Characterization of repeated DNA sequences in genomes of blue-flowered flax

Abstract

Background Members 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. Results It 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. Conclusions The 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. Electronic supplementary material The online version of this article (10.1186/s12862-019-1375-6) contains supplementary material, which is available to authorized users.

Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae)

“…A substantial fraction of nuclear plant genomes is composed of repeated DNA. These highly abundant genomic elements are influencing the function and evolution of plant genomes (e.g., Macas et al, 2011 ; Garrido-Ramos, 2015 , 2017 ), and their diversity and abundance patterns can reflect phylogenetic distances ( Dodsworth et al, 2014 , 2017 ; Bolsheva et al, 2019 ; Vitales et al, 2020 ). Here, we sequenced and analyzed repetitive elements of 15 Heliophila species proportionally representing four major infrageneric clades.…”

“…If assuming that repeat abundances are evolving through random genetic drift (Jurka et al, 2011), the abundances can be analyzed as continuous characters for phylogeny inference (Dodsworth et al, 2014). When using a genome proportion of 0.1% or higher, this method proved to be highly congruent with phylogenies inferred using other nuclear or plastome markers (Dodsworth et al, 2014(Dodsworth et al, , 2017Bolsheva et al, 2019). Recently, Vitales et al (2020) reported a novel approach of phylogenetic inference using repeats as markers.…”

Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids

“…Furthermore, satDNA together with the flanking regions of these sequences are considered to function as “hotspots” for structural chromosomal rearrangements, contributing to the generation of key variations in the genomes of closely and distantly related species [ 64 ]. It is known that satDNA families are often retained in related species during long evolutionary periods [ 65 , 66 ]. Although we expected to identify and validate new species/specific markers, all markers identified by the present study were detected in both species.…”

Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms

“…A high-quality genome can be used as a reference for genome and transcriptome assemblies of different flax cultivars/lines, and the identification of polymorphisms and differences in gene expression within L. usitatissimum genotypes (Dmitriev et al, 2019 , 2020b ; Guo et al, 2019 ; Wu et al, 2019 ). Genome sequences of flax are necessary for the identification of particular gene families or repeat classes in species of the genus Linum and cultivars/lines of L. usitatissimum (Bolsheva et al, 2019 ; Novakovskiy et al, 2019 ; Ali et al, 2020 ; Dmitriev et al, 2020a ).…”