Integration of Small RNA, Degradome, and Transcriptome Sequencing Data Illustrates the Mechanism of Low Phosphorus Adaptation in

Overview

Journal Front Plant Sci

Date 2022 Aug 18

PMID 35979079

Authors

Juanjuan Chen

Xiaojiao Han

Sicheng Ye

Linxiu Liu

Bingbing Yang

Yongqing Cao

Renying Zhuo

Xiaohua Yao

Affiliations

Soon will be listed here.

Abstract

Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in . We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (, , and ), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.

Citing Articles

Cataloging the Genetic Response: Unveiling Drought-Responsive Gene Expression in Oil Tea Camellia ( Abel.) through Transcriptomics.

Zhang Z, Xu Y, Liu C, Chen L, Zhang Y, He Z Life (Basel). 2024; 14(8).

PMID: 39202731 PMC: 11355629. DOI: 10.3390/life14080989.

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of L.

Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E Int J Mol Sci. 2024; 25(1).

PMID: 38203780 PMC: 10779315. DOI: 10.3390/ijms25010607.

Genome-Wide Detection of SPX Family and Profiling of in Regulating Low-Phosphate Stress in Tea-Oil .

Chen J, Han X, Liu L, Yang B, Zhuo R, Yao X Int J Mol Sci. 2023; 24(14).

PMID: 37511309 PMC: 10380294. DOI: 10.3390/ijms241411552.

Genome-wide identification of the WRKY gene family in and expression analysis under phosphorus deficiency.

Su W, Zhou Z, Zeng J, Cao R, Zhang Y, Hu D Front Plant Sci. 2023; 14:1082496.

PMID: 37304714 PMC: 10249505. DOI: 10.3389/fpls.2023.1082496.

Genomic and genetic advances of oiltea-camellia ().

Ye C, He Z, Peng J, Wang R, Wang X, Fu M Front Plant Sci. 2023; 14:1101766.

PMID: 37077639 PMC: 10106683. DOI: 10.3389/fpls.2023.1101766.

References

Crombez H, Motte H, Beeckman T . Tackling Plant Phosphate Starvation by the Roots. Dev Cell. 2019; 48(5):599-615. DOI: 10.1016/j.devcel.2019.01.002. View

Liu Q, Zhou Z, Wei Y, Shen D, Feng Z, Hong S . Genome-Wide Identification of Differentially Expressed Genes Associated with the High Yielding of Oleoresin in Secondary Xylem of Masson Pine (Pinus massoniana Lamb) by Transcriptomic Analysis. PLoS One. 2015; 10(7):e0132624. PMC: 4500461. DOI: 10.1371/journal.pone.0132624. View

Kvam V, Liu P, Si Y . A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. Am J Bot. 2012; 99(2):248-56. DOI: 10.3732/ajb.1100340. View

Liu Z, Wang X, Chen X, Shi G, Bai Q, Xiao K . TaMIR1139: a wheat miRNA responsive to Pi-starvation, acts a critical mediator in modulating plant tolerance to Pi deprivation. Plant Cell Rep. 2018; 37(9):1293-1309. DOI: 10.1007/s00299-018-2313-6. View

Bai Q, Wang X, Chen X, Shi G, Liu Z, Guo C . Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes. Front Plant Sci. 2018; 9:499. PMC: 5916090. DOI: 10.3389/fpls.2018.00499. View

Wang Z, Kuo H, Chiou T . Intracellular phosphate sensing and regulation of phosphate transport systems in plants. Plant Physiol. 2022; 187(4):2043-2055. PMC: 8644344. DOI: 10.1093/plphys/kiab343. View

Hsieh L, Lin S, Shih A, Chen J, Lin W, Tseng C . Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 2009; 151(4):2120-32. PMC: 2785986. DOI: 10.1104/pp.109.147280. View

Wang S, Liu L, Mi X, Zhao S, An Y, Xia X . Multi-omics analysis to visualize the dynamic roles of defense genes in the response of tea plants to gray blight. Plant J. 2021; 106(3):862-875. DOI: 10.1111/tpj.15203. View

Li A, Hu B, Chu C . Epigenetic regulation of nitrogen and phosphorus responses in plants. J Plant Physiol. 2021; 258-259:153363. DOI: 10.1016/j.jplph.2021.153363. View

10.

Jia X, Wang L, Zeng H, Yi K . Insights of intracellular/intercellular phosphate transport and signaling in unicellular green algae and multicellular land plants. New Phytol. 2021; 232(4):1566-1571. DOI: 10.1111/nph.17716. View

11.

Shi J, Zhao B, Zheng S, Zhang X, Wang X, Dong W . A phosphate starvation response-centered network regulates mycorrhizal symbiosis. Cell. 2021; 184(22):5527-5540.e18. DOI: 10.1016/j.cell.2021.09.030. View

12.

Addo-Quaye C, Miller W, Axtell M . CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics. 2008; 25(1):130-1. PMC: 3202307. DOI: 10.1093/bioinformatics/btn604. View

13.

Li Z, Xu H, Li Y, Wan X, Ma Z, Cao J . Analysis of physiological and miRNA responses to Pi deficiency in alfalfa (Medicago sativa L.). Plant Mol Biol. 2018; 96(4-5):473-492. DOI: 10.1007/s11103-018-0711-3. View

14.

Liu X, Yang Y, Wang R, Cui R, Xu H, Sun C . GmWRKY46, a WRKY transcription factor, negatively regulates phosphorus tolerance primarily through modifying root morphology in soybean. Plant Sci. 2022; 315:111148. DOI: 10.1016/j.plantsci.2021.111148. View

15.

Bao H, Chen H, Chen M, Xu H, Huo X, Xu Q . Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa. Funct Integr Genomics. 2019; 19(6):953-972. DOI: 10.1007/s10142-019-00692-1. View

16.

Peng K, Tian Y, Sun X, Song C, Ren Z, Bao Y . tae-miR399- Module Enhances Freezing Tolerance in Winter Wheat via a CBF Signaling Pathway. J Agric Food Chem. 2021; 69(45):13398-13415. DOI: 10.1021/acs.jafc.1c04316. View

17.

Dai X, Lu Q, Wang J, Wang L, Xiang F, Liu Z . MiR160 and its target genes ARF10, ARF16 and ARF17 modulate hypocotyl elongation in a light, BRZ, or PAC-dependent manner in Arabidopsis: miR160 promotes hypocotyl elongation. Plant Sci. 2021; 303:110686. DOI: 10.1016/j.plantsci.2020.110686. View

18.

Sun X, Lin L, Sui N . Regulation mechanism of microRNA in plant response to abiotic stress and breeding. Mol Biol Rep. 2018; 46(1):1447-1457. DOI: 10.1007/s11033-018-4511-2. View

19.

Ma X, Denyer T, Javelle M, Feller A, Timmermans M . Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts. Genome Res. 2021; 31(5):811-822. PMC: 8092011. DOI: 10.1101/gr.270918.120. View

20.

Wang Y, Wang F, Lu H, Liu Y, Mao C . Phosphate Uptake and Transport in Plants: An Elaborate Regulatory System. Plant Cell Physiol. 2021; 62(4):564-572. DOI: 10.1093/pcp/pcab011. View