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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.


Related in: MedlinePlus

Bioinformatic pipeline to determine the lncRNA nature of transcripts and Venn diagrams with number of lncRNA expressed by genotype. Protein coding was determined by comparing transcripts with peptide databases (TAIR 10, NCBI RefSeq and sunflower peptides); all transcript with one or more hits to peptides with a bitscore ≥ 90 and E value < 1e-6 were discarded as potential lncRNAs in (1). To determine if the transcripts had a blast hit with the draft of the sunflower genome, a threshold of bitscore ≥ 90 and E-value < 1e-6 was employed in (2). Only transcripts with a CPC score ≤ −1 and CPAT score ≤ 0.3 were considered as lncRNA by filters in (3). Venn diagrams: a) Expression of lncRNAs with significant similarity with the sunflower genome. b Expression of lncRNAs with no significant similarity with the sunflower genome. c Total number of lncRNAs detected
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Fig2: Bioinformatic pipeline to determine the lncRNA nature of transcripts and Venn diagrams with number of lncRNA expressed by genotype. Protein coding was determined by comparing transcripts with peptide databases (TAIR 10, NCBI RefSeq and sunflower peptides); all transcript with one or more hits to peptides with a bitscore ≥ 90 and E value < 1e-6 were discarded as potential lncRNAs in (1). To determine if the transcripts had a blast hit with the draft of the sunflower genome, a threshold of bitscore ≥ 90 and E-value < 1e-6 was employed in (2). Only transcripts with a CPC score ≤ −1 and CPAT score ≤ 0.3 were considered as lncRNA by filters in (3). Venn diagrams: a) Expression of lncRNAs with significant similarity with the sunflower genome. b Expression of lncRNAs with no significant similarity with the sunflower genome. c Total number of lncRNAs detected

Mentions: To test if the unidentified transcripts expressed in sunflower meiocytes were lncRNAs, we used the workflow described in Fig. 2. First, we excluded all 39,354 transcripts with protein coding potential using BLAST with protein databases (see Methods). For the remaining 34,304 unknown transcripts we performed a BLASTN search against the draft genome sequence compiled by the Sunflower Genome Project (in progress for the inbred line HA412). Among these transcripts, 90.88 % had a BLAST hit that was more than 90 % identical to the genome draft. This result suggests that most of these sequences were indeed sunflower transcripts and not assembly artifacts. On the other hand, discarding the transcripts that lacked a genome hit would be unwise, as they may be products of RNA processing or genotype-specific sequences. Thus, we tested both unknown transcripts (with and without genome hit), for their protein coding potential with two different algorithms: CPC (Coding Protein Calculator) [36] and CPAT (Coding-Potential Assessment Tool) [37], and only those transcripts that passed the thresholds of both algorithms were classified as lncRNAs (See Methods). Given that the methods used by CPC and CPAT are complementary (CPC uses a support vector machine classifier, while CPAT employs a logistic regression model), the classification of sequences as lncRNA only when both algorithms concurred can be considered highly trustworthy (see “Additional discussion of lncRNA Identification” in Additional file 1).Fig. 2


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)

Bioinformatic pipeline to determine the lncRNA nature of transcripts and Venn diagrams with number of lncRNA expressed by genotype. Protein coding was determined by comparing transcripts with peptide databases (TAIR 10, NCBI RefSeq and sunflower peptides); all transcript with one or more hits to peptides with a bitscore ≥ 90 and E value < 1e-6 were discarded as potential lncRNAs in (1). To determine if the transcripts had a blast hit with the draft of the sunflower genome, a threshold of bitscore ≥ 90 and E-value < 1e-6 was employed in (2). Only transcripts with a CPC score ≤ −1 and CPAT score ≤ 0.3 were considered as lncRNA by filters in (3). Venn diagrams: a) Expression of lncRNAs with significant similarity with the sunflower genome. b Expression of lncRNAs with no significant similarity with the sunflower genome. c Total number of lncRNAs detected
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Bioinformatic pipeline to determine the lncRNA nature of transcripts and Venn diagrams with number of lncRNA expressed by genotype. Protein coding was determined by comparing transcripts with peptide databases (TAIR 10, NCBI RefSeq and sunflower peptides); all transcript with one or more hits to peptides with a bitscore ≥ 90 and E value < 1e-6 were discarded as potential lncRNAs in (1). To determine if the transcripts had a blast hit with the draft of the sunflower genome, a threshold of bitscore ≥ 90 and E-value < 1e-6 was employed in (2). Only transcripts with a CPC score ≤ −1 and CPAT score ≤ 0.3 were considered as lncRNA by filters in (3). Venn diagrams: a) Expression of lncRNAs with significant similarity with the sunflower genome. b Expression of lncRNAs with no significant similarity with the sunflower genome. c Total number of lncRNAs detected
Mentions: To test if the unidentified transcripts expressed in sunflower meiocytes were lncRNAs, we used the workflow described in Fig. 2. First, we excluded all 39,354 transcripts with protein coding potential using BLAST with protein databases (see Methods). For the remaining 34,304 unknown transcripts we performed a BLASTN search against the draft genome sequence compiled by the Sunflower Genome Project (in progress for the inbred line HA412). Among these transcripts, 90.88 % had a BLAST hit that was more than 90 % identical to the genome draft. This result suggests that most of these sequences were indeed sunflower transcripts and not assembly artifacts. On the other hand, discarding the transcripts that lacked a genome hit would be unwise, as they may be products of RNA processing or genotype-specific sequences. Thus, we tested both unknown transcripts (with and without genome hit), for their protein coding potential with two different algorithms: CPC (Coding Protein Calculator) [36] and CPAT (Coding-Potential Assessment Tool) [37], and only those transcripts that passed the thresholds of both algorithms were classified as lncRNAs (See Methods). Given that the methods used by CPC and CPAT are complementary (CPC uses a support vector machine classifier, while CPAT employs a logistic regression model), the classification of sequences as lncRNA only when both algorithms concurred can be considered highly trustworthy (see “Additional discussion of lncRNA Identification” in Additional file 1).Fig. 2

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.


Related in: MedlinePlus