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Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan ( Daemonorops jenkinsiana )

View Article: PubMed Central - PubMed

ABSTRACT

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

No MeSH data available.


Cluster analysis of the expressed genes in D. jenkinsiana.The six groups were identified via the average log2(FPKM + 1) value. The number of genes in each group is shown in brackets. The significant GO terms are depicted based on the three GO categories, and the significant KEGG pathways are illustrated. A: CI sample; B: CD sample; C: HI sample; and D: HD sample. 1: replicate 1; 2: replicate 2. BP: biological process, CC: cellular component, MF: molecular function, and PW: KEGG pathway.
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f4: Cluster analysis of the expressed genes in D. jenkinsiana.The six groups were identified via the average log2(FPKM + 1) value. The number of genes in each group is shown in brackets. The significant GO terms are depicted based on the three GO categories, and the significant KEGG pathways are illustrated. A: CI sample; B: CD sample; C: HI sample; and D: HD sample. 1: replicate 1; 2: replicate 2. BP: biological process, CC: cellular component, MF: molecular function, and PW: KEGG pathway.

Mentions: We assumed that the same patterns contained similar trends of expressed genes, indicating that these genes may participate in similar or related biological processes. To properly classify the groups of different functional DEGs in further analysis, we performed a clustering analysis based on the DEG expression patterns (see Method and Supplementary Fig. S5). The results indicated all DEGs were clustered into 6 groups, with the gene numbers within the clusters ranging from 32 to 1,006. As shown in Fig. 4, expressed genes of the six groups shared differentially expressed patterns according to the clustering results. The GO term enrichment analyses were also performed using all of the expressed genes as the background to explore the significant GO terms for the expressed genes. The results indicated that certain expressed genes were highly enriched in the cytoskeleton- and actin-related terms for cluster 1 and the transferase- and structure-related terms in the molecular function category of clusters 2 and 3, respectively. In cluster 4, photosynthesis-related terms, such as ‘photosynthesis (GO:0015979)’, ‘thylakoid (GO:0009579)’, and ‘chlorophyll binding (GO:0016168)’, were abundant and reached statistical significance (adjusted p-value < 0.05) in the biological processes, cellular components and molecular functions categories. The related GO terms for the cell wall were enriched in cluster 5, including ‘cell wall (GO:0005618)’, and ‘cell wall organization (GO:0071555)’. Furthermore, few or no significant GO terms were identified in clusters 5 and 6 because the data were unable to meet the criteria of GO enrichment.


Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan ( Daemonorops jenkinsiana )
Cluster analysis of the expressed genes in D. jenkinsiana.The six groups were identified via the average log2(FPKM + 1) value. The number of genes in each group is shown in brackets. The significant GO terms are depicted based on the three GO categories, and the significant KEGG pathways are illustrated. A: CI sample; B: CD sample; C: HI sample; and D: HD sample. 1: replicate 1; 2: replicate 2. BP: biological process, CC: cellular component, MF: molecular function, and PW: KEGG pathway.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382692&req=5

f4: Cluster analysis of the expressed genes in D. jenkinsiana.The six groups were identified via the average log2(FPKM + 1) value. The number of genes in each group is shown in brackets. The significant GO terms are depicted based on the three GO categories, and the significant KEGG pathways are illustrated. A: CI sample; B: CD sample; C: HI sample; and D: HD sample. 1: replicate 1; 2: replicate 2. BP: biological process, CC: cellular component, MF: molecular function, and PW: KEGG pathway.
Mentions: We assumed that the same patterns contained similar trends of expressed genes, indicating that these genes may participate in similar or related biological processes. To properly classify the groups of different functional DEGs in further analysis, we performed a clustering analysis based on the DEG expression patterns (see Method and Supplementary Fig. S5). The results indicated all DEGs were clustered into 6 groups, with the gene numbers within the clusters ranging from 32 to 1,006. As shown in Fig. 4, expressed genes of the six groups shared differentially expressed patterns according to the clustering results. The GO term enrichment analyses were also performed using all of the expressed genes as the background to explore the significant GO terms for the expressed genes. The results indicated that certain expressed genes were highly enriched in the cytoskeleton- and actin-related terms for cluster 1 and the transferase- and structure-related terms in the molecular function category of clusters 2 and 3, respectively. In cluster 4, photosynthesis-related terms, such as ‘photosynthesis (GO:0015979)’, ‘thylakoid (GO:0009579)’, and ‘chlorophyll binding (GO:0016168)’, were abundant and reached statistical significance (adjusted p-value < 0.05) in the biological processes, cellular components and molecular functions categories. The related GO terms for the cell wall were enriched in cluster 5, including ‘cell wall (GO:0005618)’, and ‘cell wall organization (GO:0071555)’. Furthermore, few or no significant GO terms were identified in clusters 5 and 6 because the data were unable to meet the criteria of GO enrichment.

View Article: PubMed Central - PubMed

ABSTRACT

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

No MeSH data available.