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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 mapping to protein-coding, lncRNA or unclassified transcripts in two genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89
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Fig5: Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes mapping to protein-coding, lncRNA or unclassified transcripts in two genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89

Mentions: To establish the relationship between sRNA populations and lncRNAs, we mapped sRNAs against a mixed reference (contigs of the genome draft and the transcriptome assembled for this study), which allowed us to avoid selection bias, that is, to assign a transcript as a precursor or target of a sRNA, when the best hit for that sRNA is in a non-transcribed intergenic region (See Methods). Most 21 nt sRNAs mapped to protein coding transcripts, while the proportion of 24 nt that mapped to protein-coding transcripts was similar to that which mapped to lncRNAs (Fig. 5). sRNA reads of the wild genotype mapped to 9370 lncRNAs, while the domesticated genotype sRNA reads mapped to 8852 lncRNAs (42.69 % and 40.91 %, relative to the total lncRNAs expressed in each genotype). sRNAs reads for both genotypes mapped to the same 8852 lncRNAs. Even though the proportion of lncRNAs having sequence similarity with miRNAs is notable, it is not as high as that for maize [46].Fig. 5


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 mapping to protein-coding, lncRNA or unclassified transcripts in two 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

Fig5: Bar charts for the number of reads per length (bp) in small RNA populations of sunflower meiocytes mapping to protein-coding, lncRNA or unclassified transcripts in two genotypes. a Results for the wild genotype Ac-8. b Results for the domesticated genotype HA89
Mentions: To establish the relationship between sRNA populations and lncRNAs, we mapped sRNAs against a mixed reference (contigs of the genome draft and the transcriptome assembled for this study), which allowed us to avoid selection bias, that is, to assign a transcript as a precursor or target of a sRNA, when the best hit for that sRNA is in a non-transcribed intergenic region (See Methods). Most 21 nt sRNAs mapped to protein coding transcripts, while the proportion of 24 nt that mapped to protein-coding transcripts was similar to that which mapped to lncRNAs (Fig. 5). sRNA reads of the wild genotype mapped to 9370 lncRNAs, while the domesticated genotype sRNA reads mapped to 8852 lncRNAs (42.69 % and 40.91 %, relative to the total lncRNAs expressed in each genotype). sRNAs reads for both genotypes mapped to the same 8852 lncRNAs. Even though the proportion of lncRNAs having sequence similarity with miRNAs is notable, it is not as high as that for maize [46].Fig. 5

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.