Deep transcriptomic study reveals the role of cell wall biosynthesis and organization networks in the developing shell of peanut pod

Abstract Background Peanut (Arachis hypogaea L.) belongs to an exceptional group of legume plants, wherein the flowers are produced aerially, but the pods develop under the ground. In such a unique environment, the pod’s outer shell plays a vital role as a barrier against mechanical damage and soilborne pathogens. Recent studies have reported the uniqueness and importance of gene expression patterns that accompany peanut pods’ biogenesis. These studies focused on biogenesis and pod development during the early stages, but the late developmental stages and disease resistance aspects still have gaps. To extend this information, we analyzed the transcriptome generated from four pod developmental stages of two genotypes, Hanoch (Virginia-type) and IGC53 (Peruvian-type), which differs significantly in their pod shell characteristics and pathogen resistance. Results The transcriptome study revealed a significant reprogramming of the number and nature of differentially expressed (DE) genes during shell development. Generally, the numbers of DE genes were higher in IGC53 than in Hanoch, and the R5-R6 transition was the most dynamic in terms of transcriptomic changes. Genes related to cell wall biosynthesis, modification and transcription factors (TFs) dominated these changes therefore, we focused on their differential, temporal and spatial expression patterns. Analysis of the cellulose synthase superfamily identified specific Cellulose synthase (CesAs) and Cellulose synthase-like (Csl) genes and their coordinated interplay with other cell wall-related genes during the peanut shell development was demonstrated. TFs were also identified as being involved in the shell development process, and their pattern of expression differed in the two peanut genotypes. The shell component analysis showed that overall crude fiber, cellulose, lignin, hemicelluloses and dry matter increased with shell development, whereas K, N, protein, and ash content decreased. Genotype IGC53 contained a higher level of crude fiber, cellulose, NDF, ADF, K, ash, and dry matter percentage, while Hanoch had higher protein and nitrogen content. Conclusions The comparative transcriptome analysis identified differentially expressed genes, enriched processes, and molecular processes like cell wall biosynthesis/modifications, carbohydrate metabolic process, signaling, transcription factors, transport, stress, and lignin biosynthesis during the peanut shell development between two contrasting genotypes. TFs and other genes like chitinases were also enriched in peanut shells known for pathogen resistance against soilborne major pathogens causing pod wart disease and pod damages. This study will shed new light on the biological processes involved with underground pod development in an important legume crop.

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Differential expression patterns reveal the roles of cellulose synthase genes (CesAs) in primary and secondary cell wall biosynthesis in Miscanthus × giganteus

Industrial Crops and Products ◽

10.1016/j.indcrop.2020.112129 ◽

2020 ◽

Vol 145 ◽

pp. 112129 ◽

Cited By ~ 1

Author(s):

Xiaofei Zeng ◽

Jiajing Sheng ◽

Fenglin Zhu ◽

Lingling Zhao ◽

Xiaohu Hu ◽

...

Keyword(s):

Cell Wall ◽

Differential Expression ◽

Secondary Cell Wall ◽

Expression Patterns ◽

Cellulose Synthase ◽

Cell Wall Biosynthesis ◽

Secondary Cell Wall Biosynthesis ◽

Miscanthus Giganteus

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Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0809408105 ◽

2008 ◽

Vol 105 (51) ◽

pp. 20534-20539 ◽

Cited By ~ 55

Author(s):

M. A. Held ◽

B. Penning ◽

A. S. Brandt ◽

S. A. Kessans ◽

W. Yong ◽

...

Keyword(s):

Cell Wall ◽

Cellulose Synthase ◽

Cell Wall Biosynthesis ◽

Small Interfering Rnas ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Cellulose Synthase Gene

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AtHB7/12 Regulate Root Growth in Response to Aluminum Stress

International Journal of Molecular Sciences ◽

10.3390/ijms21114080 ◽

2020 ◽

Vol 21 (11) ◽

pp. 4080

Author(s):

Yang Liu ◽

Jiameng Xu ◽

Siyi Guo ◽

Xianzheng Yuan ◽

Shan Zhao ◽

...

Keyword(s):

Cell Wall ◽

Transcription Factors ◽

Root Growth ◽

Crop Production ◽

Expression Patterns ◽

Acid Soils ◽

Limiting Factor ◽

Aluminum Stress ◽

Al Stress

Aluminum (Al) stress is a major limiting factor for plant growth and crop production in acid soils. At present, only a few transcription factors involved in the regulation of Al resistance have been characterized. Here, we used reversed genetic approach through phenotype analysis of overexpressors and mutants to demonstrate that AtHB7 and AtHB12, two HD-Zip I transcription factors, participate in Al resistance. In response to Al stress, AtHB7 and AtHB12 displayed different dynamic expression patterns. Although both AtHB7 and AtHB12 positively regulate root growth in the absence of Al stress, our results showed that AtHB7 antagonizes with AtHB12 to control root growth in response to Al stress. The athb7/12 double mutant displayed a wild-type phenotype under Al stress. Consistently, our physiological analysis showed that AtHB7 and AtHB12 oppositely regulate the capacity of cell wall to bind Al. Yeast two hybrid assays showed that AtHB7 and AtHB12 could form homo-dimers and hetero-dimers in vitro, suggesting the interaction between AtHB7 and AtHB12 in the regulation of root growth. The conclusion was that AtHB7 and AtHB12 oppositely regulate Al resistance by affecting Al accumulation in root cell wall.

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Auxin and Cell Wall Crosstalk as Revealed by the Arabidopsis thaliana Cellulose Synthase Mutant Radially Swollen 1

Plant and Cell Physiology ◽

10.1093/pcp/pcz055 ◽

2019 ◽

Vol 60 (7) ◽

pp. 1487-1503 ◽

Cited By ~ 3

Author(s):

Thiel A. Lehman ◽

Karen A Sanguinet

Keyword(s):

Arabidopsis Thaliana ◽

Cell Wall ◽

Cellulose Synthase ◽

Cellulose Microfibrils ◽

Single Amino Acid ◽

Cell Wall Biosynthesis ◽

Restrictive Temperature ◽

Permissive Temperature ◽

Anisotropic Expansion ◽

Single Amino Acid Change

AbstractPlant cells sheath themselves in a complex lattice of polysaccharides, proteins and enzymes forming an integral matrix known as the cell wall. Cellulose microfibrils, the primary component of cell walls, are synthesized at the plasma membrane by CELLULOSE SYNTHASE A (CESA) proteins throughout cellular growth and are responsible for turgor-driven anisotropic expansion. Associations between hormone signaling and cell wall biosynthesis have long been suggested, but recently direct links have been found revealing hormones play key regulatory roles in cellulose biosynthesis. The radially swollen 1 (rsw1) allele of Arabidopsis thaliana CESA1 harbors a single amino acid change that renders the protein unstable at high temperatures. We used the conditional nature of rsw1 to investigate how auxin contributes to isotropic growth. We found that exogenous auxin treatment reduces isotropic swelling in rsw1 roots at the restrictive temperature of 30ï¿½C. We also discovered decreases in auxin influx between rsw1 and wild-type roots via confocal imaging of AUX1-YFP, even at the permissive temperature of 19ï¿½C. Moreover, rsw1 displayed mis-expression of auxin-responsive and CESA genes. Additionally, we found altered auxin maxima in rsw1 mutant roots at the onset of swelling using DII-VENUS and DR5:vYFP auxin reporters. Overall, we conclude disrupted cell wall biosynthesis perturbs auxin transport leading to altered auxin homeostasis impacting both anisotropic and isotropic growth that affects overall root morphology.

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A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis

The Plant Cell ◽

10.1105/tpc.108.061325 ◽

2008 ◽

Vol 20 (10) ◽

pp. 2763-2782 ◽

Cited By ~ 506

Author(s):

Ruiqin Zhong ◽

Chanhui Lee ◽

Jianli Zhou ◽

Ryan L. McCarthy ◽

Zheng-Hua Ye

Keyword(s):

Cell Wall ◽

Transcription Factors ◽

Secondary Cell Wall ◽

Cell Wall Biosynthesis ◽

Secondary Cell Wall Biosynthesis

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Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽

10.1186/s12864-021-08186-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jing Ma ◽

Jia-xi Dai ◽

Xiao-wei Liu ◽

Duo Lin

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Transient Expression Assay ◽

Specific Expression ◽

Tissue Specific ◽

Duplication Events ◽

Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

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Dimorphic Expression of Selected Genes in Lepidocephalus thermalis using Cross-Specific Primers

Legume Research - An International Journal ◽

10.18805/ijar.b-3895 ◽

2020 ◽

Author(s):

M. Balaganesan ◽

K. Karalmarx ◽

R. Jeya Shakila

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Developmental Stages ◽

Sex Differentiation ◽

Expression Patterns ◽

Gonadal Development ◽

Expression Study ◽

Specific Primers ◽

Qrt Pcr ◽

Dimorphic Expression

Background: The existence of two distinct forms within a species that differ in one or more characteristics is known as dimorphism. The gonads are the primary organs in teleost to show sexual dimorphism. Lepidocephalus thermalis belongs to the Cobitidae family. No expression study on the developmental stages was done on this species. Since there is no specific primers reported for L. thermalis, the study has been carried out with the help of the specific primers of catfish. Methods: qRT- PCR is an acknowledged method for gene expression analysis due to its precision and reproducibility. In the current study, the expression of 14 different transcription factors involved in sex differentiation of Indian spiny loach during different developmental stages was analyzed using qRT- PCR and has been compared among the different stages of gonadal development for that transcription factor. Results: Gene expression patterns have been obtained from the total RNA isolated from MSG (Meso nephric gonadal complex), medium stage ovary, medium stage testis, large stage ovary and large stage testis. From the study, it has been analyzed that only sf1 has higher expression in testis and all the other transcription factors has shown higher expression in ovary.

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Erratum to Development of functional modules based on co-expression patterns for cell-wall biosynthesis related genes in rice

Journal of Plant Biology ◽

10.1007/s12374-016-0901-y ◽

2016 ◽

Vol 59 (4) ◽

pp. 405-405 ◽

Cited By ~ 1

Author(s):

Anil Kumar Nalini Chandran ◽

Ho Young Jeong ◽

Ki-Hong Jung ◽

Chanhui Lee

Keyword(s):

Cell Wall ◽

Expression Patterns ◽

Cell Wall Biosynthesis ◽

Functional Modules

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Expression Patterns and Gene Analysis of the Cellulose Synthase Gene Superfamily in Eucalyptus grandis

Forests ◽

10.3390/f12091254 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1254

Author(s):

Guo Liu ◽

Yaojian Xie ◽

Xiuhua Shang ◽

Zhihua Wu

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Expression Pattern ◽

Expression Patterns ◽

Cellulose Synthase ◽

Primary Cell Wall ◽

Regulation Mechanism ◽

Cellulose Content ◽

Qrt Pcr ◽

Different Parts

Cellulose is the world’s most abundant renewable energy resource, and a variety of cellulose synthase genes are involved in the biosynthesis of cellulose. In the process of cellulose synthesis, all cellulose synthases are interrelated and act synergistically. In this study, we analyzed the contents of cellulose, hemicellulose, and lignin in the different parts and tissues of E. grandis. The results showed that the cellulose content had greater differences among three different heights. On this basis, we carried out the transcriptome-wide profiling of gene expression patterns using RNA sequencing. A total of 2066 differentially expressed genes were identified for three pairwise comparisons between three different heights, most of which were related to the programmed photosynthetic membrane and photosystem. A total of 100 transcripts of CSs (58 CesA and 42 Csl) were obtained from transcriptome libraries. The expression pattern of these genes indicated that different CS genes had a wide range of expression profiles. A phylogenetic analysis of 135 reference CS genes showed that the CSs of E. grandis were clustered into six major groups (CesA1-9, CslA, CslB/H, CslD, CslE, and CslG). Based on the weighted gene co-expression network analysis, a dual-directional regulation mechanism between Csl and CesA proteins in the cellulose biosynthesis was identified. The gene expression profile analysis, using qRT-PCR in different tissues of E. grandis, demonstrated that the CSs were highly expressed in xylem, and CesAs had a higher relative expression than Csls. The analysis of sequence similarity combined with the expression pattern indicated that the CesA1, 3, and 6 transcripts were associated with the biosynthesis of the secondary cell wall, and CesA4, 5, and 7 transcripts were more likely to associate with the biosynthesis of the primary cell wall. Finally, the qRT-PCR analysis confirmed the expression of 11 selected CSs in three different parts of E. grandis.

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