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.

Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

“…Out of total genome size of 810.6 MB,15.78 % (127,958,425 bp) of S. tuberosum has yet to be sequenced, and as for S. lyco persicum, 5 % (44,030,063 bp) out of 781.6 MB isn't still sequenced (Mehra et al, 2015). Many plant species contain repetitive elements in their genome, sometimes reaching 80 %, such as wheat.…”

“…Thus, LTR is the most abundant complex repetitive element in S. tuberosum and S. lycopersicum. Twelve chromosomes of both species are highly syntenic to each other, having high similarity for genes and repeats distribution (Mehra et al, 2015).…”

“…These results suggest that in both spe cies repetitive sequences have impact on majority of protein coding genes. Analysis of various repeat families (LINE elements RTEBovB, SINE elements and DNA transposon Stowaway) in S. tuberosum indicated big portion of repeti tive elements are located within genic regions, as well as in S. lycopersicum, where the DNA transposons hATTag1, hAT Tip100, PIFHarbinger, RC Helitron and SINEs were found in abundance in genic region, while genic region showed notable preference for LTR/ERV1 repeat family (Mehra et al, 2015).…”

“…Functions of these TFs include response to stress, light, abscisic acid, and other metabolites as well as taking part in development processes (flower development and gametophyte, embryo and seed development). Above examples indicate integration of repetitive sequences in plants is beneficial for their survival purposes, as opposed to initial speculations of them being "junks" (Mehra et al, 2015).…”

“…Transcriptional activity of repetitive elements besides controlling repetitive elements, can as well provide tissue specific expression of certain genes (Mehra et al, 2015). A fair number of expressive repetitive elements have been linked to small RNAs/siRNA biogenesis, some of which are involved in gene regulation in either cis or trans manner.…”