scholarly journals PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaojie Liu ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Early Response ◽  
Full Length ◽  
Differentially Expressed ◽  
Late Response ◽  
Response Mechanism ◽  
Necrotrophic Pathogen ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Highly Correlated

Abstract Background Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection. Results Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen V. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8139 were DETs. Total 1336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of V. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to V. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen V. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

scholarly journals PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

2020 ◽  
Author(s):  
Xiaojie Liu ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Early Response ◽  
Full Length ◽  
Differentially Expressed ◽  
Late Response ◽  
Response Mechanism ◽  
Necrotrophic Pathogen ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Highly Correlated

Abstract Background: Cytospora canker is a serious disease in the stem of Malus sieversii, caused by Cytospora mali. However, little is known about the global response mechanism in M. sieversii to C. mali infection. Results: Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen C. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8,139 were DETs. Total 1,336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3,780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of C. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions: The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to C. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen C. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

scholarly journals PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

2020 ◽  
Author(s):  
Xiaojie Liu ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Early Response ◽  
Full Length ◽  
Differentially Expressed ◽  
Late Response ◽  
Response Mechanism ◽  
Necrotrophic Pathogen ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Highly Correlated

Abstract Background Cytospora canker is a serious disease in the stem of Malus sieversii, caused by Cytospora mali. However, little is known about the global response mechanism in M. sieversii to C. mali infection. Results Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen C. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8,139 were DETs. Total 1,336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3,780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of C. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to C. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen C. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

scholarly journals PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Early Response ◽  
Full Length ◽  
Differentially Expressed ◽  
Late Response ◽  
Response Mechanism ◽  
Necrotrophic Pathogen ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Highly Correlated

Abstract Background: Cytospora canker is a serious disease in the stem of Malus sieversii, caused by Cytospora mali. However, little is known about the global response mechanism in M. sieversii to C. mali infection. Results: Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen C. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8,139 were DETs. Total 1,336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3,780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of C. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions: The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to C. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen C. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

scholarly journals Full-Length Transcriptome-Wide Characteristic and Functional Identification of WRKY Family in Malus sieversii during the Valsa Canker Disease Response

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 790
Author(s):  
Xiaojie Liu ◽  
Yiheng Zhang ◽  
Tong Zhou ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
...  
Keyword(s):  
Plant Immunity ◽  
Full Length ◽  
Future Research ◽  
Functional Identification ◽  
Disease Response ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Expression Pattern Analysis ◽  
Valsa Canker ◽  
Disease Resistances

WRKY transcription factors are one of the largest families in plants, playing important roles in regulating plant immunity. Malus sievesii has abundant genetic diversity and can offer various and high-quality gene resources. In this study, 112 putative MsWRKY proteins were identified from a full-length transcriptome of M. sieversii during the Valsa canker disease (caused by Valsa mali). The MsWRKY proteins were phylogenetically divided into three groups (I–III). Motif compositions of the MsWRKY proteins were clustered and fifteen conserved motifs were observed. Expression pattern analysis showed that thirty-four MsWRKY transcripts strongly responded to the V. mali infection, demonstrating that MsWRKY transcripts might play different roles during the response. Functional identifications were subsequently conducted with transient expressions, demonstrating that MsWRKY16, MsWRKY21, MsWRKY70, MsWRKY74 and MsWRKY85 positively regulated the resistant response. Besides, the MsWRKY21, MsWRKY70 and MsWRKY85 were dramatically induced by salicylic acid (SA), methyl-jasmonate acid (MeJA) and 1-aminocyclopropane-1-carboxylate (ACC), indicating that they play important roles in the regulatory resistance of V. mali infection. This work provides a comprehensive understanding of the WRKY family in M. sieversii and will build a foundation for future research of the potential disease resistances MsWRKY transcripts.

scholarly journals Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ping Zhou ◽  
Xiaoshuang Li ◽  
Xiaojie Liu ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Cold Acclimation ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Freezing Stress ◽  
Illumina Platform ◽  
Apple Trees ◽  
Malus Sieversii

Abstract Background Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in wild apple trees. Results Phytohormone and physiology profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that JA, IAA, and ABA accumulated in the cold acclimation stage and decreased during freezing stress in response to freezing stress. To elucidate the molecular mechanisms of freezing stress after cold acclimation, we employed single molecular real-time (SMRT) and RNA-seq technologies to study genome-wide expression profiles in wild apple. Using the PacBio and Illumina platform, we obtained 20.79G subreads. These reads were assembled into 61,908 transcripts, and 24,716 differentially expressed transcripts were obtained. Among them, 4410 transcripts were differentially expressed during the whole process of freezing stress, and these were examined for enrichment via GO and KEGG analyses. Pathway analysis indicated that “plant hormone signal transduction”, “starch and sucrose metabolism”, “peroxisome” and “photosynthesis” might play a vital role in wild apple responses to freezing stress. Furthermore, the transcription factors DREB1/CBF, MYC2, WRKY70, WRKY71, MYB4 and MYB88 were strongly induced during the whole stress period. Conclusions Our study presents a global survey of the transcriptome profiles of wild apple trees in dynamic response to freezing stress after two days cold acclimation and provides insights into the molecular mechanisms of freezing adaptation of wild apple plants for the first time. The study also provides valuable information for further research on the antifreezing reaction mechanism and genetic improvement of M. sieversii after cold acclimation.

Experimental Studies of Sedimentation Basin Dynamics

1977 ◽  
Vol 12 (1) ◽  
pp. 77-90
Author(s):  
J.F. Cordoba-Molina ◽  
P.L. Silveston ◽  
R. R. Hudgins
Keyword(s):  
Dynamic Response ◽  
Froude Number ◽  
Flow Model ◽  
Experimental Studies ◽  
Densimetric Froude Number ◽  
Number Range ◽  
The Real ◽  
Highly Correlated ◽  
Sedimentation Basins ◽  
Simple Flow

Abstract A simple Flow Model is proposed to describe the dynamic response of sedimentation basins. The response predicted by this model is linear as opposed to the real response of the basin which is nonlinear. However, the real response of the basin is highly correlated with its densimetric Froude number, and as a consequence our linear model effectively predicts the response of the basin in a restricted densimetric Froude Number range. Our experiments show that the response of the basin becomes more sluggish and erratic as the densimetric Froude number decreases.

Genes differentially expressed in broccoli as an early and late response to wounding stress

2018 ◽  
Vol 145 ◽  
pp. 172-182 ◽  
Author(s):  
Ana M. Torres-Contreras ◽  
Carolina Senés-Guerrero ◽  
Adriana Pacheco ◽  
Mauricio González-Agüero ◽  
Perla A. Ramos-Parra ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Late Response ◽  
Wounding Stress

MicroRNA expression profiles associated with pancreatic cancer.

2011 ◽  
Vol 29 (4_suppl) ◽  
pp. 153-153 ◽  
Author(s):  
N. A. Schultz ◽  
J. Werner ◽  
H. Willenbrock ◽  
A. Roslind ◽  
T. Horn ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cancer Cells ◽  
Tumor Tissue ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Ductal Adenocarcinoma ◽  
Mirna Expression Pattern ◽  
Quantile Normalisation ◽  
Highly Correlated

153 Background: The aim was: 1) to define the global microRNA (miRNA) expression pattern in pancreatic cancer (PC) and compare it with normal pancreas (NP) and chronic pancreatitis (CP); 2) to validate reported diagnostic miR profiles in PC; 3) to discover new diagnostic miRs in pancreas samples without micro-dissection of cancer cells. Methods: MiR expression patterns in FFPE tissue blocks from patients operated for pancreatic ductal adenocarcinoma (PDAC, n=170) and ampullary adenocarcinomas (A-AC, n=107) were determined using TaqMan Human miR microarrray (Applied Biosystem; 754 miRs were determined) and compared to profiles of CP (n=23) and NP (n=28). Raw Ct-values were normalized using quantile-normalisation. Results: 83miRs were differentially expressed in PDAC and NP (42 higher expression; 41 reduced expression in PDAC). 32 miRs were differentially expressed in PDAC and CP. The most differentially expressed miRs were miR-614, miR-492, miR-622, miR-135b* and miR-196. The miR signatures of PDAC and A-AC were highly correlated (0.99; only 5 miRs were significantly differentially expressed). An earlier reported diagnostic miR profile for PDAC was validated (mirR196b - miR217), and 3 other significant profiles were identified (Table). A more complex Lasso classifier using 19 miRs could separate PDAC from NP and CP (accuracy = 98%). Conclusions: We identified systematic differences in patterns of miR expressions between tumor tissue including both cancer cells and surrounding desmoplasia obtained from patients with PDAC and A-AC compared to tissue from patients with CP and NP. We validated the diagnostic miR expression profile (miR-196b, miR-217) described by Szafranska et al. (Clin Chem 2008;54:1716-24). Furthermore, we identified 5 miRs which were better to discriminate PDAC and A-AC from CP and NP. Prospective studies are needed to evaluate if this panel of miRs is useful for early diagnosis of patients with PDAC. [Table: see text] No significant financial relationships to disclose.

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