title: A Deluge of Complex Repeats: The Solanum Genome.
abstract: Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50-60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.
authors.affiliation: Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India; Academy of Scientific & Innovative Research, Chennai, India.
authors.forename: Mrigaya
authors.initials: M
authors.lastname: Mehra
authors.affiliation: Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India; Academy of Scientific & Innovative Research, Chennai, India.
authors.forename: Indu
authors.initials: I
authors.lastname: Gangwar
authors.affiliation: Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India; Academy of Scientific & Innovative Research, Chennai, India.
authors.forename: Ravi
authors.initials: R
authors.lastname: Shankar
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant; D006801:Humans; D054643:INDEL Mutation; D018551:Solanum lycopersicum / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000378:metabolism; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements / Q000235:genetics; D016415:Sequence Alignment; D011198:Solanum tuberosum / Q000235:genetics*; D013045:Species Specificity; D020079:Terminal Repeat Sequences; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D018744:DNA, Plant; D035683:MicroRNAs; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D018626:Retroelements; D014157:Transcription Factors