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.
Highlights
The hooks and grapnels of the cirrus facilitate climbing and development in a forest environment; the numerous of them increase the difficulties of cultivating, managing and harvesting rattan
differentially expressed genes (DEGs) were identified through pair-wise comparisons among the cirri at different developmental stages and the significant DEGs involved in developmental pathways, cell wall metabolism, and hook formation were detected in the analysis of cirrus development
It was noted that we performed the experiment with two replications, not three replications and more, mainly because the low density in hook sample cannot construct high-quality library and it was difficult to collect the initial stage of cirrus in tropical rainforest
Summary
The hooks and grapnels of the cirrus facilitate climbing and development in a forest environment; the numerous of them increase the difficulties of cultivating, managing and harvesting rattan. Certain molecular markers, such as simple sequence repeats based on transcriptomic data, are crucial for assisting the taxonomic classification of rattan. We mainly performed transcriptomic sequencing and transcriptome-based de novo assembling on four samples of D. jenkinsiana from two tissues (cirrus and hook) at two growth stages (initial stage and developed stage) using the Illumina platform. The loci of microsatellites were identified based on the transcriptomic data, and the developed transcriptome-based SSR markers with polymorphisms were used for molecular marker assisted taxonomy for rattan. The data provided by these analyses may provide a fundamental resource for further experimental studies on the function of genes and regulated networks, and serve as an efficient tool when performing rattan taxonomic classifications
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