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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.Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms.

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.


Related in: MedlinePlus

Transcriptionally most active repeat families on the basis of average RPKM expression.RC/Helitron and LTR/ERV1 were the transcriptionally most active repeat super-families in S. tuberosum and S. lycopersicum, respectively.
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pone.0133962.g009: Transcriptionally most active repeat families on the basis of average RPKM expression.RC/Helitron and LTR/ERV1 were the transcriptionally most active repeat super-families in S. tuberosum and S. lycopersicum, respectively.

Mentions: Repetitive elements are generally under high constraints and characterized by high DNA methylation making them silent components of the genome. Although transcriptional activity of repetitive elements has been observed under stress conditions, pathogen attack and tissue culture conditions [128,129]. Also a low level of activity for different repetitive elements has been reported in normal conditions which is one of the reasons for their amplifications in a genome. Many plant species, specially flowering plants, have been shown to possess active repetitive elements belonging to both classes of transposable elements [130,131]. Active nature of repetitive elements has been associated with the generation of small non-coding RNA (siRNAs) which through post transcriptional gene silencing mechanisms (PTGS) create a feed-back loop silencing the repetitive elements themselves [132]. Other than providing control to repetitive elements, transcriptional activity of repetitive elements may also provide tissue specific expression of certain genes [23]. These elements upon transcription can also alter the expression of certain genes by RNA interference or through antisense RNA as well as through different epigenetic modifications. Therefore, identification of active repetitive elements in these two genomes would help in defining the functional boundaries generated by these elements with regard to their host genes' expression patterns. Abundance of transcript sequences and repetitive elements was calculated using digital expression data from two different platforms. Using sequence read count based RPKM abundance measure, it was found that RC/Helitron was transcriptionally most active repeat super-family in S. tuberosum (Fig 9). Helitrons were initially discovered in A. thaliana, C. elegans and O. sativa using different in-silico methods [133,134] and since then, they have been identified in numerous eukaryotes. Helitrons transpose by rolling circle transposition rather than by traditional “cut and paste” mechanism as is followed by other DNA transposons [134,135]. Although, helitrons make only a small portion of genomes of eukaryotes, they have been known to contribute significantly to the evolution of genes by capturing exons as has been demonstrated in maize [135]. The other transcriptionally active repeat super-families in S. tuberosum on the basis of RPKM abundances include DNA transposon Harbinger and TcMar-Stowaway (Fig 9). TcMar-Stowaway was also transcriptionally most active repeat super-families identified using microarray data. DNA transposon Harbinger was the first super-family of DNA transposons to be identified in A. thaliana using in-silico analysis which was identified as the most transcriptionally active repetitive element on the basis of RPKM and microarray expression data (S1 Fig) [136]. A few of Harbinger elements have been reported to be active members of their respective genomes [137]. DNA transposons TcMar-Stowaway were first discovered in S. bicolor as the elements inserted within Tourist elements [89]. Stowaway elements can form a hairpin shaped structure [89] and have shown to be able to generate miRNAs [138]. DNA transposon TcMar-Pogo was another repeat super-family which was identified as highly transcriptionally active in S. tuberosum on the basis of microarray data (S1 Fig). Pogo super-family of repeats was first identified in Drosophila and since then has been identified in many other species [139,140]. Pogo elements have been associated with exaptation of the CENP-B gene in mammals [141] and of some MITE elements in A. thaliana [142]. SINE elements activity was also evident through S. tuberosum microarray data. However, in S. lycopersicum, a repeat super-family very similar to LTR/ERV1 repeat super-family was found as the transcriptionally most active repeat family in the RPKM based expression estimates (Fig 9). The other transcriptionally active repeat super-families according to NGS expression measures observed in S. lycopersicum belonged to SINEs and LINE element RTE-BovB, which was also observed to be transcriptionally active in microarray data (Fig 9). Other highly transcriptionally active repeat super-families in the NGS expression measures included DNA transposons CMC-EnSpm. Information regarding the annotation of repeat super-families and the method of annotation is provided in S9 Table.


A Deluge of Complex Repeats: The Solanum Genome.

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

Transcriptionally most active repeat families on the basis of average RPKM expression.RC/Helitron and LTR/ERV1 were the transcriptionally most active repeat super-families in S. tuberosum and S. lycopersicum, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133962.g009: Transcriptionally most active repeat families on the basis of average RPKM expression.RC/Helitron and LTR/ERV1 were the transcriptionally most active repeat super-families in S. tuberosum and S. lycopersicum, respectively.
Mentions: Repetitive elements are generally under high constraints and characterized by high DNA methylation making them silent components of the genome. Although transcriptional activity of repetitive elements has been observed under stress conditions, pathogen attack and tissue culture conditions [128,129]. Also a low level of activity for different repetitive elements has been reported in normal conditions which is one of the reasons for their amplifications in a genome. Many plant species, specially flowering plants, have been shown to possess active repetitive elements belonging to both classes of transposable elements [130,131]. Active nature of repetitive elements has been associated with the generation of small non-coding RNA (siRNAs) which through post transcriptional gene silencing mechanisms (PTGS) create a feed-back loop silencing the repetitive elements themselves [132]. Other than providing control to repetitive elements, transcriptional activity of repetitive elements may also provide tissue specific expression of certain genes [23]. These elements upon transcription can also alter the expression of certain genes by RNA interference or through antisense RNA as well as through different epigenetic modifications. Therefore, identification of active repetitive elements in these two genomes would help in defining the functional boundaries generated by these elements with regard to their host genes' expression patterns. Abundance of transcript sequences and repetitive elements was calculated using digital expression data from two different platforms. Using sequence read count based RPKM abundance measure, it was found that RC/Helitron was transcriptionally most active repeat super-family in S. tuberosum (Fig 9). Helitrons were initially discovered in A. thaliana, C. elegans and O. sativa using different in-silico methods [133,134] and since then, they have been identified in numerous eukaryotes. Helitrons transpose by rolling circle transposition rather than by traditional “cut and paste” mechanism as is followed by other DNA transposons [134,135]. Although, helitrons make only a small portion of genomes of eukaryotes, they have been known to contribute significantly to the evolution of genes by capturing exons as has been demonstrated in maize [135]. The other transcriptionally active repeat super-families in S. tuberosum on the basis of RPKM abundances include DNA transposon Harbinger and TcMar-Stowaway (Fig 9). TcMar-Stowaway was also transcriptionally most active repeat super-families identified using microarray data. DNA transposon Harbinger was the first super-family of DNA transposons to be identified in A. thaliana using in-silico analysis which was identified as the most transcriptionally active repetitive element on the basis of RPKM and microarray expression data (S1 Fig) [136]. A few of Harbinger elements have been reported to be active members of their respective genomes [137]. DNA transposons TcMar-Stowaway were first discovered in S. bicolor as the elements inserted within Tourist elements [89]. Stowaway elements can form a hairpin shaped structure [89] and have shown to be able to generate miRNAs [138]. DNA transposon TcMar-Pogo was another repeat super-family which was identified as highly transcriptionally active in S. tuberosum on the basis of microarray data (S1 Fig). Pogo super-family of repeats was first identified in Drosophila and since then has been identified in many other species [139,140]. Pogo elements have been associated with exaptation of the CENP-B gene in mammals [141] and of some MITE elements in A. thaliana [142]. SINE elements activity was also evident through S. tuberosum microarray data. However, in S. lycopersicum, a repeat super-family very similar to LTR/ERV1 repeat super-family was found as the transcriptionally most active repeat family in the RPKM based expression estimates (Fig 9). The other transcriptionally active repeat super-families according to NGS expression measures observed in S. lycopersicum belonged to SINEs and LINE element RTE-BovB, which was also observed to be transcriptionally active in microarray data (Fig 9). Other highly transcriptionally active repeat super-families in the NGS expression measures included DNA transposons CMC-EnSpm. Information regarding the annotation of repeat super-families and the method of annotation is provided in S9 Table.

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.Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms.

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.


Related in: MedlinePlus