Identification and functional prediction of circRNAs in Populus Euphratica Oliv. heteromorphic leaves

Li, Cailin; Qin, Shaowei; Bao, Lianghong; Guo, Zhongzhong; Zhao, Lei

doi:10.1016/j.ygeno.2019.01.013

Cited by 19 publications

(12 citation statements)

References 36 publications

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“…Soc1 and agl42 were found to be high expressed in leaves and flowers 46 , 47 , thus in P. euphratica too, leaf shape was an age-dependent mechanism 2 . Therefore it was suspected that soc1 and agl42 are important in the morphogenesis of P. hl.Additionally, Li confirmed that circRNA-0168 expression was negatively correlated with miR156 families 1 , which indicated that the ceRNA (circRNA, lncRNA)–miR156–SPL9 ( XM-011034944.1 ) plays an critical role in the miR156-SPL pathway.…”

Section: Discussionmentioning

confidence: 79%

“…Initially, the leaves of the P. euphratica are all linear (Li), with a leaf index (LI, leaf length/leaf width) ≥ 5 at the germination and seedling stages,. With increasing tree age, the leaves gradually became lanceolate (La, 5 > LI ≥ 2), ovate (Ov, 2 > LI ≥ 1), and broad-ovate (Bo, LI < 1) leaves 1 , 2 . Hence, P. euphratica is an ideal model to study leaf morphogenesis.…”

Section: Introductionmentioning

confidence: 99%

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Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

Qin¹,

Bao

He³

et al. 2022

Sci Rep

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The SQUAMOSA promoter-binding protein-like (SPL) family play a key role in guiding the switch of plant growth from juvenile to adult phases. Populus euphratica Oliv. exhibit typical heterophylly, and is therefore an ideal model for studying leaf shape development. To investigate the role and regulated networks of SPLs in the morphogenesis of P. euphratica heteromorphic leaves. In this study, 33 P. euphratica SPL (PeuSPL) genes were identified from P. euphratica genome and transcriptome data. Phylogenetic analysis depicted the classification of these SPL genes into two subgroups. The expression profiles and regulatory networks of P. euphratica SPL genes analysis displayed that major P. euphratica SPL family members gradually increases from linear to broad-ovate leaves, and they were involved in the morphogenesis regulation, stress response, transition from vegetative to reproductive growth, photoperiod, and photosynthesis etc. 14 circRNAs, and 33 lncRNAs can promote the expression of 12 of the P. euphratica SPLs by co-decoying miR156 in heteromorphic leaf morphogenesis. However, it was found that the effect of PeuSPL2-4 and PeuSPL9 in leaf shape development was contrasting to their homologous genes of Arabidopsis. Therefore, it was suggested that the SPL family were evolutionarily conserved for regulation growth, but were varies in different plant for regulation of the organ development.

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Section: Discussionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

Qin¹,

Bao

He³

et al. 2022

Sci Rep

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“…However, some researchers indicated that P. euphratica population regeneration in the lower reaches of Tarim River showed a decline type, the proportion of young plants in the population decreased significantly or even lacked, population was mostly over mature forest plants and the overall performance of the decline trend ( Zhou et al, 2018 ). Currently, most studies of P. euphratica were focus on heteromorphic leaves ( Li et al, 2020a ; Li et al, 2020b ), photosynthetic physiological characteristics ( Wang et al, 2014 ), water use efficiency ( Zhou et al, 2019 ), population structure ( Miao et al, 2020 ), etc , while few studies on the relationship between plant and rhizosphere soil fungal community composition and diversity. Therefore, the goal of our work was to (1) analyze the composition and diversity of rhizosphere soil fungi of P. euphratica at different growth stages in the lower reaches of the Tarim River; (2) explore the dominant fungi in the P. euphratica rhizosphere at different stages, and the change of rhizosphere soil physical and chemical properties; (3) elucidate the correlation between fungal community composition and environmental factors.…”

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing reveals rhizosphere fungal community composition and diversity at different growth stages of Populus euphratica in the lower reaches of the Tarim River

Dang

et al. 2022

PeerJ

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Background Populus euphratica is one of the most ancient and primitive tree species of Populus spp and plays an important role in maintaining the ecological balance in desert areas. To decipher the diversity, community structure, and relationship between rhizosphere fungi and environmental factors at different growth stages of P. euphratica demands an in-depth investigation. Methods In this study, P. euphratica at different growth stages (young, medium, overripe, and decline periods) was selected as the research object, based on the determination of the physicochemical properties of its rhizosphere soil, the fungal community structure and diversity of P. euphratica and their correlation with soil physicochemical properties were comprehensively analyzed through high-throughput sequencing technology (internal transcribed spacer (ITS)) and bioinformatics analysis methods. Results According to the analysis of OTU annotation results, the rhizosphere soil fungal communities identified in Populus euphratica were categorized into10 phyla, 36 classes, 77 orders, 165 families, 275 genera and 353 species. The alpha diversity analysis showed that there was no obvious change between the different growth stages, while beta diversity analysis showed that there were significantly differences in the composition of rhizosphere soil fungal communities between mature and overripe trees (R2 = 0.31, P = 0.001), mature and deadwood (R2 = 0.28, P = 0.001). Ascomycota and Basidiomycota were dominant phyla in the rhizosphere fungal community and the dominant genera were Geopora, Chondrostereum and unidentified_Sordariales_sp. The relative abundance of the top ten fungi at each classification level differed greatly in different stages. Canonical correspondence analysis (CCA) and Spearman’s correlation analysis showed that conductivity (EC) was the main soil factor affecting the composition of Populus euphratica rhizosphere soil fungal community (P < 0.01), followed by total dissolvable salts (TDS) and available potassium (AK) (P < 0.05). Conclusions Our data revealed that the rhizosphere fungal communities at the different growth stages of P. euphratica have differences, conductivity (EC) was the key factor driving rhizosphere fungi diversity and community structure, followed by total dissolvable salts (TDS) and available potassium (AK).

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“…In tomato (solanum lycopersicum L.), 163 circRNAs responded to low temperature stress [32]. In Populus Euphratica Oliv, 18 circRNAs participated in the stress response [33]. In Arabidopsis, overexpression of a circRNA derived from glycerol-3-p acyltransferase (ATS1), Vv-circATS1, improved cold tolerance [34].…”

Section: Introductionmentioning

confidence: 99%

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

Cui

Dai

et al. 2020

IJMS

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Sugar beet is an important sugar-yielding crop with some tolerance to salt, but the mechanistic basis of this tolerance is not known. In the present study, we have used whole-transcriptome RNA-seq and degradome sequencing in response to salt stress to uncover differentially expressed (DE) mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in both leaves and roots. A competitive endogenous RNA (ceRNA) network was constructed with the predicted DE pairs, which revealed regulatory roles under salt stress. A functional analysis suggests that ceRNAs are implicated in copper redistribution, plasma membrane permeability, glycometabolism and energy metabolism, NAC transcription factor and the phosphoinositol signaling system. Overall, we conducted for the first time a full transcriptomic analysis of sugar beet under salt stress that involves a potential ceRNA network, thus providing a basis to study the potential functions of lncRNAs/circRNAs.

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Identification and functional prediction of circRNAs in Populus Euphratica Oliv. heteromorphic leaves

Cited by 19 publications

References 36 publications

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

High-throughput sequencing reveals rhizosphere fungal community composition and diversity at different growth stages of Populus euphratica in the lower reaches of the Tarim River

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

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