A universal pipeline for mobile mRNA detection and insights into heterografting advantages under chilling stress

Wang, Ying; Wang, Lingping; Xing, Nailin; Wu, Xiaohua; Wu, Xinyi; Wang, Baogen; Lu, Zengjun; Xu, Pei; Tao, Ye; Li, Guojing; Wang, Yuhong

doi:10.1038/s41438-019-0236-1

Cited by 26 publications

(30 citation statements)

References 31 publications

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“…Similarly, Liu et al reported the differential expression of 787 genes between watermelon homo and heterograft (bottle gourd rootstock) 16 . To highlight the importance of bottle gourd as rootstock, Wang et al (2020) analyzed the transcriptome of bottle gourd (rootstock) and watermelon (scion) under chilling reatment. They reported that bottle gourd homograft, as well as hetero-graft, are tolerant to chilling stress compared to the water-melon homograft 50 .…”

Section: Discussionmentioning

confidence: 99%

“…(2020) analyzed the transcriptome of bottle gourd (rootstock) and watermelon (scion) under chilling reatment. They reported that bottle gourd homograft, as well as hetero-graft, are tolerant to chilling stress compared to the water-melon homograft 50 . Thus, in-depth analysis of GRAS transcription factors in the bottle gourd genome will be helpful for enhancing the use of bottle gourd as valuable rootstock material and could also be extended in other vegetable crops.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome

Sidhu

Pruthi

Singh

et al. 2020

Sci Rep

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GRAS genes belong to the plant-specific transcription factors (TF's) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF's. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein-protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops. Transcription factors (TFs) are the class of proteins that control the functioning of various genes by binding with their promoters and thus involved in the gene regulation process 1. Previously, more than 320K TFs belonging to 58 transcription factor families have been reported from 165 different plant species. Out of these, GRAS represents one of the major families that are involved in plant growth, development, cell signaling, and stress tolerance 2. GRAS family was first reported in bacteria and characterized by the three TFs i.e. (i) GAI (gibberellicacid insensitive); (ii) RGA (repressor of GAI), and (iii) SCR (scarecrow) with the size range from 400 to 770 amino acids 3,4. It was observed that GAI and RGA are the part of DELLA proteins that take part in gibberellin (GA) and Jasmonate (JA) response as well as light signaling. Likewise, SCR and Short Root (SHR) played a key role in the radial organization of root by forming the SCR/SHR complex 5. Previously, it has also been reported that the C-terminal region of GRAS members is highly conserved, while the N-terminal is highly divergent that might provide the specificity to each protein 6. Furthermore, the evolutionary analysis suggested the phenomenon of horizontal gene transfer (HGT) from bacteria to plants. GRAS gene family is further categorized into different subfamilies such as eight in Arabidopsis and rice 7 , while 8 to 13 in tomato, popular, castor beans, etc 8-10. Recently, Cenci et al. classified the GRAS family into 17 subfamilies such as DELLA, Lateral suppressor (LS), Hairy meristem (HAM), and SCR 11. Previous studies showed that it is one of the widely explored transcription factor family in the various plant species including tomato, potato, buckwheat, and sweet orange 12-14. Bottle gourd (Lagenaria siceraria), a member of the Cucurbitaceae family is commonly cultivated in the tropical and subtropical regions an...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome

Sidhu

Pruthi

Singh

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The homologous mRNA AtCK1 (At1G71697) was confirmed to have bidirectional mobility in grafted A. thaliana [ 25 ]. Thus, directional mRNA movement is independent of RNA abundance, RNA motifs, and mRNA length [ 44 ]. On the one hand, mRNA movement direction is dependent on the target tissue where the mRNA functions and the biological processes in which they participate.…”

Section: Discussionmentioning

confidence: 99%

Identification of Long-Distance Transmissible mRNA between Scion and Rootstock in Cucurbit Seedling Heterografts

Liu

Xiang

et al. 2020

IJMS

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Grafting has been widely used to improve plant growth and tolerance in crop production, as well as for clarifying systemic mRNA signaling from donor to recipient tissues in organ-to-organ communication. In this study, we investigated graft partner interaction mechanisms of Cucumis sativus (Csa) and Cucurbita moschata (Cmo) using a large-scale endogenous mRNA transport. The results indicated that most mobile transcripts followed an allocation pathway from source to sink. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that mRNA mobility functions are universally common and individually specific. Identification of mRNA mobility between distant tissues in heterografts with RT-PCR (reverse transcription PCR), RT-qPCR (reverse transcriptional quantitative real time PCR), and clone sequencing were used to estimate 78.75% of selected mobile transcripts. Integration of bioinformatic analysis and RT-qPCR identification allowed us to hypothesize a scion-to-rootstock-to-scion feedback signal loop of Csa move-down and Cmo move-up mRNAs, where Csa scion move-down mRNAs were involved in carbon fixation and biosynthesis of amino acid pathways, and Cmo root received Csa move-down mRNA and then delivered the corresponding Cmo upward mRNA to scion to improve photosynthesis of cucumber scion. This formed a feedback signal loop of scion-to-rootstock-to scion to explain why pumpkin rootstock enhanced cucumber production in the industry, which was utilized for organ communication and mediates photosynthesis processes in heterograft cucurbit crops.

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“…In addition, the actual research materials used are often different from those used for reference genome sequencing, resulting in many false positives and partial false negatives in bioinformatics analysis. In the study by Wang et al (2020), an important improvement in the pipeline was the inclusion of a step to correct for SNPs and indels between the experimental and reference genomes. Here, we developed a stringent bioinformatics pipeline based on the method published by Wang et al (2020) that takes most of the known technical concerns into consideration.…”

Section: Methods For the Identification Of Mobile Mrnas And Proteinsmentioning

confidence: 99%

Long‐distance communication through systemic macromolecular signaling mediates stress defense responses in plants

Zhang

Kong

2021

Physiologia Plantarum

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Land plants have a unique vascular bundle system that ranges in length from a few centimeters to hundreds of meters. These systems integrate the various organs of the whole plant, perform material exchange between different plant tissues and mediate the transmission of signals between cells or over long distances. Grafting and parasitism can reshape the vascular tissues of different ecotypes or species and represent two important systems for studying plant systemic signaling. In recent years, with the advancement of genomics and sequencing technology, the transportation, identification, and function of systemic plant macromolecules have been extensively studied. Here, we review the current body of knowledge of the transport pathways and regulatory mechanisms of macromolecules in plants and assess systemic, long‐distance signal trafficking that mediates stress responses, and plant–environment or plant–insect community interactions. Additionally, we propose several methods for identifying mobile mRNAs and proteins. Finally, we discuss the challenges facing systemic signaling research and put forth the most urgent questions that need to be answered to advance our understanding of plant systemic signaling.

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A universal pipeline for mobile mRNA detection and insights into heterografting advantages under chilling stress

Cited by 26 publications

References 31 publications

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome

Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome

Identification of Long-Distance Transmissible mRNA between Scion and Rootstock in Cucurbit Seedling Heterografts

Long‐distance communication through systemic macromolecular signaling mediates stress defense responses in plants

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