Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar

Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory...

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Main Authors: Huilin Wang, Pan Zhao, Yumei He, Yuting Su, Xinyi Zhou, Huihong Guo
Format: Article
Language:English
Published: MDPI AG 2023-11-01
Series:International Journal of Molecular Sciences
Subjects:
Online Access:https://www.mdpi.com/1422-0067/24/22/16438
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author Huilin Wang
Pan Zhao
Yumei He
Yuting Su
Xinyi Zhou
Huihong Guo
author_facet Huilin Wang
Pan Zhao
Yumei He
Yuting Su
Xinyi Zhou
Huihong Guo
author_sort Huilin Wang
collection DOAJ
description Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (<i>Populus alba</i> × <i>Populus glandulosa</i> clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-<i>PagGRFs</i>, PagmiR395c-<i>PagGA2ox1</i>/<i>PagLHW</i>/<i>PagSULTR2</i>/<i>PagPolyubiquitin</i> 1, PagmiR482d-<i>PagLAC4</i>, PagmiR167e-<i>PagbHLH62</i>, and PagmiR167f/g/h-<i>PagbHLH110</i> modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.
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spelling doaj.art-f2e8960433ba4078892534fee16a13c52023-11-24T14:47:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-11-0124221643810.3390/ijms242216438Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” PoplarHuilin Wang0Pan Zhao1Yumei He2Yuting Su3Xinyi Zhou4Huihong Guo5State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, ChinaSecondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (<i>Populus alba</i> × <i>Populus glandulosa</i> clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-<i>PagGRFs</i>, PagmiR395c-<i>PagGA2ox1</i>/<i>PagLHW</i>/<i>PagSULTR2</i>/<i>PagPolyubiquitin</i> 1, PagmiR482d-<i>PagLAC4</i>, PagmiR167e-<i>PagbHLH62</i>, and PagmiR167f/g/h-<i>PagbHLH110</i> modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.https://www.mdpi.com/1422-0067/24/22/16438“84K” poplarsecondary xylem formationtranscriptomemiRNAstranscriptional regulation
spellingShingle Huilin Wang
Pan Zhao
Yumei He
Yuting Su
Xinyi Zhou
Huihong Guo
Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
International Journal of Molecular Sciences
“84K” poplar
secondary xylem formation
transcriptome
miRNAs
transcriptional regulation
title Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
title_full Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
title_fullStr Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
title_full_unstemmed Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
title_short Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in “84K” Poplar
title_sort transcriptome and mirnas profiles reveal regulatory network and key regulators of secondary xylem formation in 84k poplar
topic “84K” poplar
secondary xylem formation
transcriptome
miRNAs
transcriptional regulation
url https://www.mdpi.com/1422-0067/24/22/16438
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