Abstract
Background and AimsLong terminal repeat-retrotransposons (LTR-RTs) comprise a large portion of plant genomes, with massive repeat blocks distributed across the chromosomes. Eleocharis species have holocentric chromosomes, and show a positive correlation between chromosome numbers and the amount of nuclear DNA. To evaluate the role of LTR-RTs in karyotype diversity in members of Eleocharis (subgenus Eleocharis), the occurrence and location of different members of the Copia and Gypsy superfamilies were compared, covering interspecific variations in ploidy levels (considering chromosome numbers), DNA C-values and chromosomal arrangements.MethodsThe DNA C-value was estimated by flow cytometry. Genomes of Eleocharis elegans and E. geniculata were partially sequenced using Illumina MiSeq assemblies, which were a source for searching for conserved proteins of LTR-RTs. POL domains were used for recognition, comparing families and for probe production, considering different families of Copia and Gypsy superfamilies. Probes were obtained by PCR and used in fluorescence in situ hybridization (FISH) against chromosomes of seven Eleocharis species.Key ResultsA positive correlation between ploidy levels and the amount of nuclear DNA was observed, but with significant variations between samples with the same ploidy levels, associated with repetitive DNA fractions. LTR-RTs were abundant in E. elegans and E. geniculata genomes, with a predominance of Copia Sirevirus and Gypsy Athila/Tat clades. FISH using LTR-RT probes exhibited scattered and clustered signals, but with differences in the chromosomal locations of Copia and Gypsy. The diversity in LTR-RT locations suggests that there is no typical chromosomal distribution pattern for retrotransposons in holocentric chromosomes, except the CRM family with signals distributed along chromatids.ConclusionsThese data indicate independent fates for each LTR-RT family, including accumulation between and within chromosomes and genomes. Differential activity and small changes in LTR-RTs suggest a secondary role in nuclear DNA variation, when compared with ploidy changes.
Highlights
The DNA C-value has been recognized as a relevant parameter for plant genome studies, especially in the context of genome evolution (Bennett and Leitch, 2011)
Since holocentric species seem to tolerate chromosome rearrangements, such as fission or fusion events (Luceño and Castroviejo, 1991; Da Silva et al, 2008), a combined analysis of chromosome counting and DNA content estimation is required to determine the relationship between chromosome number change and DNA content flexibility
Fluctuations in the amount of DNA are common during eukaryotic genome evolution, and they can be motivated by large- or small-scale rearrangements, such as polyploidy and dysploidy
Summary
The DNA C-value has been recognized as a relevant parameter for plant genome studies, especially in the context of genome evolution (Bennett and Leitch, 2011). Transposable elements are the most abundant repetitive sequences in plant genomes (SanMiguel et al, 1996; Jurka et al, 2007; Heslop-Harrison and Schwarzacher, 2011). Their proportion in dicotyledonous plants has been seen to vary from >10 % of the genome in arabidopsis to approx. 62 % of retroelements in the genome of Solanum lycopersicum (Arabidopsis Genome Initiative, 2000; Paz et al, 2017). In monocotyledonous plants, such as rice, sorghum and maize, TEs routinely range from 40 to 85 % of total DNA (Meyers et al, 2001; Matsumoto et al, 2005; Schnable et al, 2009; Devos, 2010). TEs that transpose using RNA intermediates by a ‘copy-and-paste’ process (Class 1) are commonly called by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
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