Development Of LTR Retrograde Transposon Annotation Software And Its Application In Plant Genome Evolution

LTR retrotransposons are the predominant proportion of plant genomes which play an essential role in driving genome size variation and genome structure evolution. It boasts great significance to annotate LTR retrotransposons accurately and effectively for studies on genome size variation and evolution. An LTR retrotransposons annotating software, LTRtype, was developed in this study based on homology searches. We tested the LTRtype software with the genome sequence of maize, rice and Arabidopsis, and our results showed that it could accurately and effectively mine several different LTR elements with complex structures and their nested insert events with obvious superiority to other like-kind software. We surveyed the complex elements mined by LTRtype in rice genome in details and found that, except for the complex LTR retrotransposons generated by intrachain inequality recombination and abnormal template jumping, there were at least 14 complex elements generated by the recombination before insertion. Furthermore, we found that more that 80 percent LTR retrotransposon sequences were non-autonomous elements in poplar genome and these non-autonomous elements were originated from some DNA lost/mutation events of autonomous elements. Compared with the genomes of rice and Arabidopsis, LTR retrotransposons in poplar genome experienced more serious DNA loss. In addition, LTR retrotransposons families with high copy numbers in poplar genome tended to have family amplification, and only a small part of families could contribute to the variation of genome sizes.