The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation.

Yingxin Zhang,Fangpu Han,Xiangqi Zhang,Yuhong Chen,Richard R.-C Wang,Shuangshuang Li,Zanmin Hu,Chengming Fan

doi:10.3389/fpls.2017.01706

Abstract

Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH) analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4%) of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like Abiba might play a role in their structural organization and function. All these results might help in understanding the diversity and evolution of TEs in rye, as well as their driving forces in rye genome organization and evolution.

Highlights

Transposable elements (TEs) represented a high percentage of eukaryotic genomes, 58.58% in Pinus taeda (Wegrzyn et al, 2014), 63% in Sorghum bicolor (Paterson et al, 2008), 80% in maize (Feschotte et al, 2002), and more than 72% in Secale cereale (Bauer et al, 2017)
Broad-scale patterns of TE abundance has been investigated in rye using highthroughput DNA sequencing technology (Bartoš et al, 2008; Fluch et al, 2012; Bauer et al, 2017), the accurate diversity of sequence and chromosomal distribution of TEs in rye remains enigmatic due to their dynamic nature and nested transposition
26 TE lineages were found in these identified sequences, and almost all of them could be found in chimeric sequences, which suggested wide nested transposition and recombination have happened among these TE lineages in rye genome

Summary

Introduction

Transposable elements (TEs) represented a high percentage of eukaryotic genomes, 58.58% in Pinus taeda (Wegrzyn et al, 2014), 63% in Sorghum bicolor (Paterson et al, 2008), 80% in maize (Feschotte et al, 2002), and more than 72% in Secale cereale (Bauer et al, 2017). Besides their high copy number, the serial transposition of individual TEs into previously inserted elements can form large nested structures in genomes (Bergman et al, 2006; Bousios et al, 2016). CRR (centromeric retrotransposon in rice) and CRW (centromeric retrotransposon in wheat), belonging to the same family with CRM, were proved to interact with CENH3 (Nagaki et al, 2004; Li et al, 2013), which suggesting that the Centromeric Retrotransposon (CR) family in grass species played an important role in centromere structural organization and function (Zhong et al, 2002)

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Conclusion