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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.


Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes in two genotypes. Reads were classified as ‘Unique’ for sequences found only once, or ‘Redundant’ for sequences found more than one time within genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89
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Fig4: Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes in two genotypes. Reads were classified as ‘Unique’ for sequences found only once, or ‘Redundant’ for sequences found more than one time within genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89

Mentions: We obtained around 5 million (Table AF1-2 in Additional file 1) clean reads of 20 to 25 nt, with most corresponding to reads of 24 nt (Fig. 4). These 24 nt sRNAs are typically endogenous siRNAs [27] and are the major component of sRNA populations in plants that participate in RNA-mediated chromatin-based gene silencing [56]. During maize meiosis, 24 nt phasiRNAs accumulate [30] in a way that is similar to the accumulation observed for mouse spermatogenesis [31]. Although the function of these 24 nt sRNAs is not completely understood, they may participate in genome surveillance (e.g., TE silencing pathways), or act as mobile signals and/or chromatin modifiers [30, 31].Fig. 4


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)

Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes in two genotypes. Reads were classified as ‘Unique’ for sequences found only once, or ‘Redundant’ for sequences found more than one time within genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes in two genotypes. Reads were classified as ‘Unique’ for sequences found only once, or ‘Redundant’ for sequences found more than one time within genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89
Mentions: We obtained around 5 million (Table AF1-2 in Additional file 1) clean reads of 20 to 25 nt, with most corresponding to reads of 24 nt (Fig. 4). These 24 nt sRNAs are typically endogenous siRNAs [27] and are the major component of sRNA populations in plants that participate in RNA-mediated chromatin-based gene silencing [56]. During maize meiosis, 24 nt phasiRNAs accumulate [30] in a way that is similar to the accumulation observed for mouse spermatogenesis [31]. Although the function of these 24 nt sRNAs is not completely understood, they may participate in genome surveillance (e.g., TE silencing pathways), or act as mobile signals and/or chromatin modifiers [30, 31].Fig. 4

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.