Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)

Abstract Background LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive. Results For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding. Conclusions We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.

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Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

10.1101/2021.12.09.471732 ◽

2021 ◽

Author(s):

Laszlo G Nagy ◽

Peter Jan Vonk ◽

Markus Kunzler ◽

Csenge Foldi ◽

Mate Viragh ◽

...

Keyword(s):

Cell Wall ◽

Fruiting Body ◽

Expression Patterns ◽

Schizophyllum Commune ◽

Gene Families ◽

Second Phase ◽

Fruiting Bodies ◽

Body Development ◽

Fruiting Body Development

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Key words: functional annotation; comparative genomics; cell wall remodeling; development; fruiting body morphogenesis; mushroom; transcriptome

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Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Biomolecules ◽

10.3390/biom9100609 ◽

2019 ◽

Vol 9 (10) ◽

pp. 609 ◽

Cited By ~ 1

Author(s):

Shan ◽

Yang ◽

Xu ◽

Zhu ◽

Gao

Keyword(s):

Cell Wall ◽

Gene Family ◽

Secondary Cell Wall ◽

Expression Patterns ◽

Wood Property ◽

Moso Bamboo ◽

Functional Studies ◽

Bamboo Shoots ◽

Potential Association ◽

Nac Gene Family

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

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Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development

Communications Biology ◽

10.1038/s42003-020-0969-2 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Maria Victoria Gomez Roldan ◽

Farhaj Izhaq ◽

Marion Verdenaud ◽

John Eleblu ◽

Aimen Haraghi ◽

...

Keyword(s):

Gene Networks ◽

Growth Arrest ◽

Reproductive Organs ◽

Stress Signaling ◽

Rna Seq ◽

Genome Wide Analysis ◽

Inhibition Of Growth ◽

Genome Wide ◽

Male Flowers

AbstractIn cucurbits, CmWIP1 is a master gene controlling sex determination. To bring new insight in the function of CmWIP1, we investigated two Arabidopsis WIP transcription factors, AtWIP1/TT1 and AtWIP2/NTT. Using an inducible system we showed that WIPs are powerful inhibitor of growth and inducer of cell death. Using ChIP-seq and RNA-seq we revealed that most of the up-regulated genes bound by WIPs display a W-box motif, associated with stress signaling. In contrast, the down-regulated genes contain a GAGA motif, a known target of polycomb repressive complex. To validate the role of WIP proteins in inhibition of growth, we expressed AtWIP1/TT1 in carpel primordia and obtained male flowers, mimicking CmWIP1 function in melon. Using other promoters, we further demonstrated that WIPs can trigger growth arrest of both vegetative and reproductive organs. Our data supports an evolutionary conserved role of WIPs in recruiting gene networks controlling growth and adaptation to stress.

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The role of HD-ZIP III transcription factors and miR165/166 in vascular development and secondary cell wall formation

Plant Signaling & Behavior ◽

10.1080/15592324.2015.1078955 ◽

2015 ◽

Vol 10 (10) ◽

pp. e1078955 ◽

Cited By ~ 19

Author(s):

Qian Du ◽

Huanzhong Wang

Keyword(s):

Cell Wall ◽

Transcription Factors ◽

Secondary Cell Wall ◽

Vascular Development ◽

Cell Wall Formation ◽

Secondary Cell Wall Formation ◽

Wall Formation

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The role of SND2 in the regulation of Arabidopsisfibre secondary cell wall formation

BMC Proceedings ◽

10.1186/1753-6561-5-s7-p114 ◽

2011 ◽

Vol 5 (S7) ◽

Cited By ~ 1

Author(s):

Steven Hussey ◽

Eshchar Mizrachi ◽

David Berger ◽

Alexander Myburg

Keyword(s):

Cell Wall ◽

Secondary Cell Wall ◽

Cell Wall Formation ◽

Secondary Cell Wall Formation ◽

Wall Formation

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Identification of Putative Cell Wall Synthesis Genes in Betula pendula

10.21203/rs.3.rs-33560/v2 ◽

2020 ◽

Author(s):

Song Chen ◽

Xin Lin ◽

Xiyang Zhao ◽

Su Chen

Keyword(s):

Cell Wall ◽

Betula Pendula ◽

Secondary Cell Wall ◽

Plant Cell Wall ◽

Gene Families ◽

Cellulose Synthase ◽

Wall Structure ◽

Cellulose Synthesis ◽

Cell Wall Synthesis ◽

Secondary Cell Wall Synthesis

Abstract BackgroundCellulose is an essential structural component of plant cell wall and is an important resource to produce paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues.ResultsHere, we identified 46 gene models in 7 gene families which encoding cellulose synthase and related enzymes of Betula pendula, and the transcript abundance of these genes in xylem, root, leaf and flower tissues also be determined. Based on these RNA-seq data, we have identified 8 genes that most likely participate in secondary cell wall synthesis, which include 3 cellulose synthase genes and 5 cellulose synthase-like genes. In parallel, a gene co-expression network was also constructed based on transcriptome sequencing.ConclusionsIn this study, we have identified a total of 46 cell wall synthesis genes in B. pendula, which include 8 secondary cell wall synthesis genes. These analyses will help decipher the genetic information of the cell wall synthesis genes, elucidate the molecular mechanism of cellulose synthesis and understand the cell wall structure in B. pendula.

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Cellulosic fibres of flax recruit both primary and secondary cell wall cellulose synthases during deposition of thick tertiary cell walls and in the course of graviresponse

Functional Plant Biology ◽

10.1071/fp17105 ◽

2017 ◽

Vol 44 (8) ◽

pp. 820 ◽

Cited By ~ 16

Author(s):

Natalia Mokshina ◽

Oleg Gorshkov ◽

Nadezda Ibragimova ◽

Tatyana Chernova ◽

Tatyana Gorshkova

Keyword(s):

Cell Wall ◽

Cell Walls ◽

Secondary Cell Wall ◽

Rna Seq ◽

Specific Mechanism ◽

Linum Usitatissimum L ◽

Cellulose Synthases ◽

Cellulosic Fibres ◽

Coexpression Networks ◽

Cesa Genes

Cellulose synthesising complex consists of cellulose synthase (CESA) subunits encoded by a multigene family; different sets of CESA genes are known to be expressed during primary and secondary cell wall formation. We examined the expression of LusCESAs in flax (Linum usitatissimum L.) cellulosic fibres at various stages of development and in the course of graviresponse by means of RNA-Seq and quantitative PCR. Transcripts for both primary and secondary cell wall-related CESAs were abundant in fibres depositing highly cellulosic tertiary cell walls. Gravistimulation of flax plants temporally increased the abundance of CESA transcripts, specifically in phloem fibres located at the pulling stem side. Construction of coexpression networks for LusCESAs revealed that both primary and secondary cell wall-related CESAs were involved in the joint coexpression group in fibres depositing tertiary cell walls, as distinct from other tissues, where these genes were within separate groups. The obtained data suggest that fibres depositing tertiary cell walls have a specific mechanism of cellulose biosynthesis and a specific way of its regulation.

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Coordinated analysis of exon and intron data reveals novel differential gene expression changes

Scientific Reports ◽

10.1038/s41598-020-72482-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Hamid R. Eghbalnia ◽

William W. Wilfinger ◽

Karol Mackey ◽

Piotr Chomczynski

Keyword(s):

Gene Networks ◽

Expression Data ◽

Rna Seq ◽

Data Set ◽

Exon Expression ◽

Regulatory Processes ◽

Pathway Gene ◽

Immune Pathway ◽

Archived Data

Abstract RNA-Seq expression analysis currently relies primarily upon exon expression data. The recognized role of introns during translation, and the presence of substantial RNA-Seq counts attributable to introns, provide the rationale for the simultaneous consideration of both exon and intron data. We describe here a method for the coordinated analysis of exon and intron data by investigating their relationship within individual genes and across samples, while taking into account changes in both variability and expression level. This coordinated analysis of exon and intron data offers strong evidence for significant differences that distinguish the profiles of the exon-only expression data from the combined exon and intron data. One advantage of our proposed method, called matched change characterization for exons and introns (MEI), is its straightforward applicability to existing archived data using small modifications to standard RNA-Seq pipelines. Using MEI, we demonstrate that when data are examined for changes in variability across control and case conditions, novel differential changes can be detected. Notably, when MEI criteria were employed in the analysis of an archived data set involving polyarthritic subjects, the number of differentially expressed genes was expanded by sevenfold. More importantly, the observed changes in exon and intron variability with statistically significant false discovery rates could be traced to specific immune pathway gene networks. The application of MEI analysis provides a strategy for incorporating the significance of exon and intron variability and further developing the role of using both exons and intron sequencing counts in studies of gene regulatory processes.

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A role of cotyledons and sucrose in the differentiation of primary phloem fibers in hypocotyls of sunflower seedlings

Canadian Journal of Botany ◽

10.1139/b84-238 ◽

1984 ◽

Vol 62 (8) ◽

pp. 1763-1766 ◽

Cited By ~ 1

Author(s):

Ilabanta Mukherjee ◽

Edward C. Yeung ◽

David M. Reid

Keyword(s):

Cell Wall ◽

Secondary Cell Wall ◽

Dry Weight ◽

Wall Thickening ◽

Fresh Weight ◽

Phloem Fibers ◽

Secondary Cell Wall Thickening ◽

Stimulation Of

Sucrose treatment of the hypocotyls of derooted 7-day-old sunflower seedlings stimulated growth of hypocotyls as measured by dry weight. The fresh weight of the hypocotyls was unaffected. Stimulatory effect of sucrose was much greater in the presence of the cotyledons than in their absence. Cotyledons also influenced the differentiation of primary phloem fibers in the hypocotyls of seedlings, although when cotyledons were removed, induction of some phloem fiber differentiation was possible by sucrose treatment alone. In the presence of the cotyledons, sucrose in the concentrations of 0.025 and 0.05 M greatly enhanced primary phloem fiber differentiation and secondary cell wall thickening. Stimulation of dry weight of the hypocotyls by sucrose treatment in the presence of the cotyledons may be due to enhanced secondary cell wall thickening.

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