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Transcriptome Analysis and Gene Regulation in Plant Growth Development

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 April 2023) | Viewed by 17380

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Special Issue Editors

Dr. Yi He

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Guest Editor

College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: photosynthesis; signal transduction; gene regulation; flower development
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Dali Zeng

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Guest Editor

College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: molecular breeding; gene regulation; plant genetics and genomics
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Transcriptome sequencing has become more and more important in order to understand biological phenomena, and provides a vital insight for understanding gene regulatory mechanisms in the process of plant growth development. Therefore, it is a hot topic for many plant biologists on how to efficiently explore the information underlying the transcriptome sequencing to understand the gene regulatory mechanism for the phenomenon. In addition, an integrated multi-omics framework based on transcriptome has provided insight into the gene regulatory mechanism of plant growth development, especially in some non-model plants. The importance of new mathematical and statistical methods for transcriptome analysis will also help us better understand the hidden secrets of plant growth and development. This Special Issue of Plants will highlight the new tools, methods, strategies, and perspectives of transcriptome analysis and their role in explaining gene regulatory networks.

Dr. Yi He
Prof. Dr. Dali Zeng
Guest Editors

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Keywords

plant growth
plant development
transcriptome/genome analysis
genetics
gene expression
transcriptome
signal transduction
plant genome
transcriptome
proteome
gene expression
epigenetic regulations

Related Special Issue

Transcriptome Analysis and Gene Regulation in Plant Growth Development II in Plants (4 articles)

Published Papers (10 papers)

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Research

16 pages, 2239 KiB

Open AccessArticle

Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines

by Pan Zeng, Xianhong Ge and Zaiyun Li

Plants 2023, 12(10), 2029; https://doi.org/10.3390/plants12102029 - 18 May 2023

Viewed by 957

Abstract

Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available Brassica oleracea-nigra MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived B. oleracea plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental B. oleracea, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived B. oleracea plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to B. nigra, in all five MAALs more DEGs were downregulated than upregulated. Trans-effects were likely more prevailing than cis-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that cis- and trans-mechanisms synergistically regulated alien gene transcriptions after distant hybridization. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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17 pages, 4447 KiB

Open AccessArticle

Comparative Microscopic, Transcriptome and IAA Content Analyses Reveal the Stem Growth Variations in Two Cultivars Ilex verticillata

by Sini Qin, Siyi Fu, Ying Yang, Qiumin Sun, Jingqi Wang, Yanling Dong, Xinyi Gu, Tao Wang, Xiaoting Xie, Xiaorong Mo, Hangjin Jiang, Youxiang Yu, Jijun Yan, Jinfang Chu, Bingsong Zheng and Yi He

Plants 2023, 12(10), 1941; https://doi.org/10.3390/plants12101941 - 10 May 2023

Viewed by 1605

Abstract

Ilex verticillata is not only an excellent ornamental tree species for courtyards, but it is also a popular bonsai tree. ‘Oosterwijk’ and ‘Red sprite’ are two varieties of Ilex verticillata. The former has a long stem with few branches, while the latter has a short stem. In order to explain the stem growth differences between the two cultivars ‘Oosterwijk’ and ‘Red sprite’, determination of the microstructure, transcriptome sequence and IAA content was carried out. The results showed that the xylem thickness, vessel area and vessel number of ‘Oosterwijk’ were larger than in ‘Red sprite’. In addition, our analysis revealed that the differentially expressed genes which were enriched in phenylpropanoid biosynthesis; phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis in the black and tan modules of the two varieties. We found that AST, HCT and bHLH 94 may be key genes in the formation of shoot difference. Moreover, we found that the IAA content and auxin-related DEGs GH3.6, GH3, ATRP5, IAA27, SAUR36-like, GH3.6-like and AIP 10A5-like may play important roles in the formation of shoot differences. In summary, these results indicated that stem growth variations of ‘Oosterwijk’ and ‘Red sprite’ were associated with DEGs related to phenylpropanoid biosynthesis, phenylalanine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis, as well as auxin content and DEGs related to the auxin signaling pathway. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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24 pages, 4921 KiB

Open AccessArticle

Transcriptomics and Metabolomics Analysis Provides Insight into Leaf Color and Photosynthesis Variation of the Yellow-Green Leaf Mutant of Hami Melon (Cucumis melo L.)

by Hongwei Han, Yuan Zhou, Huifang Liu, Xianjun Chen, Qiang Wang, Hongmei Zhuang, Xiaoxia Sun, Qihua Ling, Huijun Zhang, Baike Wang, Juan Wang, Yaping Tang, Hao Wang and Huiying Liu

Plants 2023, 12(8), 1623; https://doi.org/10.3390/plants12081623 - 12 Apr 2023

Cited by 3 | Viewed by 1885

Abstract

Leaf color mutants are ideal materials for studying the regulatory mechanism of chloroplast development and photosynthesis. We isolated a cucumis melo spontaneous mutant (MT), which showed yellow-green leaf phenotype in the whole growing period and could be inherited stably. We compared its leaves with the wild type (WT) in terms of cytology, physiology, transcriptome and metabolism. The results showed that the thylakoid grana lamellae of MT were loosely arranged and fewer in number than WT. Physiological experiments also showed that MT had less chlorophyll content and more accumulation of reactive oxygen species (ROS) than WT. Furthermore, the activity of several key enzymes in C₄ photosynthetic carbon assimilation pathway was more enhanced in MT than WT. Transcriptomic and metabolomic analyses showed that differential expression genes and differentially accumulated metabolites in MT were mainly co-enriched in the pathways related to photosystem-antenna proteins, central carbon metabolism, glutathione metabolism, phenylpropanoid biosynthesis and flavonoid metabolism. We also analyzed several key proteins in photosynthesis and chloroplast transport by Western blot. In summary, the results may provide a new insight into the understanding of how plants respond to the impaired photosynthesis by regulating chloroplast development and photosynthetic carbon assimilation pathways. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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18 pages, 3364 KiB

Open AccessArticle

Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen

by Chenggong Liu, Na Duan, Xiaona Chen, Xu Li, Naqi Zhao, Wenxu Cao, Huiqing Li, Bo Liu, Fengsen Tan, Xiulian Zhao and Qinghe Li

Plants 2023, 12(4), 895; https://doi.org/10.3390/plants12040895 - 16 Feb 2023

Cited by 3 | Viewed by 1253

Abstract

To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L⁻¹ nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes’ responses to increased nitrogen in the future. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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16 pages, 3330 KiB

Open AccessArticle

Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6

by Wenjia Wang, Ruizhi Huang, Gengwei Wu, Jian Sun, Ying Zhu and Hua Wang

Plants 2023, 12(4), 871; https://doi.org/10.3390/plants12040871 - 15 Feb 2023

Viewed by 1346

Abstract

Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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19 pages, 4882 KiB

Open AccessArticle

Comparative Transcriptome Analysis Reveals the Interaction of Sugar and Hormone Metabolism Involved in the Root Hair Morphogenesis of the Endangered Fir Abies beshanzuensis

by Bin Liu, Ke Liu, Xiaorong Chen, Duohong Xiao, Tingjin Wang, Yang Yang, Hui Shuai, Sumei Wu, Lu Yuan and Liping Chen

Plants 2023, 12(2), 276; https://doi.org/10.3390/plants12020276 - 06 Jan 2023

Cited by 1 | Viewed by 1284

Abstract

Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone–sucrose–root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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18 pages, 5849 KiB

Open AccessFeature PaperArticle

Reduced Expression of PRX2/ATPRX1, PRX8, PRX35, and PRX73 Affects Cell Elongation, Vegetative Growth, and Vasculature Structures in Arabidopsis thaliana

by Yu Jeong Jeong, Young-Cheon Kim, June Seung Lee, Dong-Gwan Kim and Jeong Hwan Lee

Plants 2022, 11(23), 3353; https://doi.org/10.3390/plants11233353 - 02 Dec 2022

Cited by 3 | Viewed by 1614

Abstract

Class III peroxidases (PRXs) are involved in a broad spectrum of physiological and developmental processes throughout the life cycle of plants. However, the specific function of each PRX member in the family remains largely unknown. In this study, we selected four class III peroxidase genes (PRX2/ATPRX1, PRX8, PRX35, and PRX73) from a previous genome-wide transcriptome analysis, and performed phenotypic and morphological analyses, including histochemical staining, in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi plants. The reduced mRNA levels of corresponding PRX genes in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi seedlings resulted in elongated hypocotyls and roots, and slightly faster vegetative growth. To investigate internal structural changes in the vasculature, we performed histochemical staining, which revealed alterations in cell wall structures in the main vasculature of hypocotyls, stems, and roots of each PRXRNAi plant compared to wild-type (Col-0) plants. Furthermore, we found that PRX35RNAi plants displayed the decrease in the cell wall in vascular regions, which are involved in downregulation of lignin biosynthesis and biosynthesis-regulated genes’ expression. Taken together, these results indicated that the reduced expression levels of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affected hypocotyl and root elongation, vegetative growth, and the vasculature structures in hypocotyl, stem, and root tissues, suggesting that the four class III PRX genes play roles in plant developmental processes. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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19 pages, 8869 KiB

Open AccessArticle

OsMADS58 Stabilizes Gene Regulatory Circuits during Rice Stamen Development

by Liping Shen, Feng Tian, Zhukuan Cheng, Qiang Zhao, Qi Feng, Yan Zhao, Bin Han, Yuhan Fang, Yanan Lin, Rui Chen, Donghui Wang, Wenfeng Sun, Jiaqi Sun, Hongyun Zeng, Nan Yao, Ge Gao, Jingchu Luo, Zhihong Xu and Shunong Bai

Plants 2022, 11(21), 2899; https://doi.org/10.3390/plants11212899 - 28 Oct 2022

Cited by 1 | Viewed by 1423

Abstract

Rice (Oryza sativa) OsMADS58 is a C-class MADS box protein, and characterization of a transposon insertion mutant osmads58 suggested that OsMADS58 plays a role in stamen development. However, as no null mutation has been obtained, its role has remained unclear. Here, we report that the CRISPR knockout mutant osmads58 exhibits complex altered phenotypes, including anomalous diploid germ cells, aberrant meiosis, and delayed tapetum degeneration. This CRISPR mutant line exhibited stronger changes in expression of OsMADS58 target genes compared with the osmads58 dSpm (transposon insertion) line, along with changes in multiple pathways related to early stamen development. Notably, transcriptional regulatory circuits in young panicles covering the stamen at stages 4–6 were substantially altered in the CRISPR line compared to the dSpm line. These findings strongly suggest that the pleiotropic effects of OsMADS58 on stamen development derive from a potential role in stabilizing gene regulatory circuits during early stamen development. Thus, this work opens new avenues for viewing and deciphering the regulatory mechanisms of early stamen development from a network perspective. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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14 pages, 1721 KiB

Open AccessArticle

Comparative Transcriptomics for Genes Related to Berberine and Berbamine Biosynthesis in Berberidaceae

by Neha Samir Roy, Nam-Il Park, Nam-Soo Kim, Yeri Park, Bo-Yun Kim, Young-Dong Kim, Ju-Kyung Yu, Yong-In Kim, Taeyoung Um, Soonok Kim and Ik-Young Choi

Plants 2022, 11(20), 2676; https://doi.org/10.3390/plants11202676 - 11 Oct 2022

Cited by 4 | Viewed by 1708

Abstract

Berberine and berbamine are bioactive compounds of benzylisoquinoline alkaloids (BIAs) present in Berberis species. The contents of berbamine are 20 times higher than berberine in leaf tissues in three closely related species: Berberis koreana, B. thunbergii and B. amurensis. This is the first report on the quantification of berberine compared to the berbamine in the Berberis species. Comparative transcriptome analyses were carried out with mRNAs from the leaf tissues of the three-species. The comparison of the transcriptomes of B. thunbergii and B. amurensis to those of B. koreana, B. thunbergii showed a consistently higher number of differentially expressed genes than B. amurensis in KEGG and DEG analyses. All genes encoding enzymes involved in berberine synthesis were identified and their expressions were variable among the three species. There was a single copy of CYP80A/berbamunine synthase in B. koreana. Methyltransferases and cytochrome P450 mono-oxidases (CYPs) are key enzymes for BIA biosynthesis. The current report contains the copy numbers and other genomic characteristics of the methyltransferases and CYPs in Berberis species. Thus, the contents of the current research are valuable for molecular characterization for the medicinal utilization of the Berberis species. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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16 pages, 7696 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification of R2R3-MYB Transcription Factor and Expression Analysis under Abiotic Stress in Rice

by Lihua Kang, Yangyang Teng, Qiwen Cen, Yunxia Fang, Quanxiang Tian, Xiaoqin Zhang, Hua Wang, Xian Zhang and Dawei Xue

Plants 2022, 11(15), 1928; https://doi.org/10.3390/plants11151928 - 25 Jul 2022

Cited by 12 | Viewed by 2387

Abstract

The myeloblastosis (MYB) family comprises a large group of transcription factors (TFs) that has a variety of functions. Among them, the R2R3-MYB type of proteins are the largest group in plants, which are involved in controlling various biological processes such as plant growth and development, physiological metabolism, defense, and responses to abiotic and biotic stresses. In this study, bioinformatics was adopted to conduct genome-wide identification of the R2R3-MYB TFs in rice. We identified 190 MYB TFs (99 R2R3-MYBs), which are unevenly distributed on the 12 chromosomes of rice. Based on the phylogenetic clustering and protein sequence characteristics, OsMYBs were classified into five subgroups, and 59.6% of the Os2R_MYB genes contained two introns. Analysis of cis-acting elements in the 2000 bp upstream region of Os2R_MYB genes showed that all Os2R_MYB genes contained plant hormones-related or stress-responsive elements since 91.9%, 79.8%, 79.8%, and 58.6% of Os2R_MYB genes contain ABRE, TGACG, CGTCA, and MBS motifs, respectively. Protein–protein network analysis showed that the Os2R_MYBs were involved in metabolic process, biosynthetic process, and tissue development. In addition, some genes showed a tissue-specific or developmental-stage-specific expression pattern. Moreover, the transcription levels of 20 Os2R_MYB genes under polyethylene glycol (PEG) and cadmium chloride (CdCl₂) stress inducers were dissected by qRT-PCR. The results indicated genes with an altered expression upon PEG or CdCl₂ stress induction. These results potentially supply a basis for further research on the role that Os2R_MYB genes play in plant development and stress responses. Full article

(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development)

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