Abstract
BackgroundTransposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production.ResultsWe analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations.ConclusionsThis study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance.
Highlights
Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are proposed as an ideal model to study TEs roles in the context of plant genome evolution
Evolutionary relationships of eight rice AA genomes To confirm the evolutionary relationship between the eight rice species, we performed phylogenomic analyses of 1937 orthologous and single-copy genes of at least 300 aa from the eight fully sequenced Oryza genomes, using O. meridionalis as out-group (Fig. 1a and Additional file 1: Table S1)
TEs are preferentially present in introns of expressed genes To investigate how the TEs affected gene functions, we examined gene expression levels by Cufflinks using FPKM from RNA sequencing data (RNA-seq; CPGS Oryza Genome Evolution Project, https://www.nsf.gov/ awardsearch/showAward?AWD_ID=1026200) of seven of the eight rice species
Summary
Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are proposed as an ideal model to study TEs roles in the context of plant genome evolution. While TEs are ubiquitous in all organisms [2], their contribution to genome size can change rapidly during evolution. TEs are defined as two main classes depending on their transposition mechanisms [3]. TEs have caused up to two-fold differences in genome size that sometimes arose over only a few million years [6]. TEs are often regarded as genomic “parasites” due to the potentially detrimental effects on genes by insertional inactivation and ectopic recombination of DNA [11]
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