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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.


The Venn diagram of the DEG results.Up and Down represents up-regulated genes and down-regulated genes, respectively.
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f2: The Venn diagram of the DEG results.Up and Down represents up-regulated genes and down-regulated genes, respectively.

Mentions: To deeply explore the key genes in cirrus development of rattan, we have identified some DEGs in the cirrus and hook during the developmental stages of D. jenkinsiana (see Supplementary Fig. S3c and Table S14–17). The results of the correlation analyses indicated that the replicates were significantly correlated, with the lowest correlation coefficient of 0.8747 observed in the CD sample (see Supplementary Fig. S3d). Moreover, 3,810 genes were identified as significantly enriched or depleted DEGs in the paired comparisons. Twenty-nine genes were up-regulated and 799 genes were down-regulated in the CI vs. CD comparison, whereas 772 genes were up-regulated and 2,210 genes were down-regulated in the HI vs. HD comparison (Fig. 2).


Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan ( Daemonorops jenkinsiana )
The Venn diagram of the DEG results.Up and Down represents up-regulated genes and down-regulated genes, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: The Venn diagram of the DEG results.Up and Down represents up-regulated genes and down-regulated genes, respectively.
Mentions: To deeply explore the key genes in cirrus development of rattan, we have identified some DEGs in the cirrus and hook during the developmental stages of D. jenkinsiana (see Supplementary Fig. S3c and Table S14–17). The results of the correlation analyses indicated that the replicates were significantly correlated, with the lowest correlation coefficient of 0.8747 observed in the CD sample (see Supplementary Fig. S3d). Moreover, 3,810 genes were identified as significantly enriched or depleted DEGs in the paired comparisons. Twenty-nine genes were up-regulated and 799 genes were down-regulated in the CI vs. CD comparison, whereas 772 genes were up-regulated and 2,210 genes were down-regulated in the HI vs. HD comparison (Fig. 2).

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.