Though LTR-retrotransposons represent a major component in plant genomes, they are often considered as silent, and their expression is rarely studied. The next generation sequencing methods offer an unprecedented level and unexplored potentialities of analysis, allowing a comprehensive study of the RNA expressed in different tissues and growth conditions. We evaluated the expression of LTR-retrotransposons in a poplar interspecific hybrid, Populus deltoides x P. nigra, using Illumina RNAseq and a LTR-retrotransposon database of P. trichocarpa. First, the occurrence and redundancy of P. trichocarpa retrotransposons was studied in P. deltoides and P. nigra genomes. Then, RNA was isolated from leaves of two hybrids obtained from the same parents, cultivated in control conditions or subjected to moderate or severe drought stress. Nearly all P. trichocarpa retrotransposons were found in P. deltoides and P. nigra, however large differences in retrotransposon redundancy occur between the two species, arguably because of retrotransposon activity occurred after Populus speciation. The majority of retrotransposons were not expressed in the hybrids. Expressed retrotransposon show generally low transcription level, however some of them resulted highly transcribed, i.e., with rates higher than those of genes encoding housekeeping proteins as actin, with differences during drought stress. The two hybrids, that are genetically different (being parents heterozygous), show different retrotransposon expression and such difference increases at increasing stress levels. Gypsy retrotransposons are less transcribed than Copia; the most expressed retrotransposons do not belong to any described superfamily and can be defined as LARDs or TRIMs. Retroelements that do not belong to described superfamilies and are reported as unknown show similar expression levels in control and stressed plants, contrary to Gypsy and Copia elements, whose expression is increased by drought, suggesting that these two superfamilies are more efficiently repressed in control conditions while, during drought, the repression of expression is more relaxed. Drought-related cis-acting motifs are found in higher number in LTRs of active retroelements than in those of inactive ones.

NGS Analysis of LTR Retrotransposon Redundancy and Expression in Poplar Hybrids Subjected to Water Stress

GIORDANI, TOMMASO;BARGHINI, ELENA;CAVALLINI, ANDREA;NATALI, LUCIA
2012

Abstract

Though LTR-retrotransposons represent a major component in plant genomes, they are often considered as silent, and their expression is rarely studied. The next generation sequencing methods offer an unprecedented level and unexplored potentialities of analysis, allowing a comprehensive study of the RNA expressed in different tissues and growth conditions. We evaluated the expression of LTR-retrotransposons in a poplar interspecific hybrid, Populus deltoides x P. nigra, using Illumina RNAseq and a LTR-retrotransposon database of P. trichocarpa. First, the occurrence and redundancy of P. trichocarpa retrotransposons was studied in P. deltoides and P. nigra genomes. Then, RNA was isolated from leaves of two hybrids obtained from the same parents, cultivated in control conditions or subjected to moderate or severe drought stress. Nearly all P. trichocarpa retrotransposons were found in P. deltoides and P. nigra, however large differences in retrotransposon redundancy occur between the two species, arguably because of retrotransposon activity occurred after Populus speciation. The majority of retrotransposons were not expressed in the hybrids. Expressed retrotransposon show generally low transcription level, however some of them resulted highly transcribed, i.e., with rates higher than those of genes encoding housekeeping proteins as actin, with differences during drought stress. The two hybrids, that are genetically different (being parents heterozygous), show different retrotransposon expression and such difference increases at increasing stress levels. Gypsy retrotransposons are less transcribed than Copia; the most expressed retrotransposons do not belong to any described superfamily and can be defined as LARDs or TRIMs. Retroelements that do not belong to described superfamilies and are reported as unknown show similar expression levels in control and stressed plants, contrary to Gypsy and Copia elements, whose expression is increased by drought, suggesting that these two superfamilies are more efficiently repressed in control conditions while, during drought, the repression of expression is more relaxed. Drought-related cis-acting motifs are found in higher number in LTRs of active retroelements than in those of inactive ones.
9788890457012
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11568/205985
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