Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome
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- 作者：Elena Barghini ; Flavia Mascagni ; Lucia Natali…
- 关键词：Non ; LTR retroelements ; SINEs ; Illumina sequencing ; Olive ; SINE Finder
- 刊名：Molecular Genetics and Genomics
- 出版年：2017
- 出版时间：February 2017
- 年：2017
- 卷：292
- 期：1
- 页码：53-61
- 全文大小：
- 刊物类别：Biomedical and Life Sciences
- 刊物主题：Cell Biology; Biochemistry, general; Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics;
- 出版者：Springer Berlin Heidelberg
- ISSN：1617-4623
- 卷排序：292
文摘
Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.