Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives

Abstract

The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution.

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome

“…In the chicken karyotype, several centromere-specific types of satDNA are highly similar to retrotransposons [ 127 ]. In the centromeres of Prunus species, a highly conserved monomer unit of 166 bps has been identified from assembled genomes and sequencing reads, with varying signal intensities in fluorescence in situ hybridization (FISH) experiments, which indicates that the centromeric regions of this genus are enriched with this sequence [ 128 ].…”

Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH

“…Repetitive DNA sequences, as a vital source of FISH probes, have been broadly applied in many plants [ 14 ], especially for peanut [ 17 , 58 ] and wheat [ 59 , 60 ]. However, the three probes that we identified previously could not be used for chromosome identification due to their locations at the terminus of chromosomes, which was due to the lower content or variety of tandem repeat sequences in their genomes [ 61 ]. Therefore, we used a combination of genomic data and oligo pool synthesis techniques to design a chromosome-specific single-copy oligonucleotide pool that could be used to accurately identify chromosomes.…”

“…Three oligo probes were designed from species-specific satellite sequences (monomer lengths 102 bp, 149 bp, and 159 bp) that we identified previously ( Supplementary Figure S9, Supplementary Table S2 ) [ 61 ]. Additionally, the highly conserved 45S rDNA sequences were assembled in this study, and 5S rDNA sequences obtained from the 5S rDNA database ( , accessed on 3 October 2021) were also used to design probes with their highly conserved regions using FISH.…”

A review of plant epigenetics through the lens of almond

“…Wang et al. (2022) found that repetitive sequences in genomes of species of Prunus subgenus Cerasus are positively associated with the obvious genome size expansion that occurred in cherry and Japanese plum in the last 2 million years. This evidence supports the role of TEs as genome organizers (Figure 2) and contributors to genome evolution.…”