Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper

Lee, Yeon Mi; Chae, Geun Young; Kim, Min Kyung; Kim, Seungill

doi:10.3390/plants10061039

Cited by 4 publications

(3 citation statements)

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“…Previous studies suggested that gene family analyses using advanced annotation methods could provide novel insights into the structural and functional characteristics of genes (Bayer et al, 2018;Chae et al, 2021;Lee et al, 2021;Guk et al, 2022). We also performed independent annotation updates and comparative analyses of bZIP genes in Solanaceae.…”

Section: Discussionmentioning

confidence: 99%

Two different domain architectures generate structural and functional diversity among bZIP genes in the Solanaceae family

Choi

Kim²,

Kim³

2022

Front. Plant Sci.

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The bZIP gene family is one of the largest transcription factor families and has important roles in plant growth, development, and stress responses. However, bZIP genes in the Solanaceae family have not been extensively investigated. Here, we conducted genome-wide re-annotation in nine Solanaceae species and Arabidopsis thaliana. We annotated 935 bZIP genes, including 107 (11%) that were newly identified. Structural analyses of bZIP genes in the Solanaceae family revealed that the bZIP domain displayed two types of architectures depending on the presence of an additional domain, suggesting that these architectures generate diversified structures and functions. Motif analyses indicated that the two types of bZIP genes had distinct sequences adjacent to the bZIP domain. Phylogenetic analyses suggested that the two types of bZIP genes distinctly evolved and ultimately adapted in different lineages. Transcriptome analyses in pepper (Capsicum annuum) and tomato (Solanum lycopersicum) revealed putative functional diversity between the two types of bZIP genes in response to various abiotic stresses. This study extensively updated bZIP gene family annotations and provided novel evolutionary and functional evidence for the role of bZIP genes in Solanaceae plants. Our findings provide evolutionary and functional characteristics of bZIP genes for a better understanding of their roles in Solanaceae plants.

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Section: Discussionmentioning

confidence: 99%

Two different domain architectures generate structural and functional diversity among bZIP genes in the Solanaceae family

Choi

Kim²,

Kim³

2022

Front. Plant Sci.

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“…These form membrane channel proteins which are present in all branches of life, but plants have the most diversity in aquaporin homologues. Approximately 47 aquaporins have been identified in tomato and around 73 in sweet pepper ( Reuscher et al 2013 ; Lee et al 2021 ). They possess key roles in the transportation of small neutral solutes, metal ions and gases as well as being a critical regulator in plant–water relations.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-wide modulation bySargassum vulgareandAcanthophora spiciferaextracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper

2022

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Seaweed extracts are becoming integrated into crop production systems due to their multiple beneficial effects including growth promotion and induction of defence mechanisms. However, the comprehensive molecular mechanisms of these effects are yet to be elucidated. The current study investigated the transcriptomic changes induced by seaweed extracts derived from Sargassum vulgare and Acanthophora spicifera on tomato and sweet pepper plants. Tomato and sweet pepper plants were subjected to foliar treatment with alkaline extracts prepared from the above seaweeds. Transcriptome changes in the plants were assessed 72h after treatments using RNA-sequencing. The treated plants were also analysed for defense enzyme activities, nutrient composition and phytohormonal profiles. The results showed the significant enrichment of genes associated with several growth and defense processes including photosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, plant-pathogen interaction, secondary metabolite metabolism, MAPK signaling, and amino acid biosynthesis. Activities of defense enzymes were also significantly increased in SWE-treated plants. Plant nutrient profiling showed significant increases in calcium, potassium, nitrogen, sulphur, boron, copper, iron, manganese, zinc, and phosphorous levels in seaweed-extract treated plants. Furthermore, the levels of auxins, cytokinins, and gibberellins were also significantly increased in the treated plants. In addition to these observed effects, were also significant disease reductions of bacterial leaf spot and early blight in SWE-treated plants coupled with an increase in chlorophyll content, plant growth, and fruit yield. The results demonstrated the complex effect of S. vulgare and A. spicifera extracts on the plants’ transcriptome and provide evidence of a strong role of these extracts in increasing plant growth responses while priming the plants against pathogenic attack simultaneously. The current study contributes to the understanding of the molecular mechanisms of seaweed extracts in plants and helps their usage as a viable organic input for sustainable crop production.

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“…Pepper (Capsicum annuum L.) is an agriculturally important vegetable in the Solanaceae family [14,15]. Owing to its unique cold climate advantages, Ningxia has become an important pepper-producing area in Northwest China.…”

Section: Introductionmentioning

confidence: 99%

Assessment of soil property in the Guyuan region from Ningxia Province of China and prediction of pepper blight

Hou,

Ma,

Wang

et al. 2023

PLoS ONE

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Soil quality is an important determinant of soil-use efficiency in the Loess Plateau. However, there is no in-depth study on the soil quality of the Loess Plateau. The present study compared the quality of the 0–20 cm soil layer (T0-20) and the 20–40 cm soil layer (T20-40) from the Guyuan region located in the Loess Plateau. The analysis revealed that T0-20 had a higher content of total N, total P, available P, and organic matter, and the activities of microbial enzymes, especially β-grape-glycosidase (β-GC) and sucrase (SC), than T20-40, indicating that soil quality in T0-20 was better than T20-40. Amplicon sequencing found that Pseudombrophila from Ascomycota was the most abundant microbial species and significantly differed between T0-20 (34.2%) and T20-40 (48.7%). This species and another 19 microbial species, such as Ceratobasidiaceae and Mortierellaceae, determined the diversity of soil microorganism. Further analysis of the phenotype and other parameters of pepper seedlings subjected to P. capsici infection isolated from test soil revealed that decreased organic matter content in deep soil layer is related to happening of pepper blight, and 3 h after infection was the critical time point for infection. The peroxidase (POD) activity increased after P. capsici infection and was positively correlated with infection time, suggesting this enzyme may be an indicator of pepper blight occurrence. These findings provide a theoretical foundation for planning pepper blight management and crop cultivation strategies in the Guyuan region.

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Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper

Cited by 4 publications

References 56 publications

Two different domain architectures generate structural and functional diversity among bZIP genes in the Solanaceae family

Two different domain architectures generate structural and functional diversity among bZIP genes in the Solanaceae family

Transcriptome-wide modulation bySargassum vulgareandAcanthophora spiciferaextracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper

Assessment of soil property in the Guyuan region from Ningxia Province of China and prediction of pepper blight

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