Comprehensive transcriptome analysis provides insights into metabolic and gene regulatory networks in trichomes of Nicotiana tabacum

Nautiyal, Abhishek Kumar; Gani, Umar; Sharma, Priyanka; Kundan, Maridul; Fayaz, Mohd; Lattoo, Surrinder K.; Misra, Prashant

doi:10.1007/s11103-020-00968-2

Cited by 15 publications

(6 citation statements)

References 54 publications

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“…The log 2 transformed RPKM values were applied to perform Hierarchical clustering using Pearson’s correlation distance ( Chen et al, 2021 ). The significantly expressed genes were defined as RPKM value > 1, the organ-enhanced genes were defined as RPKM value is 5-fold above the average RPKM values of other organs, whereas organ-enriched genes were defined as RPKM value is 5-fold above the RPKM values of any other organs ( Uhlén et al, 2016 ; Nautiyal et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

et al. 2022

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Common bermudagrass (Cynodon dactylon L.) is an important perennial warm-season turfgrass species with great economic value. However, the reference genome is still deficient in C. dactylon, which severely impedes basic studies and breeding studies. In this study, a high-quality haplotype-resolved genome of C. dactylon cultivar Yangjiang was successfully assembled using a combination of multiple sequencing strategies. The assembled genome is approximately 1.01 Gb in size and is comprised of 36 pseudo chromosomes belonging to four haplotypes. In total, 76,879 protein-coding genes and 529,092 repeat sequences were annotated in the assembled genome. Evolution analysis indicated that C. dactylon underwent two rounds of whole-genome duplication events, whereas syntenic and transcriptome analysis revealed that global subgenome dominance was absent among the four haplotypes. Genome-wide gene family analyses further indicated that homologous recombination-regulating genes and tiller-angle-regulating genes all showed an adaptive evolution in C. dactylon, providing insights into genome-scale regulation of polyploid genome stability and prostrate growth. These results not only facilitate a better understanding of the complex genome composition and unique plant architectural characteristics of common bermudagrass, but also offer a valuable resource for comparative genome analyses of turfgrasses and other plant species.

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Section: Methodsmentioning

confidence: 99%

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

et al. 2022

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“…For the gene expression quantification, the read numbers of each gene were counted using featureCounts v1.5.0-p3, and the fragments per kilobase of transcript per million mapped reads (FPKM) of each gene were calculated for comparison among different samples ( Nautiyal et al, 2020 ). The DESeq2 R package was employed for analyzing the differentially expressed genes (DEGs) between the three samples, i.e., genes with an adjusted p -value ( p adj) ≤ 0.05 and | log2(FoldChange) | ≥ 0 were assigned as differentially expressed.…”

Section: Methodsmentioning

confidence: 99%

Translocation of Foliar Absorbed Zn in Sunflower (Helianthus annuus) Leaves

Wang

et al. 2022

Front. Plant Sci.

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Foliar zinc (Zn) fertilization is an important approach for overcoming crop Zn deficiency, yet little is known regarding the subsequent translocation of this foliar-applied Zn. Using synchrotron-based X-ray fluorescence microscopy (XFM) and transcriptome analysis, the present study examined the translocation of foliar absorbed Zn in sunflower (Helianthus annuus) leaves. Although bulk analyses showed that there had been minimal translocation of the absorbed Zn out of the leaf within 7 days, in situ analyses showed that the distribution of Zn in the leaf had changed with time. Specifically, when Zn was applied to the leaf for 0.5 h and then removed, Zn primarily accumulated within the upper and lower epidermal layers (when examined after 3 h), but when examined after 24 h, the Zn had moved to the vascular tissues. Transcriptome analyses identified a range of genes involved in stress response, cell wall reinforcement, and binding that were initially upregulated following foliar Zn application, whereas they were downregulated after 24 h. These observations suggest that foliar Zn application caused rapid stress to the leaf, with the initial Zn accumulation in the epidermis as a detoxification strategy, but once this stress decreased, Zn was then moved to the vascular tissues. Overall, this study has shown that despite foliar Zn application causing rapid stress to the leaf and that most of the Zn stayed within the leaf over 7 days, the distribution of Zn in the leaf had changed, with Zn mostly located in the vascular tissues 24 h after the Zn had been applied. Not only do the data presented herein provide new insight for improving the efficiency of foliar Zn fertilizers, but our approach of combining XFM with a transcriptome methodological system provides a novel approach for the study of element translocation in plants.

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“…The log 2 transformed FPKM values were applied to perform Hierarchical clustering using Pearson’s correlation distance in the Pvclust software package with default settings ( Suzuki and Shimodaira, 2006 ). The significantly expressed unigenes were defined as FPKM value ≥ 1 ( Nautiyal et al, 2020 ). The stably expressed unigenes were defined as the FPKM ratio (minimal versus maximal FPKM value in different organ samples) > 0.8 and the coefficient of variation (C.V., standard deviation divided by the average FPKM value) < 0.3 ( Klepikova et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Cynodon dactylon L.)

Chen

et al. 2021

Front. Genet.

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As an important warm-season turfgrass and forage grass species with wide applications, bermudagrass (Cynodon dactylon L.) simultaneously has shoot, stolon and rhizome, three types of stems with different physiological functions. To better understand how the three types of stems differentiate and specialize, we generated an organ-specific transcriptome dataset of bermudagrass encompassing 114,169 unigenes, among which 100,878 and 65,901 could be assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) terms, respectively. Using the dataset, we comprehensively analyzed the gene expression of different organs, especially the shoot, stolon and rhizome. The results indicated that six organs of bermudagrass all contained more than 52,000 significantly expressed unigenes, however, only 3,028 unigenes were enrich-expressed in different organs. Paired comparison analyses further indicated that 11,762 unigenes were differentially expressed in the three types of stems. Gene enrichment analysis revealed that 39 KEGG pathways were enriched with the differentially expressed unigenes (DEGs). Specifically, 401 DEGs were involved in plant hormone signal transduction, whereas 1,978 DEGs were transcription factors involved in gene expression regulation. Furthermore, in agreement with the starch content and starch synthase assay results, DEGs encoding starch synthesis-related enzymes all showed the highest expression level in the rhizome. These results not only provided new insights into the specialization of stems in bermudagrass but also made solid foundation for future gene functional studies in this important grass species and other stoloniferous/rhizomatous plants.

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Comprehensive transcriptome analysis provides insights into metabolic and gene regulatory networks in trichomes of Nicotiana tabacum

Cited by 15 publications

References 54 publications

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

Translocation of Foliar Absorbed Zn in Sunflower (Helianthus annuus) Leaves

Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Cynodon dactylon L.)

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