Sequencing and Functional Annotation of Competing Endogenous RNAs and MicroRNAs in Tea Leaves During Infection by <i>Lasiodiplodia theobromae</i>

Guo, Di; Xia, Zhongqiu; Jiang, Xinyue; Huang, Hongbin; Yang, Yuqin; Jiang, Shilong; Wang, Delu; Chen, Zhuo

doi:10.1094/phytofr-11-21-0075-a

Cited by 5 publications

(3 citation statements)

References 52 publications

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“…A total of 102 mRNA sequencing datasets encompassing seven fungal pathogen treatments, i.e. Colletotrichum camelliae 14 , Didymella bellidis , Didymella segeticola 18 , Epicoccum sorghinum 19 , Lasiodiplodia theobromae 16 , Pestalotiopsis trachicarpicola 13 and Pseudopestalotiopsis sp. 17 at multiple time intervals including uninfected or control samples were obtained from NCBI-SRA and categorized accordingly (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…A total of 102 RNA-seq datasets were harvested from the NCBI-SRA, comprising the raw sequence reads of mRNAs originating from tea leaves uninfected and infected groups of seven fungal pathogens viz. C. camelliae (BioProject: PRJNA396805) 14 , D. bellidis (BioProject: PRJNA800776), D. segeticola (BioProject: PRJNA528172) 18 , E. sorghinum (BioProject: PRJNA799860) 19 , L. theobromae (BioProject: PRJNA752965) 16 P. trachicarpicola (BioProject: PRJNA756832) 13 and Pseudopestalotiopsis sp. (BioProject: PRJNA564655) 17 .…”

Section: Methodsmentioning

confidence: 99%

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Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Hazra,

Ghosh,

Naskar

et al. 2023

Sci Rep

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Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host–pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Hazra,

Ghosh,

Naskar

et al. 2023

Sci Rep

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“…Eleven genes specifically related to drought stress and abscisic acid (ABA) signaling in other species included the following: a calmodulin-binding receptor-like cytoplasmic kinase 3 (Yang et al, 2010; Sun et al, 2021) on ZPchr0004; a calcium-dependent protein kinase family protein (Campo et al, 2014; Wei et al, 2014) on ZPchr0005; two copies of coatomer subunit beta’-1 isoform X1 (Mirzaei et al, 2014), a zinc finger CCCH domain-containing protein 43 (Peng et al, 2012), and a receptor-like protein kinase At5g2005 (Marshall et al, 2012) on ZPchr0006; a CBL-interacting protein kinase 32 (Tai et al, 2016) on ZPchr0011; two copies of ras-related protein RABC2a (Mérida-Garcia et al, 2020) and E3 ubiquitin-protein ligase RZFP34 isoform X2 (Ding et al, 2015; Shu and Yang, 2017) on ZPchr0013; methyltransferase-like protein 13 isoform X2 (Gupta et al, 2020) on ZPchr0015. We also identified five genes in these regions known to confer disease resistance in other species including a LRR receptor-like serine/threonine-protein kinase At1g06840 isoform X1 (Kumar et al, 2018; Guo et al, 2022), a respiratory burst oxidase homolog protein H (Sagi et al, 2004; Wang et al, 2018), a hydrolase, NUDIX family protein (Bartsch et al, 2006; Ge and Xia, 2008), a 60S ribosomal protein L3 (Di et al, 2010; Kant et al, 2012), and the barley B recombinant-like protein A (Ameen et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)

Haas

McGilp

Shao

et al. 2022

Preprint

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Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of the United States and Canada. Understanding the genetic diversity of NWR is essential to conservation efforts. In this study, we assembled and genotyped a diverse collection of 789 NWR individuals using genotyping-by-sequencing and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations, some of which were collected temporally, a representative sampling of cultivated NWR germplasm, and a Zizania aquatica population (outgroup). Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their lake or river of origin as well as larger clustering patterns based on watershed assignment. Contextualizing some clustering patterns with historical knowledge of ecosystem management helped to unravel some of the complexity of the population structure of wild populations. Cultivated materials were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. Estimates of linkage disequilibrium (LD) in NWR demonstrated that LD decays quickly across the genome and provided insights into the quality of the reference genome assembly of NWR. The first genome-wide scans of putative selection events in cultivated NWR were also evaluated. Overall, this study presents a large set of new SNP markers for use in NWR genetic studies as well as new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

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CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis ‘Shuchazao’)

Zhao,

Qiao,

Zhang

et al. 2024

International Journal of Biological Macromolecules

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Sequencing and Functional Annotation of Competing Endogenous RNAs and MicroRNAs in Tea Leaves During Infection by Lasiodiplodia theobromae

Cited by 5 publications

References 52 publications

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)

CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis ‘Shuchazao’)

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