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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.


Venn diagrams showing overlap of differentially expressed genes (DEGs) between different developmental stages.(a) Venn diagram of DEGs between sexual and apomictic Boehmeria tricuspis at particular stages. (b) Venn diagram of DEGs in sexual B. tricuspis at four stages. (c) Venn diagram of DEGs in apomictic B. tricuspis at four stages. (d) Number of DEGs identified in sexual and apomictic B. tricuspis.
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f4: Venn diagrams showing overlap of differentially expressed genes (DEGs) between different developmental stages.(a) Venn diagram of DEGs between sexual and apomictic Boehmeria tricuspis at particular stages. (b) Venn diagram of DEGs in sexual B. tricuspis at four stages. (c) Venn diagram of DEGs in apomictic B. tricuspis at four stages. (d) Number of DEGs identified in sexual and apomictic B. tricuspis.

Mentions: The normalised expression level (expected number of fragments per kilobase of transcript sequence per millions of base pairs sequenced, FPKMs) of each transcript was estimated in all the analysed samples. To characterise the developmental events of gene expression profiles, differences in gene expression at four stages during floral development in two genotypes were examined by comparing normalised expression values. Differentially expressed genes (DEGs) were identified by pairwise comparisons of different stages in the same genotype and of the same stages between different genotypes (Table 2). The number of DEGs detected in same-stage comparisons between the two genotypes was generally higher than that detected from same-genotype comparisons at different stages. Comparisons of different genotypes at the four stages identified 4,594 DEGs for AI vs. SI, 7,630 for AII vs. SII, 3,836 for AIII vs. SIII, and 4,674 for AIV vs. SIV. Additionally, different stages had specific DEGs: 2,358 in stage I, 4,119 in II, 753 in III, and 1,300 in IV (Fig. 4a). Comparisons of the four stages in S identified 1,732, 633, and 188 DEGs between SI and SII, SII and SIII, and SIII and SIV, respectively (Fig. 4b). Comparisons of the four stages in A identified 7,052, 257, and 2,210 DEGs between AI and AII, AII and AIII, and AIII and AIV, respectively (Fig. 4c). In total, 18,899 genes were differentially expressed in A and S at the four stages. Of these DEGs, 15,482 were differentially expressed in both genotypes during ovule development, whereas 2949 and 468 genes were differentially expressed in A and S, respectively (Fig. 4d).


Diplosporous development in Boehmeria tricuspis : Insights from de novo transcriptome assembly and comprehensive expression profiling
Venn diagrams showing overlap of differentially expressed genes (DEGs) between different developmental stages.(a) Venn diagram of DEGs between sexual and apomictic Boehmeria tricuspis at particular stages. (b) Venn diagram of DEGs in sexual B. tricuspis at four stages. (c) Venn diagram of DEGs in apomictic B. tricuspis at four stages. (d) Number of DEGs identified in sexual and apomictic B. tricuspis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Venn diagrams showing overlap of differentially expressed genes (DEGs) between different developmental stages.(a) Venn diagram of DEGs between sexual and apomictic Boehmeria tricuspis at particular stages. (b) Venn diagram of DEGs in sexual B. tricuspis at four stages. (c) Venn diagram of DEGs in apomictic B. tricuspis at four stages. (d) Number of DEGs identified in sexual and apomictic B. tricuspis.
Mentions: The normalised expression level (expected number of fragments per kilobase of transcript sequence per millions of base pairs sequenced, FPKMs) of each transcript was estimated in all the analysed samples. To characterise the developmental events of gene expression profiles, differences in gene expression at four stages during floral development in two genotypes were examined by comparing normalised expression values. Differentially expressed genes (DEGs) were identified by pairwise comparisons of different stages in the same genotype and of the same stages between different genotypes (Table 2). The number of DEGs detected in same-stage comparisons between the two genotypes was generally higher than that detected from same-genotype comparisons at different stages. Comparisons of different genotypes at the four stages identified 4,594 DEGs for AI vs. SI, 7,630 for AII vs. SII, 3,836 for AIII vs. SIII, and 4,674 for AIV vs. SIV. Additionally, different stages had specific DEGs: 2,358 in stage I, 4,119 in II, 753 in III, and 1,300 in IV (Fig. 4a). Comparisons of the four stages in S identified 1,732, 633, and 188 DEGs between SI and SII, SII and SIII, and SIII and SIV, respectively (Fig. 4b). Comparisons of the four stages in A identified 7,052, 257, and 2,210 DEGs between AI and AII, AII and AIII, and AIII and AIV, respectively (Fig. 4c). In total, 18,899 genes were differentially expressed in A and S at the four stages. Of these DEGs, 15,482 were differentially expressed in both genotypes during ovule development, whereas 2949 and 468 genes were differentially expressed in A and S, respectively (Fig. 4d).

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.