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Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates.

Flórez-Zapata NM, Reyes-Valdés MH, Martínez O - BMC Genomics (2016)

Bottom Line: Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis.To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome. lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO)/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821, Irapuato, Guanajuato, México.

ABSTRACT

Background: Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.

Results: Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome.

Conclusions: lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

No MeSH data available.


Expression overview of genes grouped by coding class (Protein-coding, lncRNA or Unclassified) in somatic and meiocyte transcriptomes. a Bar chart showing the coding class proportions by transcriptome. b Bar chart comparing the number of genes exclusively expressed in somatic or meiocyte transcriptomes by coding class. c Box plots for the distributions of the decimal log expression of genes in meiocytes and somatic transcriptomes by coding class
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Fig3: Expression overview of genes grouped by coding class (Protein-coding, lncRNA or Unclassified) in somatic and meiocyte transcriptomes. a Bar chart showing the coding class proportions by transcriptome. b Bar chart comparing the number of genes exclusively expressed in somatic or meiocyte transcriptomes by coding class. c Box plots for the distributions of the decimal log expression of genes in meiocytes and somatic transcriptomes by coding class

Mentions: To gain insight into the function of sunflower lncRNAs, we examined their expression behavior in the meiocyte and somatic transcriptomes of the domesticated sunflower genotype HA89 [17]. In HA89 meiocytes, the proportion of lncRNAs was significantly higher (P < 0.01) than that of the somatic transcriptome (Fig. 3a). Likewise, as mentioned above, high expression levels of lncRNAs in reproductive structures have been described in plants [46] and animals [43, 45]. Given the high number of lncRNAs expressed in sunflower meiocytes, many are likely involved in meiosis, and therefore the expression (and possible role) of lncRNAs in meiosis could be highly conserved.Fig. 3


Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates.

Flórez-Zapata NM, Reyes-Valdés MH, Martínez O - BMC Genomics (2016)

Expression overview of genes grouped by coding class (Protein-coding, lncRNA or Unclassified) in somatic and meiocyte transcriptomes. a Bar chart showing the coding class proportions by transcriptome. b Bar chart comparing the number of genes exclusively expressed in somatic or meiocyte transcriptomes by coding class. c Box plots for the distributions of the decimal log expression of genes in meiocytes and somatic transcriptomes by coding class
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940957&req=5

Fig3: Expression overview of genes grouped by coding class (Protein-coding, lncRNA or Unclassified) in somatic and meiocyte transcriptomes. a Bar chart showing the coding class proportions by transcriptome. b Bar chart comparing the number of genes exclusively expressed in somatic or meiocyte transcriptomes by coding class. c Box plots for the distributions of the decimal log expression of genes in meiocytes and somatic transcriptomes by coding class
Mentions: To gain insight into the function of sunflower lncRNAs, we examined their expression behavior in the meiocyte and somatic transcriptomes of the domesticated sunflower genotype HA89 [17]. In HA89 meiocytes, the proportion of lncRNAs was significantly higher (P < 0.01) than that of the somatic transcriptome (Fig. 3a). Likewise, as mentioned above, high expression levels of lncRNAs in reproductive structures have been described in plants [46] and animals [43, 45]. Given the high number of lncRNAs expressed in sunflower meiocytes, many are likely involved in meiosis, and therefore the expression (and possible role) of lncRNAs in meiosis could be highly conserved.Fig. 3

Bottom Line: Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis.To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome. lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO)/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821, Irapuato, Guanajuato, México.

ABSTRACT

Background: Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.

Results: Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome.

Conclusions: lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

No MeSH data available.