bearing the most expected continuations; it does not depend on the length of strings contained in a dictionary. Various genomes exhibit a multi-minima pattern of the dependence of information capacity on the string length, thus reflecting an order within a sequence. The strings with significant deviation of an expected frequency from the real one are the words of increased information value. Such words exhibit a non-random distribution alongside a sequence, thus making it possible to retrieve the correlation between a structure, and a function encoded within a sequence.

Chloroplast genomes have eight-cluster structuredness, in triplet frequency space. Small fragments of a genome converted into a triplet frequency dictionaries are the elements to be clustered. Typical structure consists of eight clusters: six of them correspond to three different positions of a reading frame shifted for 0, 1 and 2 nucleotides (in two opposing strands), the seventh cluster corresponds to a junk regions of a genome, and the eighth cluster is comprised by the fragments with excessive GC-content bearing specific RNA genes. The structure exhibits a specific symmetry.

No abstract

The information capacity of sequences is considered through the calculation of specific entropy of their frequency dictionary. The specific entropy was calculated against the reconstructed dictionary which bears the most probable continuations of shorter strings. The measure developed allows to distinguish the sequences both from the random ones, and those with high level of (rather simple) order. Some applications of the developed methodology to genetics, bioinformatics, and linguistics are discussed.

No abstract

Anisotropy is assumed to be the difference of a plane object observed in different dimensions. For digital images, anisotropy is determined in two ways. The first one is based on the comparison of mosaics bearing rectangular smalts developed in different (perpendicular, to be exact) directions. The comparison is provided through an intermediate mosaic called palette, that is the mosaic with the frequency of smalts equal to arithmetic mean of the frequency of smalts of compared mosaics. The latter is based on the calculation of the information capacity of the mosaics developed in different directions. The information capacity is the specific entropy of real mosaic calculated against the reconstructed one bearing the most probable expansions of smaller smalts. The problem of test object is discussed.