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

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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.


Clustering analysis of differentially expressed genes (DEGs).(a) Hierarchical clustering of DEGs. (b) Clustering of DEGs based on their expression patterns.
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f5: Clustering analysis of differentially expressed genes (DEGs).(a) Hierarchical clustering of DEGs. (b) Clustering of DEGs based on their expression patterns.

Mentions: To further investigate gene expression profiles, we performed hierarchical clustering of all DEGs using the Euclidean distance method and complete linkage (Fig. 5a, b). Twenty clusters were plotted with distinctive expression patterns. Subclusters 1 and 6 containing 4,623 and 4,485 genes, respectively, possessed most of the DEGs, and the genes in the two clusters had similar expression patterns. Subclusters 4, 10, and 17 were characterised by peak expression in AII, and most of these genes were only expressed in A, indicating that the development stages were associated with specific gene clusters. Subcluster 13 included 255 genes that were progressively upregulated in both genotypes from stage I to IV, and the expression level of these genes in A was lower than in S. Most of the genes in subclusters 14, 15, and 16 were downregulated in both genotypes at later developmental stages, and the expression level in S was higher than in A.


Diplosporous development in Boehmeria tricuspis : Insights from de novo transcriptome assembly and comprehensive expression profiling
Clustering analysis of differentially expressed genes (DEGs).(a) Hierarchical clustering of DEGs. (b) Clustering of DEGs based on their expression patterns.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Clustering analysis of differentially expressed genes (DEGs).(a) Hierarchical clustering of DEGs. (b) Clustering of DEGs based on their expression patterns.
Mentions: To further investigate gene expression profiles, we performed hierarchical clustering of all DEGs using the Euclidean distance method and complete linkage (Fig. 5a, b). Twenty clusters were plotted with distinctive expression patterns. Subclusters 1 and 6 containing 4,623 and 4,485 genes, respectively, possessed most of the DEGs, and the genes in the two clusters had similar expression patterns. Subclusters 4, 10, and 17 were characterised by peak expression in AII, and most of these genes were only expressed in A, indicating that the development stages were associated with specific gene clusters. Subcluster 13 included 255 genes that were progressively upregulated in both genotypes from stage I to IV, and the expression level of these genes in A was lower than in S. Most of the genes in subclusters 14, 15, and 16 were downregulated in both genotypes at later developmental stages, and the expression level in S was higher than in A.

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.