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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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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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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