Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns.

Douglas S Domingues,Guilherme M Q Cruz,Cristiane De S Alves,Fabio T S Nogueira,Cushla J Metcalfe,Renato Vicentini,Marie-Anne Van Sluys

doi:10.1186/1471-2164-13-137

Abstract

BackgroundSugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out.ResultsSixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements.ConclusionsIndividual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

Highlights

Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source
Characterization of LTR retrotransposons in sugarcane: phylogeny and structural features Plant Long Terminal Repeat retrotransposons (LTR-reverse transcriptase (RT)) evolutionary lineage names are not used consistently within the literature [6,7,8], we chose to include sequences from more than one source, so that we could directly compare our results with published data
Of the sixty full-length sequences extracted from sugarcane BAC sequences, thirty-two sequences were assigned to the Copia superfamily and twenty-eight to the Gypsy superfamily (Table 1; Figures 1 and 2)

Summary

Introduction

Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Based on the massive amounts of genomic sequence data released in the last 15 years, phylogenetic analysis of plant LTR-RTs has identified distinct evolutionary lineages within Gypsy and Copia, the two main plant LTR-RT superfamilies [5]. These lineages are widespread in both monocot and eudicot genomes. Sugarcane is an important crop worldwide, being a major source of sugar, and is increasingly being used for the production of renewable energy sources such as ethanol. Modern cultivars are highly polyploid and have one of the largest (10Gb) and most complex crop genomes, and chromosome numbers varying between 100-130 [10]

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