De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Abstract

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

“…As shown in Table 1 , among the 1440 orthologous gene sets of Embryophyta, 90.8% (1308 BUSCOs) were “complete” BUSCO copies (including 504 (35.0%) single-copy and 804 (55.8%) duplicated), 4.5% (65 BUSCOs) were “fragmented”, and the remaining 4.7% (67 BUSCOs) were “missing” which shows the good quality of the assembled transcriptome. Organism distribution in the final transcriptome was searched through BLASTx and BLASTp, and Arabidopsis thaliana was identified as the species with the most homologous genes as R. stylosa that is consistent with the previous report for a close relative mangrove species, B. gymnorhiza [ 8 ] and different from what was reported for another Rhizophora species ( R. apiculata ) for which Medicago truncatula was assigned as the species with most homologous genes, however Arabidopsis thaliana was also found among the top species with high similarity [ 24 ] ( Figures S2 and S3, Tables S6–S9 ).…”

“…The assembled transcripts ranged from the 300 bp cut-off value to the maximum length of 13,191 bp. Most of the final transcripts ranged from 300–500 and 501–1000 bp, and the frequency of longer transcripts gradually decreased ( Figure S1 ), which is a common pattern reported for the transcriptome assemblies of other plant species as well [ 8 , 16 ].…”

“…The number of the retrieved unitranscripts and unigenes, the N50, the average and the maximum length of the transcripts were all higher than what has been reported so far for other mangrove species. In addition, the GC content of the assembled unitranscripts (41.44%) was in the same range as the other mangroves [ 8 , 24 ]. The mapping rate of the RNA-Seq reads to the final transcriptome indicated a high quality for the assembly, with the overall alignment rate of >94.02%, covering 96.46% of the reference sequences ( Table S5 ).…”

“…Salinity is one of the top and most challenging environmental stressors for plants, and it even leads to other chains of pressures such as osmotic and oxidative stress [ 3 , 4 ]. Many studies in different plant species have reported the changes in expression of salt tolerance genes in response to high salinity (e.g., [ 5 , 6 , 7 , 8 ]). As salt tolerant plants that encounter with constant daily fluctuation of salinity level caused by tidal oscillations, mangroves are a very good model system for studying gene expression changes under natural alteration of salt stress and may help to identify potential salt- and other abiotic-stress response genes [ 9 , 10 ].…”

“…Lira-Medeiros et al [ 11 ] reported an association between phenology of a mangrove tree ( Laguncularia racemosa ) and DNA methylation, where trees growing in salt marsh environment were strikingly smaller than the trees growing next to a river in freshwater. A recent transcriptome study has reported differential expression of stress-responsive genes between two populations of Bruguiera gymnorhiza in their natural environment as well [ 8 ]. In addition, an epigenetic study of the same species showed DNA hypermethylation in transposable elements (TEs) in B. gymnorhiza plants experiencing high-salinity stress, and suggested suppression of TEs in mangroves under high salt stress [ 12 ].…”