De novo transcriptome assembly of Coffea liberica reveals phylogeny and expression atlas of phenylalanine ammonia-lyase genes in Coffea species

Huang, Xing; Bai, Xuehui; Xie, Zhouli; Fahad, Shah; Gbokie, Thomas; Lu, Ying; Guo, Tieying; Li, Jinhong; Zhang, Zhirun; Wu, Weihuai; Yi, Kexian

doi:10.1016/j.indcrop.2022.116029

Cited by 3 publications

(1 citation statement)

References 44 publications

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“…The mechanisms underpinning SA biosynthesis mainly include the phenylalanine ammonia lyase (PAL) pathway and the isochorismate synthase (ICS) pathway. When the enzymatic activity of PAL or ICS is inhibited, the susceptibility of plants to pathogens is enhanced and disease resistance is weakened [10,11]. Moreover, expression of specific genes (e.g., nahG) causes a loss of the biological functions of SA, inhibits the accumulation of SA, and distinctly reduces disease resistance in plants [12].…”

Section: Introductionmentioning

confidence: 99%

Reactive Oxygen Species and Salicylic Acid Mediate the Responses of Pear to Venturia nashicola Infection

Liu,

Zheng,

Zhou

et al. 2024

Agronomy

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Reactive oxygen species (ROS) and salicylic acid (SA) are essential signaling molecules in plant cells that participate in responses to biotic and abiotic stresses. Changes in ROS and SA signals during interactions between pear and the pear scab pathogen Venturia nashicola remain unclear. Herein, we analyzed the roles of ROS in the signal transduction pathway of pear scab resistance using the highly resistant Huangguan and susceptible Xuehua cultivars of pear (Pyrus bretschneideri Rehd). Protoplasts, calluses, and leaves were obtained from 14-year-old pear trees and treated with V. nashicola for different periods. The results showed that ROS rapidly accumulated in protoplasts of both cultivars within a 120-min treatment period, but the fluorescence intensity of ROS differed between cultivars. The H2O2 content in fruit-derived calluses of Huangguan peaked at 48 h post-infection at levels 1.85 times higher than those in Xuehua. Induction of H2O2 by V. nashicola in Huangguan was more intense than in Xuehua over a 96-h treatment period. At 96 h post-infection, the malondialdehyde content in leaves of Huangguan was significantly lower than in Xuehua, while the activities of superoxide dismutase, peroxidase, and catalase, and the relative expression levels of PbMnSOD, PbPOD, and PbCAT genes were higher in Huangguan than Xuehua. V. nashicola infection also caused a continuous increase in the leaf SA content of Huangguan, which was 6.76 times higher than in Xuehua at 96 h post-infection, and V. nashicola exposure upregulated the expression of PbPAL, PbICS, PbPR1, and PbPR5. In summary, both ROS and SA participated in the responses of pear trees to V. nashicola infection and played vital roles in the signal transduction pathway of pear scab resistance.

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Section: Introductionmentioning

confidence: 99%

Reactive Oxygen Species and Salicylic Acid Mediate the Responses of Pear to Venturia nashicola Infection

Liu,

Zheng,

Zhou

et al. 2024

Agronomy

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Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets

Sergio Alberto,

Maximo,

Andres

et al. 2024

Bioinform Biol Insights

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De novo assembly of transcriptomes from species without reference genome remains a common problem in functional genomics. While methods and algorithms for transcriptome assembly are continually being developed and published, the quality of de novo assemblies using short reads depends on the complexity of the transcriptome and is limited by several types of errors. One problem to overcome is the research gap regarding the best method to use in each study to obtain high-quality de novo assembly. Currently, there are no established protocols for solving the assembly problem considering the transcriptome complexity. In addition, the accuracy of quality metrics used to evaluate assemblies remains unclear. In this study, we investigate and discuss how different variables accounting for the complexity of RNA-Seq data influence assembly results independently of the software used. For this purpose, we simulated transcriptomic short-read sequence datasets from high-quality full-length predicted transcript models with varying degrees of complexity. Subsequently, we conducted de novo assemblies using different assembly programs, and compared and classified the results using both reference-dependent and independent metrics. These metrics were assessed both individually and combined through multivariate analysis. The degree of alternative splicing and the fragment size of the paired-end reads were identified as the variables with the greatest influence on the assembly results. Moreover, read length and fragment size had different influences on the reconstruction of longer and shorter transcripts. These results underscore the importance of understanding the composition of the transcriptome under study, and making experimental design decisions related to the need to work with reads and fragments of different sizes. In addition, the choice of assembly software will positively impact the final assembly outcome. This selection will affect the completeness of represented genes and assembled isoforms, as well as contribute to error reduction.

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Agave schidigera Transcriptome Reveals Stress-Responsive Phenylalanine ammonia-lyase Genes in Agave

Wang,

Hu,

Lin

et al. 2024

Agronomy

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Agave is a significant fiber crop in tropical regions, known for its high fiber strength. Lignin is closely associated with fiber strength, and phenylalanine ammonia-lyase (PAL) serves as the initial enzyme in biosynthesis of lignin. Hence, it is of considerable significance to study the genes of PAL family to analyze the characteristics and mechanism of sisal fiber development. In this research, we conducted a transcriptomic analysis of Agave schidigera, a widely recognized ornamental plant in agave. Approximately 29.85 million clean reads were acquired through Illumina sequencing. In total, 116,602 transcripts including 72,160 unigenes were assembled, and 22.06~63.56% of those unigenes were annotated in public databases. Two, six, six and six PAL genes were successfully identified and cloned from A. schidigera, A. deserti, A. tequilana and A. H11648, respectively. After phylogenetic analysis, these genes were clustered into two branches. Genes AhPLA2a and AhPLA2c exhibited higher expression levels compared to other genes but had different expression patterns. Moreover, AhPLA2a and AhPLA2c were expressed at high levels under full-nutrient, nitrogen-free and phosphorus-free stresses. Most PAL genes were induced by Phytophthora nicotianae Breda, especially AhPAL1a, AhPAL1b, AhPAL2b and AhPAL2c. This research is the first work to present a de novo transcriptome dataset for A. schidigera, enriching its bioinformation of transcripts. The cloned PAL genes and the expression analyses will form the basis of future research on lignin biosynthesis, the relationship between lignin and fiber strength, and stress resistance in Agave species.

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De novo transcriptome assembly of Coffea liberica reveals phylogeny and expression atlas of phenylalanine ammonia-lyase genes in Coffea species

Cited by 3 publications

References 44 publications

Reactive Oxygen Species and Salicylic Acid Mediate the Responses of Pear to Venturia nashicola Infection

Reactive Oxygen Species and Salicylic Acid Mediate the Responses of Pear to Venturia nashicola Infection

Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets

Agave schidigera Transcriptome Reveals Stress-Responsive Phenylalanine ammonia-lyase Genes in Agave

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