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Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns.
BMC Genomics. 2012 Apr 16; 13:137.BG

Abstract

BACKGROUND

Sugarcane 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.

RESULTS

Sixty 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.

CONCLUSIONS

Individual 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.

Authors+Show Affiliations

GaTE Lab, Depto, de Botânica, Inst, de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22507400

Citation

Domingues, Douglas S., et al. "Analysis of Plant LTR-retrotransposons at the Fine-scale Family Level Reveals Individual Molecular Patterns." BMC Genomics, vol. 13, 2012, p. 137.
Domingues DS, Cruz GM, Metcalfe CJ, et al. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics. 2012;13:137.
Domingues, D. S., Cruz, G. M., Metcalfe, C. J., Nogueira, F. T., Vicentini, R., Alves, C. d. e. . S., & Van Sluys, M. A. (2012). Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics, 13, 137. https://doi.org/10.1186/1471-2164-13-137
Domingues DS, et al. Analysis of Plant LTR-retrotransposons at the Fine-scale Family Level Reveals Individual Molecular Patterns. BMC Genomics. 2012 Apr 16;13:137. PubMed PMID: 22507400.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. AU - Domingues,Douglas S, AU - Cruz,Guilherme M Q, AU - Metcalfe,Cushla J, AU - Nogueira,Fabio T S, AU - Vicentini,Renato, AU - Alves,Cristiane de S, AU - Van Sluys,Marie-Anne, Y1 - 2012/04/16/ PY - 2011/10/27/received PY - 2012/04/16/accepted PY - 2012/4/18/entrez PY - 2012/4/18/pubmed PY - 2012/9/13/medline SP - 137 EP - 137 JF - BMC genomics JO - BMC Genomics VL - 13 N2 - BACKGROUND: Sugarcane 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. RESULTS: Sixty 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. CONCLUSIONS: Individual 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/22507400/Analysis_of_plant_LTR_retrotransposons_at_the_fine_scale_family_level_reveals_individual_molecular_patterns_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-137 DB - PRIME DP - Unbound Medicine ER -