Genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase I (FNSI) in Apiaceae

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Qi-Zhi Wang ◽  
Stephen R. Downie ◽  
Zhen-Xi Chen
Keyword(s):  
Positive Selection ◽  
Function Analysis ◽  
Gene Families ◽  
Genome Wide ◽  
Key Enzyme ◽  
Flavone Synthase ◽  
Flavone Synthase Ii ◽  
Site Identification ◽  
Identification Analysis ◽  
Significant Positive Selection

Flavone synthase is a key enzyme for flavone biosynthesis and is encoded by two gene families: flavone synthase I (FNSI) and flavone synthase II (FNSII). FNSII is widely distributed in plants, while FNSI has been reported in rice (Oryza sativa) and seven species of Apiaceae. FNSI has likely evolved from the duplication of flavanone 3β-hydroxylase (F3H). In this study, we used multiple bioinformatics tools to identify putative FNSI and F3H genes from 42 publicly available genome and transcriptome datasets. Results showed that rice FNSI does not share a common ancestral sequence with other known FNSI genes and that FNSI is absent from species outside of Apiaceae. Positive selection site identification analysis revealed that four sites within the FNSI tree branches of Apiaceae evolved under significant positive selection. The putative F3H genes identified in this study provide a valuable resource for further function analysis of flavone synthase.

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

2020 ◽  
Author(s):  
Yuxin Pan ◽  
Jinpeng Wang ◽  
Zhenyi Wang ◽  
Hengwei Liu ◽  
Lan Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Cotton Species ◽  
Expressional Analysis ◽  
Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

Enzymatic Synthesis of 4′-and 3′, 4′ -Hydroxylated Flavanones and Flavones with Flower Extracts of Sinningia cardinalis

1987 ◽  
Vol 42 (11-12) ◽  
pp. 1193-1199 ◽  
Author(s):  
K. Stich ◽  
G. Forkmann
Keyword(s):  
Enzymatic Synthesis ◽  
Microsomal Fraction ◽  
Chalcone Synthase ◽  
Condensation Reaction ◽  
Flavonoid Biosynthesis ◽  
Hydroxylase Activity ◽  
Key Enzyme ◽  
Flavone Synthase ◽  
Flavone Synthase Ii ◽  
Cytochrome P 450

Flowers of Sinningia (syn. Rechsteineria) cardinalis contain glycosides of the flavones apigenin (4′-OH) and luteolin (3′,4′-OH) respectively, and of the related 3-deoxyanthocyanidins apigeninidin and luteolinidin. Studies on substrate specificity of the key enzyme of flavonoid biosynthesis, chalcone synthase, revealed that the 3′,4′-hydroxylated flavonoids are formed by hydroxylation of flavonoid compounds rather than by incorporation of caffeoyl-CoA into the flavonoid skeleton during the condensation reaction. In fact, flavonoid 3′-hydroxylase activity could be demonstrat­ed in the microsomal fraction of the flower extracts. The enzyme catalyses hydroxylation of naringenin and apigenin in the 3′-position to eriodictyol and luteolin, respectively, with NADPH as cofactor. Besides flavanone 3′-hydroxylase a further NADPH-dependent enzyme activity (flavone synthase II) was observed in the microsomal fraction catalysing the oxidation of naringenin to apigenin and of eriodictyol to luteolin. The Cytochrome P-450 inhibitor ancymidol was found to abolish completely flavone synthase II activity, whereas flavonoid 3′-hydroxylase activity was not impaired.

scholarly journals Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

2020 ◽  
Author(s):  
Muhammad Zulfiqar Ahmad ◽  
Xiangsheng Zeng ◽  
Qiang Dong ◽  
Sehrish Manan ◽  
Huanan Jin ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Plant Defence ◽  
Constitutive Expression ◽  
Gene Families ◽  
Strong Positive Selection ◽  
Genome Wide ◽  
A Genome ◽  
Bahd Acyltransferase

Abstract Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

scholarly journals Flavone Synthase II (CYP93B) of Antarctic Plant Colobanthus quitensis (Kunth) Bartl.

2018 ◽  
Vol 4 (2) ◽  
pp. 196-198 ◽  
Author(s):  
Rodrigo A. Contreras ◽  
Gustavo E. Zúñiga
Keyword(s):  
Molecular Farming ◽  
Ph Stability ◽  
Biotechnological Applications ◽  
In Vitro Production ◽  
Antarctic Plants ◽  
Potential Applications ◽  
Key Enzyme ◽  
Flavone Synthase ◽  
Flavone Synthase Ii

The role of flavonoids in plant-environmental stress has many biotechnological applications, in this way Antarctic plants have an important potential for molecular farming. However, the concentration and exploitation of resource are highly restricted, for this reason the use of enzymatic machinery of the Antarctic plants have importance for in vitro flavonoid production for different biotechnological applications. Despite their potential applications, key enzymes for flavonoid biosynthesis are poorly studied in non-model plants. In this work, we studied the flavonoid key enzyme, flavone synthase II (FNS II) in C. quitensis. The results show a cooperative kinetic model for NADPH and naringenin. The temperature and pH stability assays show optimal temperature between 20-30 °C, with an operative range from 2 to 37 °C, pH stability shows an optimum of 7.0 to 8.0, with operative range from 3.0 to 8.0, demonstrating a big thermal and pH-stability, an interesting characteristic to in vitro production of flavones.

scholarly journals Adaptive evolution driving the young duplications in six Rosaceae species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Zhong ◽  
Xiaohui Zhang ◽  
Qinglong Shi ◽  
Zong-Ming Cheng
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Families ◽  
Whole Genome Sequencing Data ◽  
Duplicate Genes ◽  
Plant Genomes ◽  
Rosaceae Species ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Species Specific

Abstract Background In plant genomes, high proportions of duplicate copies reveals that gene duplications play an important role in the evolutionary processes of plant species. A series of gene families under positive selection after recent duplication events in plant genomes indicated the evolution of duplicates driven by adaptive evolution. However, the genome-wide evolutionary features of young duplicate genes among closely related species are rarely reported. Results In this study, we conducted a systematic survey of young duplicate genes at genome-wide levels among six Rosaceae species, whose whole-genome sequencing data were successively released in recent years. A total of 35,936 gene families were detected among the six species, in which 60.25% were generated by young duplications. The 21,650 young duplicate gene families could be divided into two expansion types based on their duplication patterns, species-specific and lineage-specific expansions. Our results showed the species-specific expansions advantaging over the lineage-specific expansions. In the two types of expansions, high-frequency duplicate domains exhibited functional preference in response to environmental stresses. Conclusions The functional preference of the young duplicate genes in both the expansion types showed that they were inclined to respond to abiotic or biotic stimuli. Moreover, young duplicate genes under positive selection in both species-specific and lineage-specific expansions suggested that they were generated to adapt to the environmental factors in Rosaceae species.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-wide identification and expression profiling of thes MAPK, MAPKK, and MAPKKK gene families in Ophiocordyceps sinensis

Gene ◽  
2022 ◽  
Vol 807 ◽  
pp. 145930
Author(s):  
Pan Yue ◽  
Han Zhang ◽  
Xinxin Tong ◽  
Ting Peng ◽  
Pan Tang ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Gene Families ◽  
Ophiocordyceps Sinensis ◽  
Genome Wide
Sign in / Sign up

Export Citation Format

Share Document