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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.


Diagram showing the numbers and proportions of differentially expressed genes (DEG) between the domesticated and wild genotypes grouped by coding class. Global percentage of DEGs (first row) was calculated based on the total number of genes (59,058). Percentages of genes with and without protein coding potential were calculated with reference to number of DEGs (29,469). Percentages of lncRNA and unclassified genes were calculated with reference to non-protein coding genes (18,767). Last row in the diagram presents percentages in each category with reference to the total DEG number (29,469)
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Fig1: Diagram showing the numbers and proportions of differentially expressed genes (DEG) between the domesticated and wild genotypes grouped by coding class. Global percentage of DEGs (first row) was calculated based on the total number of genes (59,058). Percentages of genes with and without protein coding potential were calculated with reference to number of DEGs (29,469). Percentages of lncRNA and unclassified genes were calculated with reference to non-protein coding genes (18,767). Last row in the diagram presents percentages in each category with reference to the total DEG number (29,469)

Mentions: We found 29,469 (49.87 %) differentially expressed genes (DEGs) between the domesticated and wild genotype using a False Discovery Rate (FDR) of 1 %. The majority (63.62 %) of these genes could not be identified via BLAST (Fig. 1), which is consistent with our previous study wherein transcripts that could not be identified were more abundant in meiocytes than in the somatic transcriptome, and also exhibited more tissue-specific expression [17]. Thus, we focused on these unidentified transcripts to investigate how many could be classified as lncRNAs that may play a regulatory role in homologous recombination during meiosis.Fig. 1


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)

Diagram showing the numbers and proportions of differentially expressed genes (DEG) between the domesticated and wild genotypes grouped by coding class. Global percentage of DEGs (first row) was calculated based on the total number of genes (59,058). Percentages of genes with and without protein coding potential were calculated with reference to number of DEGs (29,469). Percentages of lncRNA and unclassified genes were calculated with reference to non-protein coding genes (18,767). Last row in the diagram presents percentages in each category with reference to the total DEG number (29,469)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Diagram showing the numbers and proportions of differentially expressed genes (DEG) between the domesticated and wild genotypes grouped by coding class. Global percentage of DEGs (first row) was calculated based on the total number of genes (59,058). Percentages of genes with and without protein coding potential were calculated with reference to number of DEGs (29,469). Percentages of lncRNA and unclassified genes were calculated with reference to non-protein coding genes (18,767). Last row in the diagram presents percentages in each category with reference to the total DEG number (29,469)
Mentions: We found 29,469 (49.87 %) differentially expressed genes (DEGs) between the domesticated and wild genotype using a False Discovery Rate (FDR) of 1 %. The majority (63.62 %) of these genes could not be identified via BLAST (Fig. 1), which is consistent with our previous study wherein transcripts that could not be identified were more abundant in meiocytes than in the somatic transcriptome, and also exhibited more tissue-specific expression [17]. Thus, we focused on these unidentified transcripts to investigate how many could be classified as lncRNAs that may play a regulatory role in homologous recombination during meiosis.Fig. 1

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.