Structural, Functional, and Evolutionary Analysis of the Unusually Large Stilbene Synthase Gene Family in Grapevine

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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The effect of salicylic acid on phenylalanine ammonia-lyase and stilbene synthase gene expression in Vitis amurensis Cell Culture

Russian Journal of Plant Physiology ◽

10.1134/s1021443710030143 ◽

2010 ◽

Vol 57 (3) ◽

pp. 415-421 ◽

Cited By ~ 17

Author(s):

K. V. Kiselev ◽

A. S. Dubrovina ◽

G. A. Isaeva ◽

Y. N. Zhuravlev

Keyword(s):

Gene Expression ◽

Cell Culture ◽

Salicylic Acid ◽

Phenylalanine Ammonia Lyase ◽

Stilbene Synthase ◽

Vitis Amurensis ◽

Stilbene Synthase Gene

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Evolutionary Analysis of Cellulose Gene Family in Grasses

Communications in Computer and Information Science - Information Computing and Applications ◽

10.1007/978-3-642-27452-7_24 ◽

2011 ◽

pp. 178-183 ◽

Cited By ~ 1

Author(s):

Yakun Wang ◽

Li Wang ◽

Ling Jin ◽

Jinpeng Wang ◽

Dianchuan Jin

Keyword(s):

Gene Family ◽

Evolutionary Analysis

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A New Stilbene Synthase Gene from Muscadine (Vitis rotundifolia) Grape Berry

2007 Frontiers in the Convergence of Bioscience and Information Technologies ◽

10.1109/fbit.2007.155 ◽

2007 ◽

Cited By ~ 1

Author(s):

Hemanth KN. Vasanthaiah ◽

Ramesh Katam ◽

Sheikh M. Basha

Keyword(s):

Stilbene Synthase ◽

Grape Berry ◽

Vitis Rotundifolia ◽

Stilbene Synthase Gene

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INCREASED DISEASE RESISTANCE IN PAPAYA BY TRANSFORMING A PATHOGEN-INDUCIBLE STILBENE SYNTHASE GENE

Acta Horticulturae ◽

10.17660/actahortic.2005.692.13 ◽

2005 ◽

pp. 107-114 ◽

Cited By ~ 1

Author(s):

Y.J. Zhu ◽

C.S. Tang ◽

P. Moore

Keyword(s):

Disease Resistance ◽

Stilbene Synthase ◽

Stilbene Synthase Gene

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SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽

10.3390/plants9030354 ◽

2020 ◽

Vol 9 (3) ◽

pp. 354

Author(s):

Shaokun Li ◽

Li Li ◽

Yang Jiang ◽

Jun Wu ◽

Honghua Sun ◽

...

Keyword(s):

Gene Family ◽

Panax Ginseng ◽

Interaction Analysis ◽

Binding Protein ◽

Expression Patterns ◽

Evolutionary Analysis ◽

Main Function ◽

Squamosa Promoter Binding Protein ◽

Expression Characteristics ◽

Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

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