Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant<i>Ferula assafoetida</i>

Amini, Hajar; Naghavi, Mohammad Reza; Shen, Tong; Wang, Yanhong; Nasiri, Jaber; Khan, Ikhlas A.; Fiehn, Oliver; Zerbe, Philipp; Maloof, Julin

doi:10.1534/g3.118.200852

Cited by 34 publications

(16 citation statements)

References 66 publications

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“…Detailed results are displayed in Table S2, Supplementary Materials . The level of transcriptome completeness depends on the amount of tissues and developmental stages within the samples [ 14 ]. Therefore, we would expect a limited set of detected BUSCOs in our tissue-specific analysis of meristematic embryo cells.…”

Section: Resultsmentioning

confidence: 99%

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

Boudichevskaia

Ruban

Thiel

et al. 2020

IJMS

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Some eukaryotes exhibit dramatic genome size differences between cells of different organs, resulting from programmed elimination of chromosomes. Here, we present the first transcriptome analysis of programmed chromosome elimination using laser capture microdissection (LCM)-based isolation of the central meristematic region of Aegilops speltoides embryos where B chromosome (B) elimination occurs. The comparative RNA-seq analysis of meristematic cells of embryos with (Bplus) and without Bs (B0) allowed the identification of 14,578 transcript isoforms (35% out of 41,615 analyzed transcript isoforms) that are differentially expressed during the elimination of Bs. A total of 2908 annotated unigenes were found to be up-regulated in Bplus condition. These genes are either associated with the process of B chromosome elimination or with the presence of B chromosomes themselves. GO enrichment analysis categorized up-regulated transcript isoforms into 27 overrepresented terms related to the biological process, nine terms of the molecular function aspect and three terms of the cellular component category. A total of 2726 annotated unigenes were down-regulated in Bplus condition. Based on strict filtering criteria, 341 B-unique transcript isoforms could be identified in central meristematic cells, of which 70 were functionally annotated. Beside others, genes associated with chromosome segregation, kinetochore function and spindle checkpoint activity were retrieved as promising candidates involved in the process of B chromosome elimination.

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Section: Resultsmentioning

confidence: 99%

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

Boudichevskaia

Ruban

Thiel

et al. 2020

IJMS

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“…By analysing the DEGs in the root, researchers revealed the pathway of tanshinone biosynthesis in S. miltiorrhiza [29]. Tissue-speci c genes, play important roles in plant defence, stress response, plant development and material metabolism [41,42,[80][81][82][83]. In Ferula asafetida, genes involved in terpenoid and phenylpropanoid metabolism tended to be expressed in the owers [83].…”

Section: Discussionmentioning

confidence: 99%

“…Tissue-speci c genes, play important roles in plant defence, stress response, plant development and material metabolism [41,42,[80][81][82][83]. In Ferula asafetida, genes involved in terpenoid and phenylpropanoid metabolism tended to be expressed in the owers [83]. In the study of tomato (Solanum pennellii), researchers concluded that tissue-speci c genes play important regulatory roles during fruit development [41].…”

Section: Discussionmentioning

confidence: 99%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

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“…Further, differential expression analysis between the corm, leaf and flower provides a reduced set of uncharacterised genes that narrows down the list of genes possibly imparting medicinal properties to the corm. Cross-tissue transcriptomic analyses have been performed in the past to identify candidate genes involved in the biosynthesis of secondary metabolites in medicinal plants like Ferula asafoetida, Dysphania schraderiana and Salvia miltiorrhiza [21][22][23]. In this study, aside from transcriptomic analyses, proteomic profiling was performed on the flower, leaf and corm tissues from Hypoxis hemerocallidea.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

et al. 2021

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The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.

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Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal PlantFerula assafoetida

Cited by 34 publications

References 66 publications

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

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