Transcriptome analysis of low phosphate stress response in the roots of masson pine (Pinus massoniana) seedlings

Abstract Background: Masson pine (Pinus massoniana) is primarily present within subtropical and tropical areas in China, and a number of these regions have a severe deficiency in inorganic phosphate (Pi). As a macronutrient, phosphorus plays a crucial role in plant development. Although several studies have studied the responses of masson pine to Pi starvation at the global level using RNA-Seq and comparative proteomic analyses, the detailed features in the roots that primarily respond to low Pi stress have not yet been studied. Results: This study examined the masson pine of the response of masson pine roots to a deficiency in Pi. Approximately 1,117 unigenes were shown to respond to Pi-deficiency by differential expression when analyzed using RNA-Seq. A total of 819 and 298 of these transcripts were up- and down-regulated, respectively. The results identified several phosphate transporters (PHT1, PHO88), ABC transporters and metal transporters. In particular, the ethylene response factor (ERF) was the most abundant transcription factor. Analyses of these genes, including gene ontology enrichment and the KEGG pathway analysis, indicated that the metabolic processes are the most enriched under abiotic stresses, including Pi-deficiency. Conclusions: This study provided abundant transcriptomic information to functionally dissect the response of masson pine roots to a deficiency of Pi, which will provide additional aid to elucidate the biological regulatory mechanisms that the pines use to respond to low Pi stress.

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

10.21203/rs.3.rs-16720/v1 ◽

2020 ◽

Author(s):

Fuhua Fan ◽

Xianwen Shang ◽

Guijie Ding ◽

Zijing Zhou ◽

Jianhui Tan

Keyword(s):

Differential Expression Analysis ◽

Differentially Expressed Gene ◽

Pinus Massoniana ◽

Dynamic Responses ◽

Masson Pine ◽

Pine Seedlings ◽

Low Pi Stress ◽

Pi Deficiency ◽

Abstract Background Masson pine ( Pinus massoniana ) is primarily present in subtropical and tropical areas of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, different tissues, especially the roots, that exhibit primary responses to low-Pi stress, have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi-deficient conditions. Results Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporters and nitrate transporters, reflecting the crosstalk between nitrate and Pi homeostasis in plants. The MYB family was the most abundant transcription factor family identified. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families, including novel miRNA families in Masson pine, were dramatically changed in response to Pi starvation. GO and KEGG analyses of these mRNAs and targets of miRNAs indicated that metabolic processes were most enriched under Pi deficiency. Conclusions This study provided abundant spatiotemporal transcriptomic information to functionally dissect the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

BMC Genomics ◽

10.1186/s12864-021-07481-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Pawel Sega ◽

Katarzyna Kruszka ◽

Dawid Bielewicz ◽

Wojciech Karlowski ◽

Przemyslaw Nuc ◽

...

Keyword(s):

Small Rnas ◽

Plant Stress ◽

Regulatory Elements ◽

Proximal Promoter ◽

Rna Seq ◽

Nutrient Mobilization ◽

Pi Starvation ◽

Low Pi Stress ◽

Abstract Background Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3′-5′ exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools. Conclusions Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

10.21203/rs.2.24665/v2 ◽

2020 ◽

Author(s):

Pawel Sega ◽

Katarzyna Kruszka ◽

Dawid Bielewicz ◽

Wojciech Karlowski ◽

Przemyslaw Nuc ◽

...

Keyword(s):

Small Rnas ◽

Plant Stress ◽

Regulatory Elements ◽

Proximal Promoter ◽

Rna Seq ◽

Nutrient Mobilization ◽

Pi Starvation ◽

Low Pi Stress ◽

Abstract Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms19072145 ◽

2018 ◽

Vol 19 (7) ◽

pp. 2145 ◽

Cited By ~ 6

Author(s):

Houqing Zeng ◽

Xiajun Zhang ◽

Xin Zhang ◽

Erxu Pi ◽

Liang Xiao ◽

...

Keyword(s):

Calcium Signaling ◽

Rna Sequencing ◽

Rna Seq ◽

Short Term ◽

Transcriptomic Response ◽

Low Pi Stress ◽

Soybean Leaves ◽

Pi Deprivation ◽

Low phosphate (Pi) availability is an important limiting factor affecting soybean production. However, the underlying molecular mechanisms responsible for low Pi stress response and tolerance remain largely unknown, especially for the early signaling events under low Pi stress. Here, a genome-wide transcriptomic analysis in soybean leaves treated with a short-term Pi-deprivation (24 h) was performed through high-throughput RNA sequencing (RNA-seq) technology. A total of 533 loci were found to be differentially expressed in response to Pi deprivation, including 36 mis-annotated loci and 32 novel loci. Among the differentially expressed genes (DEGs), 303 were induced and 230 were repressed by Pi deprivation. To validate the reliability of the RNA-seq data, 18 DEGs were randomly selected and analyzed by quantitative RT-PCR (reverse transcription polymerase chain reaction), which exhibited similar fold changes with RNA-seq. Enrichment analyses showed that 29 GO (Gene Ontology) terms and 8 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were significantly enriched in the up-regulated DEGs and 25 GO terms and 16 KEGG pathways were significantly enriched in the down-regulated DEGs. Some DEGs potentially involved in Pi sensing and signaling were up-regulated by short-term Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation and cell wall modification were affected at the early stage of Pi deprivation. The cis-elements of PHO (phosphatase) element, PHO-like element and P responsive element were present more frequently in promoter regions of up-regulated DEGs compared to that of randomly-selected genes in the soybean genome. Our transcriptomic data showed an intricate network containing transporters, transcription factors, kinases and phosphatases, hormone and calcium signaling components is involved in plant responses to early Pi deprivation.

Genetic diversity and population structure of masson pine (Pinus massoniana Lamb.) superior clones in South China as revealed by EST-SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01112-9 ◽

2021 ◽

Author(s):

Lina Mei ◽

Xiaopeng Wen ◽

Fuhua Fan ◽

Zhangqi Yang ◽

Weibin Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

South China ◽

Pinus Massoniana ◽

Masson Pine ◽

Pinus Massoniana Lamb ◽

Superior Clones

Role of Suillus placidus in Improving the Drought Tolerance of Masson Pine (Pinus massoniana Lamb.) Seedlings

Forests ◽

10.3390/f12030332 ◽

2021 ◽

Vol 12 (3) ◽

pp. 332

Author(s):

Min Li ◽

Haoyun Wang ◽

Xizhou Zhao ◽

Zhongke Lu ◽

Xueguang Sun ◽

...

Keyword(s):

Drought Stress ◽

Defense Mechanism ◽

Southern China ◽

Dry Weight ◽

Pinus Massoniana ◽

Photosynthetic Performance ◽

Ectomycorrhizal Fungus ◽

Severe Drought ◽

Masson Pine ◽

Pine Seedlings

Masson pine is an important afforestation species in southern China, where seasonal drought is common. The present study focused on the effects of Suillus placidus, an ectomycorrhizal fungus, inoculation on the growth and physiological and biochemical performance of masson pine seedlings under four different watering treatments (well-watered, mild drought, moderate drought, and severe drought) to evaluate the symbiotic relationship between S. placidus and masson pine seedlings. Ectomycorrhizal-inoculated (ECM) and non-inoculated (NM) seedlings were grown in pots and maintained for 60 days using the weighing method. Results showed that seedlings’ growth, dry weight, RWC, chlorophyll content, PSII efficiency, and photosynthesis decreased as drought stress intensified in both ECM and NM plants. This suggests that drought stress significantly limits the growth and photosynthetic performance of masson pine seedlings. Nevertheless, increased An/gs and proline contents in both NM and ECM prevented oxidative damage caused by drought stress. In addition, increased peroxidase (POD) activity is an essential defense mechanism of ECM seedling under drought stress. Compared with NM, ECM seedlings showed faster growth, higher RWC, and photosynthetic performance, and lower lipid peroxidation in cell membranes under drought stress, as indicated by higher POD activity and lower proline and malondialdehyde (MDA). Our experiment found that S. placidus inoculation can enhance the drought resistance of masson pine seedlings by increasing antioxidant enzyme activity, water use efficiency, and proline content, thereby enhancing growth under water-deficiency conditions. S. placidus can be used to cultivate high-quality seedlings and improve their survival in regions that experience seasonal droughts.

Thinning effects on forest evolution in Masson pine (Pinus massoniana Lamb.) conversion from pure plantations into mixed forests

Forest Ecology and Management ◽

10.1016/j.foreco.2020.118503 ◽

2020 ◽

Vol 477 ◽

pp. 118503

Author(s):

Cheng Deng ◽

Shougong Zhang ◽

Yuanchang Lu ◽

Robert E. Froese ◽

Xiaojun Xu ◽

...

Keyword(s):

Pinus Massoniana ◽

Mixed Forests ◽

Masson Pine ◽

Pinus Massoniana Lamb

Soil propagule bank of ectomycorrhizal fungi associated with Masson pine (Pinus massoniana) grown in a manganese mine wasteland

PLoS ONE ◽

10.1371/journal.pone.0198628 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0198628 ◽

Cited By ~ 1

Author(s):

Jian Huang ◽

Qisheng Han ◽

Junjian Li

Keyword(s):

Ectomycorrhizal Fungi ◽

Pinus Massoniana ◽

Masson Pine ◽

Propagule Bank

Insights into the BRT (Boosted Regression Trees) Method in the Study of the Climate-Growth Relationship of Masson Pine in Subtropical China

Forests ◽

10.3390/f10030228 ◽

2019 ◽

Vol 10 (3) ◽

pp. 228 ◽

Cited By ~ 8

Author(s):

Hongliang Gu ◽

Jian Wang ◽

Lijuan Ma ◽

Zhiyuan Shang ◽

Qipeng Zhang

Keyword(s):

Tree Growth ◽

General Circulation ◽

Growth Response ◽

Circulation Model ◽

Regression Trees ◽

Pinus Massoniana ◽

Boosted Regression Trees ◽

Climate Factors ◽

Masson Pine ◽

Hydroclimatic Variability

Dendroclimatology and dendroecology have entered mainstream dendrochronology research in subtropical and tropical areas. Our study focused on the use of the chronology series of Masson pine (Pinus massoniana Lamb.), the most widely distributed tree species in the subtropical wet monsoon climate regions in China, to understand the tree growth response to ecological and hydroclimatic variability. The boosted regression trees (BRT) model, a nonlinear machine learning method, was used to explore the complex relationship between tree-ring growth and climate factors on a larger spatial scale. The common pattern of an asymptotic growth response to the climate indicated that the climate-growth relationship may be linear until a certain threshold. Once beyond this threshold, tree growth will be insensitive to some climate factors, after which a nonlinear relationship may occur. Spring and autumn climate factors are important controls of tree growth in most study areas. General circulation model (GCM) projections of future climates suggest that warming climates, especially temperatures in excess of those of the optimum growth threshold (as estimated by BRT), will be particularly threatening to the adaptation of Masson pine.