Transcriptome analysis of the Taxodium ‘Zhongshanshan 405’ roots in response to salinity stress

Yu, Chang Yeon; Xu, Sheng; Yin, Yongguang

doi:10.1016/j.plaphy.2016.01.009

Cited by 34 publications

(37 citation statements)

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“…Poly (A) mRNA was enriched referring to the previous method (Yu et al, 2016) by using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and fragmented to short pieces. These short fragments were as applied as the templates for cDNA.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

Wang

et al. 2017

Front. Plant Sci.

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Lycoris aurea, a medicinal species of the Amaryllidaceae family, is used in the practice of traditional Chinese medicine (TCM) because of its broad pharmacological activities of Amaryllidaceae alkaloids. Despite the officinal and economic importance of Lycoris species, the secondary mechanism for this species is relatively deficient. In this study, we attempted to characterize the transcriptome profiling of L. aurea seedlings with the methyl jasmonate (MeJA) treatment to uncover the molecular mechanisms regulating plant secondary metabolite pathway. By using short reads sequencing technology (Illumina), two sequencing cDNA libraries prepared from control (Con) and 100 μM MeJA-treated (MJ100) samples were sequenced. A total of 26,809,842 and 25,874,478 clean reads in the Con and MJ100 libraries, respectively, were obtained and assembled into 59,643 unigenes. Among them, 41,585 (69.72%) unigenes were annotated by basic local alignment search tool similarity searches against public sequence databases. These included 55 Gene Ontology (GO) terms, 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups (COG) families. Additionally, 4,175 differentially expressed genes (DEGs; false discovery rate ≤ 0.001 and |log2 Ratio| ≥ 1) with 2,291 up-regulated and 1,884 down-regulated, were found to be affected significantly under MeJA treatment. Subsequently, the DEGs encoding key enzymes involving in the secondary metabolite biosynthetic pathways, transcription factors, and transporter proteins were also analyzed and summarized. Meanwhile, we confirmed the altered expression levels of the unigenes that encode transporters and transcription factors using quantitative real-time PCR (qRT-PCR). With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of L. aurea may be improved. Additionally, the genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of L. aurea.

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Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

Wang

et al. 2017

Front. Plant Sci.

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“…The unigene sequences of Taxodium 'Zhongshanshan' were derived from the previously determined salinity stress transcriptome (Yu et al, 2016), short-term waterlogging transcriptome (Qi et al, 2014), and adventitious roots transcriptome (Wang et al, 2019). Hidden Markov Model (HMM) profiles (PF00069, PF01453, PF00139, PF00059), which correspond to kinase, G-type lectin, L-type lectin, and C-type lectin domains, respectively, were downloaded from the Pfam database (http://pfam.xfam.org/) (El-Gebali et al, 2019).…”

Section: Identification Of Thzlecrlk Sequencesmentioning

confidence: 99%

“…For ThzLecRLK gene expression analysis, RNA-seq data of different tissues and treatments of Taxodium 'Zhongshanshan' were obtained from the pre-laboratory development of the stress transcriptome (Yu et al, 2016) and short-term waterlogging transcriptome (Qi et al, 2014). The waterlogging stress related transcriptome analysis included four groups of data: the untreated root, the untreated stem, the root after one hour of soil waterlogging, and the stem after one hour of soil waterlogging.…”

Section: Transcriptional Profile Analysismentioning

confidence: 99%

“…Taxodium 'Zhongshanshan' has been found to show strong adaptability in China, and is now widely used for wetland ecological restoration, coastal shelter forest construction, saline-alkali land afforestation, urban and rural afforestation, and farmland forest networks (Changxiao et al, 2005), offering great landscaping and ecological values. Recently, exploring the stress resistance of Taxodium at the molecular level has become a research focus (Yu et al, 2016;Fan et al, 2018;Wang et al, 2017;Qi et al, 2014). Because of their inability to move, plant can only passively withstand changes in the external environment and various stimuli.…”

Section: Introductionmentioning

confidence: 99%

“…Conifers are rarely reported due to the lack of genomic information. With the development of high-throughput sequencing technology, the transcriptome of Taxodium has been published (Qi et al, 2014;Yu et al, 2016;Wang et al, 2019), which has laid a foundation for the identification of large gene families. Here, we conducted a comprehensive bioinformatics analysis of ThzLecRLK gene family based on transcriptome data and analyzed the expression of 15 representative LecRLKs in different tissues and under various stressors.…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #2 of "Identification and functional analysis of LecRLK genes in Taxodium ‘Zhongshanshan’ (v0.1)"

2019

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Background. Lectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported. Methods. Putative LecRLK genes were identified in the transcriptome of Taxodium 'Zhongshanshan.' The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes as well as co-expressed genes were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions. Results. In total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of Land C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups. Conclusions. This is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium.

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Effects of cadmium stress on the antioxidant system and chlorophyll fluorescence characteristics of two Taxodium clones

et al. 2018

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The T.118 and T.406 seedlings showed strong adaptability under Cd concentrations ≤ 50 µM. The mechanisms of photoprotection in T.118 and T.406 differed in high-Cd concentrations. To explore the physiological response characteristics of Taxodium hybrids to cadmium (Cd) stress and provide basis for screening of Cd-tolerant species, the hydroponic cultivation of T.118 and T.406 seedlings was conducted to demonstrate the effects of Cd stress on seedling growth, antioxidant system, and chlorophyll fluorescence parameters. After 35 days of Cd stress at a concentration ≤ 50 µM, the dry weight biomass of the two clones did not significantly differ from that of the control. T.406 exhibited a significant increase in POD activity compared to T.118 and maintained high SOD activity after exposure to high concentrations of Cd, whereas MDA levels showed little changes. Under low-Cd stress, chlorophyll content and fluorescence parameters remained stable, especially for T.406. Under high-Cd concentration stress, the above parameters were lower than the control, with a more significant decrease in T.118 than in T.406. The non-photochemical quenching coefficient (NPQ) of both clones increased with increasing Cd concentration. T.118 showed a greater increase than T.406, particularly under high-Cd concentration stress. The T.118 and T.406 seedlings adapted to low-Cd concentration stress by enhancing their antioxidant enzyme activity to maintain the balance of reactive oxygen metabolism and reduce cellular damage. The photochemical activity of mesophyll cells remained high to maintain photosynthetic capacity and normal seedling growth. T.406 showed stronger resistance to Cd than T.118. T.406 prevented photodamage by promoting the photochemical utilization of the excitation energy and maintaining a strong antioxidant stress ability. Enhancement of heat dissipation capability may be the main photoprotection mechanism of T.118.

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Transcriptome analysis of the Taxodium ‘Zhongshanshan 405’ roots in response to salinity stress

Cited by 34 publications

References 38 publications

Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

Peer Review #2 of "Identification and functional analysis of LecRLK genes in Taxodium ‘Zhongshanshan’ (v0.1)"

Effects of cadmium stress on the antioxidant system and chlorophyll fluorescence characteristics of two Taxodium clones

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