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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

Gain/loss of Transcription factor binding sites (TFBS) in the upstream regions of orthologous genes in S. tuberosum and S. lycopersicum.Plot showing the percentage of TFBS gained in orthologous genes contributed by repetitive elements.
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pone.0133962.g006: Gain/loss of Transcription factor binding sites (TFBS) in the upstream regions of orthologous genes in S. tuberosum and S. lycopersicum.Plot showing the percentage of TFBS gained in orthologous genes contributed by repetitive elements.

Mentions: Compared to the influence of repetitive elements over structural variations in genes, some previous studies have given enough reasons for speciation through regulatory variability caused by the repetitive elements. The contribution of repetitive elements has been acknowledged widely for gene regulations by exaptation of various cis-regulatory elements, enhancers and silencers [103,104]. Evolution of Brassica species has been associated with regulatory evolution carried out through TEs like MITE elements [105]. Similarly, the evolution of sunflower has also been attributed to transposable elements like LTR elements [103]. In P. abies, the large genome size has been attributed to slow accumulation transposable elements [106], while in olive genome, accumulation of tandem repeats has influenced its genome size [107]. In mammalian and primate genomes, several studies have reported about some major roles being played by the repetitive elements in the distribution and evolution of regulatory sites [50,51,108,109]. Therefore, it becomes imperative to assess the possible regulatory impacts of the repetitive elements over the Solanum genomes, especially when it is found that >95% genes of these two Solanum species are associated with the repetitive elements. The TFBS gained/lost in the 2kb upstream regions of orthologous genes and present within the repetitive elements were identified. Probability of gain/loss of TFBS for every TF in every orthologous gene pair was elucidated using binomial test. In this analysis, hypotheses assumed was that there was no significant gain/loss of TFBS in the 2kb upstream region of orthologous genes due to repetitive element. From this analysis, only those TFBS which showed significant p-value (≤ 0.05) for gain/loss of TFBS while being present within repeat sequences were retained, rejecting the hypothesis. In S. tuberosum, it was found that of the total binding sites of I-box gained/lost in the 2kb upstream region of the genes, ~36% were found overlapping with repetitive elements (Fig 6). The I-box promoter motif has been found to be present in the upstream region of genes involved in light based responses. I-box has been found associated with tomato genes and classified as a member of Myb-group of transcription factors. Similarly, another transcription factor (TF), SORLIP2 (Sequences Over-Represented in Light-Induced Promoters (SORLIPs)), was found to have a significant gain of their TFBS in the orthologous genes of S. tuberosum with ~23% of the gained sites occurring within the repetitive regions (Fig 6). This transcription factor has been associated with light-induced genes in cotyledon and roots of plants including A. thaliana. Another TF G-Box, which has been found involved in the regulation of expression of genes in response to light, anaerobic stress, abscissic acid and other metabolites. It was identified that 13% of the gained sites of G-box were within the repeat overlapping regions. Also, MADS family of transcription factors had ~14% of the TFBS gained in S. tuberosum. MADS TF possesses the MADS domain and these transcription factors have been associated critically with all sorts of development processes in plants, including flower development and gametophyte, embryo and seed development.


A Deluge of Complex Repeats: The Solanum Genome.

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

Gain/loss of Transcription factor binding sites (TFBS) in the upstream regions of orthologous genes in S. tuberosum and S. lycopersicum.Plot showing the percentage of TFBS gained in orthologous genes contributed by repetitive elements.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133962.g006: Gain/loss of Transcription factor binding sites (TFBS) in the upstream regions of orthologous genes in S. tuberosum and S. lycopersicum.Plot showing the percentage of TFBS gained in orthologous genes contributed by repetitive elements.
Mentions: Compared to the influence of repetitive elements over structural variations in genes, some previous studies have given enough reasons for speciation through regulatory variability caused by the repetitive elements. The contribution of repetitive elements has been acknowledged widely for gene regulations by exaptation of various cis-regulatory elements, enhancers and silencers [103,104]. Evolution of Brassica species has been associated with regulatory evolution carried out through TEs like MITE elements [105]. Similarly, the evolution of sunflower has also been attributed to transposable elements like LTR elements [103]. In P. abies, the large genome size has been attributed to slow accumulation transposable elements [106], while in olive genome, accumulation of tandem repeats has influenced its genome size [107]. In mammalian and primate genomes, several studies have reported about some major roles being played by the repetitive elements in the distribution and evolution of regulatory sites [50,51,108,109]. Therefore, it becomes imperative to assess the possible regulatory impacts of the repetitive elements over the Solanum genomes, especially when it is found that >95% genes of these two Solanum species are associated with the repetitive elements. The TFBS gained/lost in the 2kb upstream regions of orthologous genes and present within the repetitive elements were identified. Probability of gain/loss of TFBS for every TF in every orthologous gene pair was elucidated using binomial test. In this analysis, hypotheses assumed was that there was no significant gain/loss of TFBS in the 2kb upstream region of orthologous genes due to repetitive element. From this analysis, only those TFBS which showed significant p-value (≤ 0.05) for gain/loss of TFBS while being present within repeat sequences were retained, rejecting the hypothesis. In S. tuberosum, it was found that of the total binding sites of I-box gained/lost in the 2kb upstream region of the genes, ~36% were found overlapping with repetitive elements (Fig 6). The I-box promoter motif has been found to be present in the upstream region of genes involved in light based responses. I-box has been found associated with tomato genes and classified as a member of Myb-group of transcription factors. Similarly, another transcription factor (TF), SORLIP2 (Sequences Over-Represented in Light-Induced Promoters (SORLIPs)), was found to have a significant gain of their TFBS in the orthologous genes of S. tuberosum with ~23% of the gained sites occurring within the repetitive regions (Fig 6). This transcription factor has been associated with light-induced genes in cotyledon and roots of plants including A. thaliana. Another TF G-Box, which has been found involved in the regulation of expression of genes in response to light, anaerobic stress, abscissic acid and other metabolites. It was identified that 13% of the gained sites of G-box were within the repeat overlapping regions. Also, MADS family of transcription factors had ~14% of the TFBS gained in S. tuberosum. MADS TF possesses the MADS domain and these transcription factors have been associated critically with all sorts of development processes in plants, including flower development and gametophyte, embryo and seed development.

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