Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

Abstract

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.

Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only few fast-evolving satellite DNAs

“…As with EulaSat4, an explanation for the short arrays may be an association with transposable elements. We have observed partially mixed RepeatExplorer clusters that may point towards an embedment within retrotransposons, also often observed for short satDNA arrays (Meštrović et al, 2015; Satović et al, 2016; Belyayev et al, 2020; Sultana et al, 2020). Similarly, concatenated TEs or part from TEs may have satDNA-like properties, but tend to occur dispersedly along chromosomes (Maiwald et al, 2020; Vondrak et al, 2020).…”

“…We have observed partially mixed RepeatExplorer clusters that may point towards an embedment within retrotransposons, also often observed for short satDNA arrays (Meštrović et al, 2015;Satović et al, 2016;Belyayev et al, 2020;Sultana et al, 2020).…”

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

“…As with EulaSat4, an explanation for the short arrays may be an association with transposable elements. We have observed partially mixed RepeatExplorer clusters that may point toward an embedment within retrotransposons and also often observed for short satDNA arrays ( Meštrović et al, 2015 ; Satović et al, 2016 ; Belyayev et al, 2020 ; Sultana et al, 2020 ). Similarly, concatenated TEs or part from TEs may have satDNA-like properties, but tend to occur dispersedly along chromosomes ( Vondrak et al, 2020 ; Maiwald et al, 2021 ).…”

The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”

“…Scanning was performed with the “search for motifs” command of the GP program, with a maximum of zero nucleotide mismatches. There could be a multitude of dispersed repeats in the genome [ 24 ], but they are of low copy numbers and can be considered genetic noise in most cases. Therefore, the existence of arrays for a specific satDNA was crucial for the conformation of the presence of that satDNA family in the genome of a single species.…”