The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass,Cenchrus ciliaris

Abstract

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found and we analysed here a 2n=4×+3=39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. About a third of Ty1-copia sites overlapped or spanned centromeric DAPI positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methycytosine signals, except some Ty3-gypsy on the arms of chromosomes which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. Probes developed from RepeatExplorer clusters gave strong signals mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris likely having different repeat sequence variants amplified before the genome came together in the tetraploid.

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

“…The allopolyploid condition enables intra-and inter-genomic reshuffling of chromosomal segments and genes through translocations, recombination, transposition or introgressions (Kenton et al, 1993;Levy and Feldman, 2002;Patokar et al, 2016;Martin et al, 2021;Tomaszewska and Kosina, 2021;Tomaszewska et al, 2022). This unique feature, especially widespread in grasses, increases genome plasticity and enables to create new genetic combinations and genome arrangements.…”

“…A certain advantage of the repetitive DNA probes over the whole genomic DNA probes used for in situ hybridization is observed (Tomaszewska et al, 2022). Despite the often perfect discrimination of genomes in allopolyploids/amphiploids using total genomic DNA isolated from a diploid species (Tomaszewska and Kosina, 2021), such probes are not applicable to distinguish closely related genomes such as those observed in Brassica (Alix et al, 2008), Triticum (Tang et al, 2018), Cenchrus and Urochloa tropical forage grasses (Rathore et al, 2022;Tomaszewska et al, 2022) or highly homologous A and D genomes in Avena (Linares et al, 1998).…”

“…A certain advantage of the repetitive DNA probes over the whole genomic DNA probes used for in situ hybridization is observed (Tomaszewska et al, 2022). Despite the often perfect discrimination of genomes in allopolyploids/amphiploids using total genomic DNA isolated from a diploid species (Tomaszewska and Kosina, 2021), such probes are not applicable to distinguish closely related genomes such as those observed in Brassica (Alix et al, 2008), Triticum (Tang et al, 2018), Cenchrus and Urochloa tropical forage grasses (Rathore et al, 2022;Tomaszewska et al, 2022) or highly homologous A and D genomes in Avena (Linares et al, 1998). The parental species of amphiploids studied here are meiotically compatible in the crossing process, exhibiting sometimes partial sterility (Loskutov, 2001), and these data together with established genome composition of hybrids and amphiploids contribute to a better understanding of the complex evolutionary processes within the genus Avena.…”

“…The combination of molecular cytogenetic and genomic or bioinformatic methods are promising to identify the processes occurring when genomes come together in polyploids (Heslop-Harrison and Schwarzacher, 2011;Tomaszewska et al, 2022). We can then address features of polyploidy that may be related to evolutionary adaptation (Barker et al, 2016) and test the hypotheses that chromosomal rearrangements, including intergenomic translocations, occur early in polyploid evolution.…”