The Full-Length Transcriptome of Spartina alterniflora Reveals the Complexity of High Salt Tolerance in Monocotyledonous Halophyte

Abstract Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.

Download Full-text

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

10.1101/680819 ◽

2019 ◽

Cited By ~ 2

Author(s):

Wenbin Ye ◽

Taotao Wang ◽

Wei Wei ◽

Shuaitong Lou ◽

Faxiu Lan ◽

...

Keyword(s):

Gene Expression ◽

Salt Stress ◽

Alternative Splicing ◽

Salt Tolerance ◽

Protein Kinases ◽

Spartina Alterniflora ◽

High Salt ◽

Full Length ◽

Salt Tolerant ◽

High Salt Tolerance

ABSTRACTSpartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used PacBio full-length single molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt-gradient experiments (0, 350, 500 and 800 mM NaCl). We systematically analyzed the gene expression diversity and deciphered possible roles of ion transporters, protein kinases and photosynthesis in salt tolerance. Moreover, the co-expression network analysis revealed several hub genes in salt stress regulatory networks, including protein kinases such as SaOST1, SaCIPK10 and three SaLRRs. Furthermore, high salt stress affected the gene expression of photosynthesis through down-regulation at the transcription level and alternative splicing at the post-transcriptional level. In addition, overexpression of two Spartina salt-tolerant genes SaHSP70-I and SaAF2 in Arabidopsis significantly promoted the salt tolerance of transgenic lines. Finally, we built the SAPacBio website for visualizing the full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes, and alternative splicing events in Spartina. Overall, this study sheds light on the high salt tolerance mechanisms of monocotyledonous-halophyte and demonstrates the potential of Spartina genes for engineering salt-tolerant plants.

Download Full-text

A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis

10.1101/2020.09.30.320101 ◽

2020 ◽

Author(s):

Wei Zhou ◽

Yaxing Zhou ◽

Guoli Zhu ◽

Yun Wang ◽

Zhibiao He ◽

...

Keyword(s):

Transcription Factors ◽

Comparative Analysis ◽

Alternative Splicing ◽

Rna Sequencing ◽

Transcriptome Sequencing ◽

Full Length ◽

Transcriptional Analysis ◽

Sequencing Analysis ◽

Short Read ◽

Alternative Splicing Events

AbstractBackground and ObjectivesCastor (Ricinus communis L.) is an important non-edible oilseed crop. Lm type female strains and normal amphiprotic strains are important castor cultivars, and are mainly different in inflorescence structures and leaf shapes. To better understand the mechanisums underling these differences at the molecular level, we performed comparative transcriptional analysis.Materials and MethodsFull-length transcriptome sequencing and short-read RNA sequencing were employed.ResultsA total of 76,068 and 44,223 non-redundant transcripts were obtained from high-quality transcripts of Lm type female strains and normal amphiprotic strains, respectively. In Lm female strain and normal amphiprotic strains 51,613 and 20,152 alternative splicing events were found, respectively. There were 13,239 transcription factors identified from the full-length transcriptomes. Comparative analysis showed great different gene expression of common and unique transcription factors between the two cultivars. Meanwhile, functional analysis of isoform was conducted. Full-length sequences were used as a reference genome, and short-read RNA sequencing analysis was performed to conduct differential gene analysis. Furthermore, the function of DEGs were performed to annotation analysis.ConclusionsThe results revealed considerable difference and expression diversity between two cultivars, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two cultivars.HighlightUsing the full-length transcriptome sequencing technology, we performed comparative analysis of transcription factors of two castor cultivars, analyzed alternative splicing events, and identified their lncRNAs.

Download Full-text

The influence of high salt stress on starch, sucrose and degradative enzymes of twoglycine maxvarieties that differ in salt tolerance

Journal of Plant Nutrition ◽

10.1080/01904168509363336 ◽

1985 ◽

Vol 8 (3) ◽

pp. 199-209 ◽

Cited By ~ 9

Author(s):

G. Rathert

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

High Salt ◽

Degradative Enzymes ◽

High Salt Stress

Download Full-text

Survival mechanism of a novel marine multistress-tolerant Meyerozyma guilliermondii GXDK6 under high NaCl stress as revealed by integrative omics analysis

10.1101/2021.06.28.450280 ◽

2021 ◽

Author(s):

Chengjian Jiang ◽

Xinghua Cai ◽

Huijie Sun ◽

Huashan Bai ◽

Yanyi Chen ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Inositol Phosphate ◽

High Salt ◽

Differentially Expressed ◽

Glycerol Metabolism ◽

Salt Tolerant ◽

Meyerozyma Guilliermondii ◽

Survival Mechanism ◽

High Salt Stress

A novel strain named Meyerozyma guilliermondii GXDK6 was provided in this work, which was confirmed to survive independently under high salt stress (12% NaCl) or co-stress condition of strong acid (pH 3.0) and high salts (10% NaCl) without sterilization. Its survival mechanism under high salt stress was revealed by integrated omics for the first time. Whole-genome analysis showed that 14 genes (e.g., GPD1 and FPS1) of GXDK6 relevant to salt tolerance were annotated and known to belong to various salt-resistant mechanisms (e.g., regulation of cell signal transduction and glycerol metabolism controls). Transcriptome sequencing results indicated that 1220 genes (accounting for 10.15%) of GXDK6 were differentially transcribed (p < 0.05) when GXDK6 growth was under 10% stress for 16 h, including important novel salt-tolerant-related genes (e.g., RTM1 and YHB1). Proteomics analysis demonstrated that 1005 proteins (accounting for 27.26%) of GXDK6 were differentially expressed (p < 0.05) when GXDK6 was stressed by 10% NaCl. Some of the differentially expressed proteins were defined as the novel salt-tolerant related proteins (e.g., sugar transporter STL1 and NADPH-dependent methylglyoxal reductase). Metabolomic analysis results showed that 63 types of metabolites (e.g., D-mannose, glycerol and inositol phosphate) of GXDK6 were up- or downregulated when stressed by 10% NaCl. Among them, D-mannose is one of the important metabolites that could enhance the salt-tolerance survival of GXDK6.

Download Full-text

OsNAC45 is Involved in ABA Response and Salt Tolerance in Rice

Rice ◽

10.1186/s12284-020-00440-1 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Xiang Zhang ◽

Yan Long ◽

Jingjing Huang ◽

Jixing Xia

Keyword(s):

Transcription Factors ◽

Salt Stress ◽

Salt Tolerance ◽

Stress Responses ◽

Crop Yields ◽

Plant Stress ◽

Root Cells ◽

Nac Transcription Factors ◽

Rice Plants ◽

Plant Stress Responses

Abstract Background Salt stress threatens crop yields all over the world. Many NAC transcription factors have been reported to be involved in different abiotic stress responses, but it remains unclear how loss of these transcription factors alters the transcriptomes of plants. Previous reports have demonstrated that overexpression of OsNAC45 enhances salt and drought tolerance in rice, and that OsNAC45 may regulate the expression of two specific genes, OsPM1 and OsLEA3–1. Results Here, we found that ABA repressed, and NaCl promoted, the expression of OsNAC45 in roots. Immunostaining showed that OsNAC45 was localized in all root cells and was mainly expressed in the stele. Loss of OsNAC45 decreased the sensitivity of rice plants to ABA and over-expressing this gene had the opposite effect, which demonstrated that OsNAC45 played an important role during ABA signal responses. Knockout of OsNAC45 also resulted in more ROS accumulation in roots and increased sensitivity of rice to salt stress. Transcriptome sequencing assay found that thousands of genes were differently expressed in OsNAC45-knockout plants. Most of the down-regulated genes participated in plant stress responses. Quantitative real time RT-PCR suggested that seven genes may be regulated by OsNAC45 including OsCYP89G1, OsDREB1F, OsEREBP2, OsERF104, OsPM1, OsSAMDC2, and OsSIK1. Conclusions These results indicate that OsNAC45 plays vital roles in ABA signal responses and salt tolerance in rice. Further characterization of this gene may help us understand ABA signal pathway and breed rice plants that are more tolerant to salt stress.

Download Full-text

Study on Stress Resistance of n-Hexadecane Degrading Bacteria under High Salt Stress

Proceedings of the 2019 9th International Conference on Biomedical Engineering and Technology - ICBET' 19 ◽

10.1145/3326172.3326173 ◽

2019 ◽

Author(s):

Shaojun Zhang ◽

Mingyu Wang ◽

Chunxiao Jiang ◽

Enrui Zhao ◽

Jianqiang Shi

Keyword(s):

Salt Stress ◽

Stress Resistance ◽

High Salt ◽

Degrading Bacteria ◽

High Salt Stress

Download Full-text

Transcriptomic Analysis of Betula halophila in Response to Salt Stress

International Journal of Molecular Sciences ◽

10.3390/ijms19113412 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3412 ◽

Cited By ~ 10

Author(s):

Fenjuan Shao ◽

Lisha Zhang ◽

Iain Wilson ◽

Deyou Qiu

Keyword(s):

Cell Wall ◽

Salt Stress ◽

Salt Tolerance ◽

Expression Patterns ◽

Soil Salinization ◽

Sphingolipid Metabolism ◽

Sequencing Platform ◽

Resistant Varieties ◽

High Salt Tolerance ◽

Salt Overly Sensitive

Soil salinization is a matter of concern worldwide. It can eventually lead to the desertification of land and severely damage local agricultural production and the ecological environment. Betula halophila is a tree with high salt tolerance, so it is of importance to understand and discover the salt responsive genes of B. halophila for breeding salinity resistant varieties of trees. However, there is no report on the transcriptome in response to salt stress in B. halophila. Using Illumina sequencing platform, approximately 460 M raw reads were generated and assembled into 117,091 unigenes. Among these unigenes, 64,551 unigenes (55.12%) were annotated with gene descriptions, while the other 44.88% were unknown. 168 up-regulated genes and 351 down-regulated genes were identified, respectively. These Differentially Expressed Genes (DEGs) involved in multiple pathways including the Salt Overly Sensitive (SOS) pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. The gene ontology (GO) enrichments suggested that the DEGs were mainly involved in a plant-type cell wall organization biological process, cell wall cellular component, and structural constituent of cell wall molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that the top-four enriched pathways were ‘Fatty acid elongation’, ‘Ribosome’, ‘Sphingolipid metabolism’ and ‘Flavonoid biosynthesis’. The expression patterns of sixteen DEGs were analyzed by qRT-PCR to verify the RNA-seq data. Among them, the transcription factor AT-Hook Motif Nuclear Localized gene and dehydrins might play an important role in response to salt stress in B. halophila. Our results provide an important gene resource to breed salt tolerant plants and useful information for further elucidation of the molecular mechanism of salt tolerance in B. halophila.

Download Full-text