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Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses

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Book cover Plant Transposable Elements

Part of the book series: Topics in Current Genetics ((TCG,volume 24))

Abstract

Sugarcane is an important crop worldwide for sugar and biofuel production. Modern sugarcane cultivars have large, highly complex, polyploid genomes, and like other grasses, have a significant transposable element (TE) content. Four sugarcane TE superfamilies, hAT, Mutator, Gypsy and Copia, were first described from an EST database and, with the availability of genomic sequence, further characterised and compared with TEs from other grasses. Here we summarise previous work and extend the knowledge of the structure, diversity, evolutionary history, age, transcriptional activity and genomic distribution of sugarcane TEs. We also compare and contrast sugarcane TEs with homologous sequences in rice and sorghum, as well as analyse the age and genomic distribution of sugarcane TEs with related lineages from sorghum and rice. Finally, we discuss the importance of defining sugarcane TE lineages for understanding the contribution of ancestral genomes to modern cultivars, for genome sequencing and annotation and in applied genetics.

Article Note

Both authors contributed equally to this paper and are joint first co-authors.

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Abbreviations

BAC:

Bacterial Artificial Chromosome

BLASTn:

Basic Local Alignment Search Tool nucleotide

EST:

Expressed Sequence Tag

FISH:

Fluorescent In Situ Hybridisation

LTR:

Long Terminal Repeats

my:

millions of years

mya:

millions of years ago

MuLES :

Mutator-Like ElementS

NCBI:

National Center for Biotechnology Information

QTL:

Quantitative Trait Loci

SChAT:

SugarCane hAT sequences

sRNA:

small RNA

TE:

Transposable Elements

TIRs:

Terminal Inverted Repeats

WGD:

Whole Genome Duplication

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Acknowledgements

We gratefully acknowledge funding from FAPESP-BIOEN (08/52074-0) and CNPq to MAVS. NS, CJM and GMQC are supported by FAPESP fellowships; EAOC is supported by CNPq fellowship.

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  1. Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil

    Nathalia de Setta, Cushla J. Metcalfe, Guilherme M. Q. Cruz, Edgar A. Ochoa & Marie-Anne Van Sluys

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  1. Nathalia de Setta
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  3. Guilherme M. Q. Cruz
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  4. Edgar A. Ochoa
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Correspondence to Marie-Anne Van Sluys .

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  1. , Institut Jean-Pierre Bourgin (IJPB), INRA Versailles, UMR 1318, Versailles Cedex, 78026, France

    Marie-Angèle Grandbastien

  2. , Centre de Recerca en Agrigenomica (CRAG), CSIC-RTA-UAB, Barcelona, 08193, Spain

    Josep M. Casacuberta

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de Setta, N., Metcalfe, C.J., Cruz, G.M.Q., Ochoa, E.A., Van Sluys, MA. (2012). Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses. In: Grandbastien, MA., Casacuberta, J. (eds) Plant Transposable Elements. Topics in Current Genetics, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31842-9_10

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