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Diplosporous development in Boehmeria tricuspis : Insights from de novo transcriptome assembly and comprehensive expression profiling

View Article: PubMed Central - PubMed

ABSTRACT

Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages. By classifying the transcripts into gene ontology categories of differentially expressed genes, we showed that differential plant hormone signal transduction, cell cycle regulation, and transcription factor regulation are possibly involved in apomictic development and/or a polyploidization response in B. tricuspis. Furthermore, we suggest that specific gene families are possibly related to apomixis and might have important effects on diplosporous floral development. These results make a notable contribution to our understanding of the molecular basis of diplosporous development in B. tricuspis.

No MeSH data available.


Heatmap showing expression profile of selected enriched GO terms and KEGG pathways of differentially expressed genes (DEGs).(a) The significances of the most represented GO-slims in each main comparison are indicated using log-transformed P-values (red). (b) The significances of the most represented KEGG pathways in each main comparison are indicated using log-transformed P-values (red).
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f6: Heatmap showing expression profile of selected enriched GO terms and KEGG pathways of differentially expressed genes (DEGs).(a) The significances of the most represented GO-slims in each main comparison are indicated using log-transformed P-values (red). (b) The significances of the most represented KEGG pathways in each main comparison are indicated using log-transformed P-values (red).

Mentions: We used GO assignments to classify DEG functions in pairwise comparisons of cDNA libraries between different genotypes and between different ovule developmental stages (see Supplementary Fig. S2). We selected 25 over-represented GO terms that were enriched in at least five comparisons to construct a heatmap showing expression profiles (Fig. 6a). No terms were significantly enriched in comparisons between AII and AIII, and only two were enriched for SIII vs. SIV. Genes in the categories of cell wall, cell wall organisation, external encapsulating structure organisation, carboxylic ester hydrolase activity, and pectinesterase activity were significantly enriched in eight pairwise comparisons. Four GO terms, pectinesterase activity, external encapsulating structure organisation, carboxylic ester hydrolase activity, and cell wall organisation, were significantly enriched in pairwise comparisons between the two genotypes at all four stages.


Diplosporous development in Boehmeria tricuspis : Insights from de novo transcriptome assembly and comprehensive expression profiling
Heatmap showing expression profile of selected enriched GO terms and KEGG pathways of differentially expressed genes (DEGs).(a) The significances of the most represented GO-slims in each main comparison are indicated using log-transformed P-values (red). (b) The significances of the most represented KEGG pathways in each main comparison are indicated using log-transformed P-values (red).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382578&req=5

f6: Heatmap showing expression profile of selected enriched GO terms and KEGG pathways of differentially expressed genes (DEGs).(a) The significances of the most represented GO-slims in each main comparison are indicated using log-transformed P-values (red). (b) The significances of the most represented KEGG pathways in each main comparison are indicated using log-transformed P-values (red).
Mentions: We used GO assignments to classify DEG functions in pairwise comparisons of cDNA libraries between different genotypes and between different ovule developmental stages (see Supplementary Fig. S2). We selected 25 over-represented GO terms that were enriched in at least five comparisons to construct a heatmap showing expression profiles (Fig. 6a). No terms were significantly enriched in comparisons between AII and AIII, and only two were enriched for SIII vs. SIV. Genes in the categories of cell wall, cell wall organisation, external encapsulating structure organisation, carboxylic ester hydrolase activity, and pectinesterase activity were significantly enriched in eight pairwise comparisons. Four GO terms, pectinesterase activity, external encapsulating structure organisation, carboxylic ester hydrolase activity, and cell wall organisation, were significantly enriched in pairwise comparisons between the two genotypes at all four stages.

View Article: PubMed Central - PubMed

ABSTRACT

Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages. By classifying the transcripts into gene ontology categories of differentially expressed genes, we showed that differential plant hormone signal transduction, cell cycle regulation, and transcription factor regulation are possibly involved in apomictic development and/or a polyploidization response in B. tricuspis. Furthermore, we suggest that specific gene families are possibly related to apomixis and might have important effects on diplosporous floral development. These results make a notable contribution to our understanding of the molecular basis of diplosporous development in B. tricuspis.

No MeSH data available.