Evolution Of Tomato Long Non-Coding RNA And Identification Of InDels During Tomato Domestication Base On The Fragment Similarity

Long non-coding RNA(lncRNA), with a transcript length between 200 nt and 100000 nt, has not the capability of protein coding RNA fragments. LncRNA initially are considered to be transcription "noise", the by-product of RNA polymerase II and junk sequence without biologically functional. In recent years, lncRNAs have been widely studied with the development of sequencing technology. But the lncRNA expression and origin in plant are still unclear. In order to understand the lncRNA expression features and evolution patterns in plants. In our study, we identified 413 and 709 multi-exon noncoding transcripts from 353 and 595 loci of the cultivar tomato Heinz1706 and its wild relative LA1589, respectively. Systematic comparison of the sequence and expression of lnc RNAs showed that they are poorly conserved in Solanaceae, with only < 0.4% lncRNAs present in all sequenced genomes of tomato and potato. About 75% of Lycopersicon-specific lncRNA loci contain one or more insertion/deletion in their transcribed or promoter regions compared with that in the genome of S. pennellii and the origin of some lncRNAs are closely related to transposable events. Further analysis a fruit-specific expressed lncRNA(named lncRNA-314), revealed that it originated through two evolutionary events: speciation of S. pennellii resulted in insertion of a long terminal repeat(LTR) retrotransposon into chromosome 10 and contributed to most of the transcribed region of lncRNA-314; and a 102 kb deletion in Lycopersicon generated the promoter region and part of the transcribed region of lncRNA-314. Coexpression analysis indicated that a neighbouring ABC transport gene which located upstream and coexpressed with lncRNA-314, maybe as a target gene of lncRNA-314. These results provide novel insights into the evolution and regulatory function of lncRNAs in plants.Insertion and deletion(InDel) polymorphism are widely distributed in the genome, and only second to the SNP polymorphism in number. With many species genome have been sequenced and the development of high-throughput sequencing technology, it is possible to identify InDel markers in genome, especially the InDel markers in intergenic regions. More important, genotypes can be distinguished according to the size of InDel marker by gel electrophoresis. But, the identification of InDel not only need a lot of sequenced data, but the analysis method is edious and the results have a high false discovery rate. So it is not suitable for the conventionality breeding and map-based cloning. In our study, 29,618 InDel polymorphism were identified between LA1589 and Heinz1706 by comparative genome. Due to a high linkage disequilibrium, a piple was developed to infer the possibility of InDel in any region base on the similarity method and SNP dataset. Combining with the experimental verification, the InDel polymorphism accuracy identified by this piple could reach 40%-80% and the identification of InDel markers by experiment was left out. Further analysis show that this method could also conclude the possible hybrid region in genome. In a word, a mass of InDel molecular markers were obtained in our research and these markers were wildly used in conventional breeding and map-based cloning, etc.