Exploring the adaptive mechanism of Passiflora edulis in karst areas via an integrative analysis of nutrient elements and transcriptional profiles

Xu, Mengxuan; Li, Anding; Teng, Yun; Sun, Zimou; Xu, Meng

doi:10.1186/s12870-019-1797-8

Cited by 10 publications

(6 citation statements)

References 53 publications

(51 reference statements)

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“…In addition, functional genes of P. edulis have not been well studied, especially by relative quantitative analysis of functional genes, and research on reference genes in P. edulis has not been reported. [1,2]. To enhance the reliability of functional gene expression research, we systematically selected reliable internal control genes for RT-qPCR data normalization in multiple tissue samples and cold-treated samples of P. edulis.…”

Section: Discussionmentioning

confidence: 99%

“…Passi ora edulis (P. edulis), or passion fruit, is a perennial vine that belongs to the Passi oraceae family. P. edulis, which origined in South America, is now widely cultivated in southern China because of its high edible value, medicinal e cacy and ornamental properties; additionally, P. edulis is an important raw material in the juice and pulp industry [1][2][3][4][5][6]. Passion fruit, a tropical fruit, provides a variety of nutrients, such as carbohydrates, vitamins and minerals, which are essential for biological activities [5].…”

Section: Introductionmentioning

confidence: 99%

“…P. edulis was introduced in China at the beginning of the last century [2]. In recent years, researchers have studied the adaptability of P. edulis to cold environments, providing a theoretical basis for expanding the cultivation area of P. edulis in China [1,2]. Although the edible value and medicinal e cacy of P. edulis have increased, only a few studies on the functional genes of P. edulis have been reported, especially on gene expression patterns under cold conditions.…”

Section: Introductionmentioning

confidence: 99%

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Reference gene selection in multiple Passiflora edulis tissues and under cold stress for RT- qPCR analysis

Tu¹,

Fan²,

Li³

et al. 2020

Preprint

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Background: Passiflora edulis is a tropical fruit with high edible and medicinal values that is widely cultivated in southern China. The development of new P. edulis variety with cold resistance and research on the mechanism of cold resistance are the basis for further promoting the cultivation of this species. In a previous study, our laboratory discovered a cold-resistant variety Pingtang 1, which is used as a material for the study of cold resistance mechanism in P. edulis. However, functional genes of P. edulis have not been well studied, especially via relative quantitative analysis. In addition, research on reference genes in P. edulis has not been reported.Results: We used three tools to test the expression stability of 10 candidate reference genes in multiple tissue samples and cold-treated samples of P. edulis. We found that Ts and EF1 showed the highest expression stability in all samples. Further analysis showed that HIS and EF1 were stably expressed in tissue samples, whereas UBQ and EF1 were stably expressed in cold-treated samples. Interestingly, EF1 was stably expressed in not only multiple tissue samples but also cold-treated samples. To validate the selected reference genes, we used the target gene ICE1 and investigated its expression level in cold-treated leaves. Interestingly, the expression of ICE1 increased with increasing cold treatment times.Conclusions: In this study, we successfully selected reference genes from among 10 candidates for P. edulis RT-qPCR data normalization. We selected Ts and EF1 as reference genes for normalization in all samples. HIS and EF1 were ideal for data normalization in tissue samples, whereas UBQ and EF1 were ideal for cold-treated samples. Our work substantially benefits the study of functional genes in P. edulis.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Reference gene selection in multiple Passiflora edulis tissues and under cold stress for RT- qPCR analysis

Tu¹,

Fan²,

Li³

et al. 2020

Preprint

Self Cite

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“…The expression profiles of the 34 identified PeCER genes in different tissues of yellow and purple passion fruit cultivars were evaluated through the available public data. The RNA-Seq raw reads were downloaded from the NCBI Sequence Read Archive database ( http://www.ncbi.nlm.nih.gov/sra ) with the following accession numbers: SRP150688 (Xu et al, 2019 ) and PRJNA634206 (Wu et al, 2021 ). The passion fruit sample information for the NCBI raw reads was as follows: peel tissue samples were from yellow ( P. edulis .…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Rizwan

Waheed

et al. 2022

Front. Plant Sci.

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Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.

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“…Plants in karst areas have been adapted to grow in a drought and high calcium environment for a long time through their own physiological processes and structural adjustments in the evolution. Soil moisture and calcium carbonate content have the greatest impact on vegetation spectral characteristics in karst areas [10].…”

Section: Introductionmentioning

confidence: 99%

Exploring the adaptive mechanism of Camellia limonia in karst high calcium environment via an integrative analysis of metabolomics and metagenomics

Liu

Huang

et al. 2021

Preprint

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Background: Yellow Camellia is a kind of rare plant with high economic and medicinal value. It is known as the "giant panda" of the botanical world. Camellia group of plants (Camellia Sect. Chrysantha Chang) is the only golden flower of Theaceae. Compared with Camellia nitidissima, Camellia limonia grows in karst areas, where the soil has the characteristic of high calcium content. However, there are few studies about the Camellia limonia in karst soil environment and the adaptation mechanism is no clear. Results: In this study, we found that under high calcium treatment, the chlorophyll content and leaf areas of Camellia limonia increased, while those of Camellia nitidissima decreased. The photosynthetic efficiency of Camellia limonia was more stable and higher than Camellia nitidissima. Compared with Camellia nitidissima, the conductance was larger and the degree of leaf shrinkage was smaller in Camellia limonia. The metabolomics analysis showed that the kaempferol-3-o-rutinoside, tyrosol, 6-o-methyldeacetylisoipecoside and (r)-mandelic acid are the main differently metabolic compounds . The results of karst high calcium soil metagenomics showed that microbacterium-testaceum, intrasporangium-calvum and rubrivivax-gelatinosus significantly changed. Through metabonomics and metagenomics integrative analysis, flavone and flavonol biosynthesis is suggested to be the main regulation pathway, which is regulated by apigenin, kaempferol, astragalin, isoquercitrin metabolites and TT7, UGT78D1, UGT78D2 genes. This metabolic pathway involves the synthesis of flavonoids. Flavonoids have the functions in drought and salt resistance, which play an important role in the adaptation of Camellia limonia in karst high calcium environment.Conclusion: This omics study identified key regulation metabolites and genes for Camellia and provided important basis for the adaptive mechanism of plants to adapt to the high-calcium environment and the protection of Camellia species.

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Exploring the adaptive mechanism of Passiflora edulis in karst areas via an integrative analysis of nutrient elements and transcriptional profiles

Cited by 10 publications

References 53 publications

Reference gene selection in multiple Passiflora edulis tissues and under cold stress for RT- qPCR analysis

Reference gene selection in multiple Passiflora edulis tissues and under cold stress for RT- qPCR analysis

Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Exploring the adaptive mechanism of Camellia limonia in karst high calcium environment via an integrative analysis of metabolomics and metagenomics

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