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

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.

The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

“…Reverse transcription was conducted with a Reverse Transcription System (Promega, USA). The extracted RNA was treated with RNase-free DNase I for 30 minutes at 37°C to remove residual DNA, as described previously [ 33 ], and then, the pooled libraries were sequenced using the BGISEQ-500 platform with short 100PE reads. When preprocessing the transcriptomic data, adaptor sequences and low-quality reads were filtered using SOAPnuke (version 1.5.6) [ 34 ] with the following parameters: “-n 0.001 -l 20 -q 0.4 -Q 2.” The clean reads of all samples were assembled using Trinity (version 2.0.6) [ 35 ] with the following parameters: (1) group_pairs_distance 500, (2) min_contig_length 200, (3) min_kmer_cov 2, (4) min_glue 2, (5) bfly_opts -V 5, (6) edge-thr = 0.1, (7) stderr, and (8) SS_lib_type RF.…”

Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

“…RNA was reverse transcribed using a reverse transcription system (Promega, Madison, WI, United States). As described previously (Zhao et al, 2017a), the extracted RNA was treated with RNase-free DNase I for 30 min at 37 • C to remove residual DNA before reverse transcription. The pooled libraries were then sequenced using a BGISEQ-500 platform (Beijing Genomics Institute, Shenzhen, China), with 100-bp paired-end reads.…”

“…The pooled libraries were then sequenced using a BGISEQ-500 platform (Beijing Genomics Institute, Shenzhen, China), with 100-bp paired-end reads. Furthermore, four additional in-house samples of cirri were collected from D. jenkinsiana, which had previously been sequenced by RNA-seq (Zhao et al, 2017a). Thus, a total of 24 and 36 in-house transcriptome datasets, covering different developmental stages of cirri, were processed for C. simplicifolius and D. jenkinsiana, respectively.…”

“…They are characterized by whiplike cirri containing hooks and grapnels that assist in climbing and development in a forest environment (Raj et al, 2014). However, in most cases, this makes it difficult to cultivate, manage, and harvest rattan, resulting in the high cost of rattan products (Zhao et al, 2017a). The genetic regulatory mechanism of cirrus formation is thus of great concern.…”

Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs

“…For instance, MYB1 [ 35 ] and MYB4 [ 36 ] in Pinus taeda L. and MYB2 [ 37 ] in Eucalyptus grandis can bind to the AC element in the promoter region of the lignin biosynthesis genes and have been shown to regulate the pathway. However, few studies have explored NAC and MYB in regulating lignin biosynthesis pathways in the rattan [ 38 ].…”