Impact of Retroelements in Shaping the Petunia Genome

The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes

“…Our analysis of repetitive elements from genomes of four Petunia species (P. axillaris, P. inflata, P. hybrida, and P. parodii) identified seven tandem repeat or satellite families (PSAT1, PSAT3, PSAT4, PSAT5, PSAT6, PSAT7, and PSAT8) not found in the Solanaceae crown group genera (Nicotiana, Solanum, and Capsicum) and showed their abundance and diversity using complementary tools (graph-based repeat clustering using unassembled raw reads, k-mer analysis, read mapping, sequence assemblies, in situ hybridization, and chromosome studies). In total, all repetitive elements represented 64%-68% of the Petunia genomes, consistent with the measurements reported by Bombarely et al (2016) in P. axillaris N and P. inflata S6, and was composed of abundant DNA transposons, LTR retroelements, and retrotransposons including pararetroviruses, as seen in other Solanaceae species (Hansen and Heslop-Harrison, 2004;Staginnus and Richert-Pöggeler, 2006;Staginnus et al, 2007;Richert-Pöggeler and Schwarzacher, 2009). A very low proportion of the genome, approximately 0.8% (10 Mb of the c. 1,400 Mb genomes, excluding the rDNA and short tandem repeats or simple sequence repeats), was represented by a limited number of tandemly repeated (satellite DNA) families, each less than 0.3% of the genome (Table 1).…”

“…They undergo frequent hybridization and backcrossing events as evidenced by P. hybrida in nature and breeding programs, allowing frequent exchange of sequences. Not surprisingly, we found no species-specific retroelements (Richert-Pöggeler and Schwarzacher, 2009) and no species-specific satellite repeats or variants and limited variation in their abundance or chromosomal distribution (this study), unlike the sister genus Nicotiana (Gazdováet al, 1995;Lim et al, 2006) or Solanum (Tang et al, 2014;Gaiero et al, 2019). There seems to be a variable relationship between repetitive DNA, dispersed and tandemly repeated satellite DNAs, and genome size as different rates of evolution and strong phylogenetic signal of major repeat sequences, and up and down genome sizing can occur in diploid species (McCann et al, 2020;Chase et al, 2023).…”

“…In contrast, many other plant species have conspicuous bands, considered heterochromatin and rich in satellite repeats, at centromeric, sub-telomeric, or intercalary positions on chromosomes (e.g., Contento et al, 2005;Hemleben et al, 2007;Moscone et al, 2007;Mlinarec et al, 2019;de Souza et al, 2022). In Petunia, as in many other species (Heslop-Harrison and Schwarzacher, 2011), the peri-centromeric regions are characterized by retroelement-related sequences (Richert-Pöggeler and Schwarzacher, 2009;Bombarely et al, 2016). In our analysis, we found no satellite repeat that was prominent at all centromeres or contained centromere-like motifs that would indicate CenH3 binding sites typical for centromere-specific tandem repeats (Heslop-Harrison et al, 1999;Gong et al, 2012;Kirov et al, 2018;Pesǩa et al, 2019).…”

“…In Petunia, DNA transposable elements have been studied, but little is known about other repeats (Shepherd et al, 1990;Richert-Pöggeler and Schwarzacher, 2009). In the P. axillaris and P. inflata assemblies (Bombarely et al, 2016), approximately 60% of the genome was repeats, with a relatively high proportion of DNA transposons and unassigned low copy sequences.…”