Characterization of Repetitive DNA in Saccharum officinarum and Saccharum spontaneum by Genome Sequencing and Cytological Assays.

Kai Wang,Hui Zhang,Ayman M H Esh,Dong Xiang,Bo Sun,Kai Xia,Haris Khurshid

doi:10.3389/fpls.2022.814620

Abstract

In most plant species, DNA repeated elements such as satellites and retrotransposons are composing the majority of their genomes. Saccharum officinarum (2n = 8x = 80) and S. spontaneum (2n = 40–128) are the two fundamental donors of modern sugarcane cultivars. These two species are polyploids with large genome sizes and are enriched in repetitive elements. In this work, we adopted a de novo strategy to isolate highly repetitive and abundant sequences in S. officinarum LA Purple and S. spontaneum SES208. The findings obtained from alignment to the genome assemblies revealed that the vast majority of the repeats (97.9% in LA Purple and 96.5% in SES208) were dispersed in the respective genomes. Fluorescence in situ hybridization assays were performed on 27 representative repeats to investigate their distributions and abundances. The results showed that the copies of some highly repeated sequences, including rDNA and centromeric or telomeric repeats, were underestimated in current genome assemblies. The analysis of the raw read mapping strategy showed more copy numbers for all studied repeats, suggesting that copy number underestimation is common for highly repeated sequences in current genome assemblies of LA Purple and SES208. In addition, the data showed that the centromeric retrotransposons in all SES208 centromeres were absent in certain S. spontaneum clones with different ploidies. This rapid turnover of centromeric DNA in sugarcane provides new clues regarding the pattern of centromeric retrotransposon formation and accumulation.

Highlights

In eukaryotes, repetitive sequences in genomes are ubiquitous (Treangen and Salzberg, 2012; Wicker et al, 2018) and often present as a major component (Feschotte and Pritham, 2007)
A total of 161,028 and 90,804 repeat clusters were obtained from LA Purple and SES208, respectively (Supplementary Figure 1), using RepeatExplorer
338 and 305 clusters that accounted for 44.9 and 42.4% of the total 33 million genomic reads were relatively enriched in LA Purple and SES208, respectively and were annotated to characterize the most repeat families

Summary

Introduction

Repetitive sequences ( referred to as repeats) in genomes are ubiquitous (Treangen and Salzberg, 2012; Wicker et al, 2018) and often present as a major component (Feschotte and Pritham, 2007). Repetitive DNAs in Sugarcane (Garbus et al, 2015) Despite their pervasiveness, it is still a lot to be understood about the mechanisms by which repetitive elements emerge and rapidly accumulate. Tandem repeating DNAs and transposable elements (TEs) are the two typical repeats in eukaryotes. There are three well-known types of tandem repeats: centromeric satellite repeats, telomeric satellite repeats, and ribosomal DNA (5S and 45S rDNAs) (de Koning et al, 2011; Biscotti et al, 2015). Long terminal repeat (LTR)-type retrotransposons are typically the most type of TE in plants, especially for species with large genome sizes, such as sugarcane, wheat, maize, and cotton (Schnable et al, 2009; Appels et al, 2018; Zhang et al, 2018; Yang et al, 2020). LTR-type retrotransposons can move via ‘copy and paste’ mechanisms and was enriched in the centromeres of plants (Presting, 2018)

Methods

Results

Conclusion