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A Deluge of Complex Repeats: The Solanum Genome.

Mehra M, Gangwar I, Shankar R - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Length distribution plot of the sRNA reads mapping to repetitive elements.sRNA reads of length 24 bp were observed to be most enriched in S. lycopersicum, while in S. tuberosum, 17 bp long sRNAs were more prevalent.
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pone.0133962.g012: Length distribution plot of the sRNA reads mapping to repetitive elements.sRNA reads of length 24 bp were observed to be most enriched in S. lycopersicum, while in S. tuberosum, 17 bp long sRNAs were more prevalent.

Mentions: A large number of expressing repetitive elements have been reported to be involved in small RNAs/siRNA biogenesis [147,148]. Several of such sRNAs regulate the genes in either cis or trans manner. While some sRNAs are involved in post transcriptional gene silencing [148], a good number of such small RNAs are involved in de novo DNA methylation in plant genome [147,149–151]. Measuring the abundance of such small RNAs could also mirror the expression of repetitive elements which could have regulatory roles in the system. The small RNA sequencing reads were mapped to the repetitive elements as mentioned in the Methods section. Out of 35,992,757 unique small RNA reads in S. tuberosum and 9,620,265 unique reads in S. lycopersicum, ~0.23% (85,013) and ~33.41% (3,214,301) unique reads mapped to different repetitive elements, respectively. It was also found that most of the sRNA reads mapped to LTR/Gypsy elements in both species (Fig 11). To further verify the nature of these small RNAs, length distribution plot of the small RNA reads was made and it was identified that a high percentage of sRNA reads in S. tuberosum and S. lycopersicum were around 24bp, a length most prevalent with small regulatory RNAs like endogenous siRNAs and miRNAs (Fig 12). The overall comparison between the coverage of repeat family, the average abundance of repeat families and the percentage of sRNA reads mapped has been illustrated in Fig 13. It appears that expression of a repeat family is not correlated to its genomic prevalence.


A Deluge of Complex Repeats: The Solanum Genome.

Mehra M, Gangwar I, Shankar R - PLoS ONE (2015)

Length distribution plot of the sRNA reads mapping to repetitive elements.sRNA reads of length 24 bp were observed to be most enriched in S. lycopersicum, while in S. tuberosum, 17 bp long sRNAs were more prevalent.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524691&req=5

pone.0133962.g012: Length distribution plot of the sRNA reads mapping to repetitive elements.sRNA reads of length 24 bp were observed to be most enriched in S. lycopersicum, while in S. tuberosum, 17 bp long sRNAs were more prevalent.
Mentions: A large number of expressing repetitive elements have been reported to be involved in small RNAs/siRNA biogenesis [147,148]. Several of such sRNAs regulate the genes in either cis or trans manner. While some sRNAs are involved in post transcriptional gene silencing [148], a good number of such small RNAs are involved in de novo DNA methylation in plant genome [147,149–151]. Measuring the abundance of such small RNAs could also mirror the expression of repetitive elements which could have regulatory roles in the system. The small RNA sequencing reads were mapped to the repetitive elements as mentioned in the Methods section. Out of 35,992,757 unique small RNA reads in S. tuberosum and 9,620,265 unique reads in S. lycopersicum, ~0.23% (85,013) and ~33.41% (3,214,301) unique reads mapped to different repetitive elements, respectively. It was also found that most of the sRNA reads mapped to LTR/Gypsy elements in both species (Fig 11). To further verify the nature of these small RNAs, length distribution plot of the small RNA reads was made and it was identified that a high percentage of sRNA reads in S. tuberosum and S. lycopersicum were around 24bp, a length most prevalent with small regulatory RNAs like endogenous siRNAs and miRNAs (Fig 12). The overall comparison between the coverage of repeat family, the average abundance of repeat families and the percentage of sRNA reads mapped has been illustrated in Fig 13. It appears that expression of a repeat family is not correlated to its genomic prevalence.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.