De novo sequencing, assembly, and analysis of the Taxodium‘Zhongshansa’ roots and shoots transcriptome in response to short-term waterlogging

Abstract

BackgroundTaxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further exploration of its underlying flood-tolerance mechanism. Taxodium ‘Zhongshansa’ is an interspecies hybrid of T. distichum and T. mucronatum, and has been widely planted in southeastern China. To understand the genetic basis of its flood tolerance, we analyzed the transcriptomes of Taxodium ‘Zhongshansa’ roots and shoots in response to short-term waterlogging.ResultsRNA-seq was used to analyze genome-wide transcriptome changes of Taxodium ‘Zhongshansa 406’ clone root and shoot treated with 1 h of soil-waterlogging stress. After de novo assembly, 108,692 unigenes were achieved, and 70,260 (64.64%) of them were annotated. There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected. Under waterlogging stress, the primary reaction of hypoxic-treated root was to activate the antioxidative defense system to prevent cells experiencing reactive oxygen species (ROS) poisoning. As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant. The glycolysis and fermentation pathway was activated to maintain ATP production in the hypoxic root. Constantly, the demand for carbohydrates increased, and carbohydrate metabolism were accumulated in the root as well as the shoot, possibly indicating that systemic communications between waterlogged and non-waterlogged tissues facilated survival. Amino acid metabolism was also greatly influenced, with down-regulation of genes involvedin serine degradation and up-regulation of aspartic acid degradation. Additionally, a non-symbiotic hemoglobin class 1 gene was up-regulated, which may also help the ATP production. Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.ConclusionsWe conclude that ROS detoxification and energy maintenance were the primary coping mechanisms of ‘Zhongshansa’ in surviving oxygen deficiency, which may be responsible for its remarkable waterlogging tolerance. Our study not only provided the first large-scale assessment of genomic resources of Taxodium but also guidelines for probing the molecular mechanism underlying ‘Zhongshansa’ waterlogging tolerance.

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

“…In the transcriptome of T. 'zhongshansa', 143,636 transcripts with a total of 106.3 Mb were assembled, of which 31,665 were long transcripts (≥1 kb). Besides, the mean length and N50 length of all transcripts in Taxodium transcriptome were 740 and 1324 bp, respectively, (Qi et al 2014). Compared with the transcriptomes of pepper (Ashrafi et al 2012) and seashore paspalum (Jia et al 2015), the In addition to the quality of transcriptome, the frequency and density of SSRs were also affected by the search criteria set to identify SSRs, SSR search tools, datasets for the database mining, and the nature of species (Durand et al 2010).…”

“…The genus Taxodium is well known for its extreme tolerance to waterlogging, thus having great ecological and economic potential (Qi et al 2014). Taxodium 'zhongshansa' are interspecies hybrid clones generated from three Taxodium species, Taxodium mucronatum, Taxodium distichum, and Taxodium ascendens (Yu et al 2011).…”

“…The transcriptome data of 'zhongshansa 406' were obtained by Illumina sequencing (Qi et al 2014). MIcroSAtellite (MISA) was used to detect SSR loci in the ESTs (Thiel et al 2003), and Primer3.0 was used for designing primers to amplify EST-SSR molecular markers (Cardle et al 2000).…”

Cultural Extension Of Taxodium In The Territory Of Slovakia And Its Genetic-Genomical Notes

“…Druh Taxodium je známy svojou významnou toleranciou voči stresu zavodnenia, z čoho vyplýva jeho veľký ekologický a ekonomický potenciál (Qi et al, 2014). Taxodium, patrí do čeľade Taxodiaceaetisovcovité (Mareček et al, 2001).…”

“…Neznáša zatienenie, znečistené ovzdušie znáša dobre (Hieke, 2008;Mareček et al, 2001). Napriek výraznému ekologickému a ekonomickému potenciálu, genomické informácie tohto druhu sú limitované, čo značne spomaľuje tvorbu molekulových markérov a ďalšie poznávanie mechanizmov tolerancie daného druhu voči podmienkam zamokrenia (Qi et al, 2014).…”