Isolation and characterization of Ty1-copia retrotransposons in Saccharum officinarum

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1 National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
2 Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
3 State Key Laboratory for protection and utilization of subtropical agro-bioresources Guangxi University, Nanning 530004, China
DOI
10.7287/peerj.preprints.27092v1
Published
Accepted
Subject Areas
Agricultural Science, Genetics, Plant Science
Keywords
Saccharum officinarum, Ty1-copia retrotransposons, phylogenetic diversity, chromosomal organization, genome
Copyright
© 2018 Chen et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Chen K, Yu F, Huang Y, Wu X, Yang S, Li X, Zeng K, Hu X, Huang F, Deng Z, Zhang M. 2018. Isolation and characterization of Ty1-copia retrotransposons in Saccharum officinarum. PeerJ Preprints 6:e27092v1

Abstract

Background. Saccharum officinarum is the most significant resource for sugar and high-yield genes in sugarcane breeding programs. However, the unknown information of evolution and genome organization remain largely in the sugarcane, which has limited progress in sugarcane breeding. Retrotransposons occupy a large proportion of the plant genome; therefore, characterization of Ty1-copia retrotransposons will improve understanding of the evolution and organization of plant genomes.

Methods. The present study isolated conserved domains of Ty1-copia retrotransposon-encoded reverse transcriptase genes from S. officinarum to characterize their phylogenetic diversity, genomic abundance, and chromosomal distribution.

Results. In total, 42 Ty1-copia reverse transcriptase sequences with 35-100% similarity and high levels of heterogeneity were obtained. Of them, 11 (26%) were disrupted by stop codons and/or frameshift mutations. Phylogenetic analysis revealed these sequences could be split into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Sire/Maximus, and Retrofit/Ale). Dot blot analysis showed that Ty1-copia retrotransposons represent a significant portion of the S. officinarum genome, with copy numbers as high as 1.7 × 105. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons were dispersed within heterochromatic regions among all S. officinarum chromosomes, with around 30 obvious signals clustering in terminal regions. However, Ty1-copia retrotransposons were not found in nucleolar organizing regions of 45S rDNA.

Discussion. These results serve to enhance our understanding of the chromosomal distribution and evolution of the S. officinarum genome as well as promote possible utilization of retrotransposons in sugarcane breeding programs.

Author Comment

This is a submission to PeerJ for review.

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