Abstract
BackgroundMembers of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method.ResultsIt was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes.ConclusionsThe evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.
Highlights
Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes
General characteristics of genomes The analysis of genome size and repeatomes showed that species from different sections differed significantly in genome size and repeatome composition (Table 2)
Stellerolinum, diploid species L. stelleroides, had the largest genome (1C = 1376 M bp), 39.47% of which was represented by mobile elements, and only 0.55% of satellite DNA
Summary
Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Even though the study of repetitive sequences is essential for understanding the principles of functional regulation and evolution of genomes, until recently information on the structure, organization and abundance of repetitive sequences in genomes was very fragmentary. This situation was mainly related to the technical difficulties of studying the repetitive elements in genomes [15]. A set of software tools called “Repeat Explorer”, which allows identifying repetitive sequences using raw WGS reads [16, 17], was developed Based on this approach, the repeatomes of many plant species have already been successfully investigated [18,19,20,21,22,23,24,25,26,27]
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