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Bao Y, Nie T, Wang D, Chen Q. Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression. BMC PLANT BIOLOGY 2022; 22:228. [PMID: 35508980 PMCID: PMC9066749 DOI: 10.1186/s12870-022-03557-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/22/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Anthocyanins, which account for color variation and remove reactive oxygen species, are widely synthesized in plant tissues and organs. Using targeted metabolomics and nanopore full-length transcriptomics, including differential gene expression analysis, we aimed to reveal potato leaf anthocyanin biosynthetic pathways in different colored potato varieties. RESULTS Metabolomics analysis revealed 17 anthocyanins. Their levels varied significantly between the different colored varieties, explaining the leaf color differences. The leaves of the Purple Rose2 (PurpleR2) variety contained more petunidin 3-O-glucoside and malvidin 3-O-glucoside than the leaves of other varieties, whereas leaves of Red Rose3 (RedR3) contained more pelargonidin 3-O-glucoside than the leaves of other varieties. In total, 114 genes with significantly different expression were identified in the leaves of the three potato varieties. These included structural anthocyanin synthesis-regulating genes such as F3H, CHS, CHI, DFR, and anthocyanidin synthase and transcription factors belonging to multiple families such as C3H, MYB, ERF, NAC, bHLH, and WRKY. We selected an MYB family transcription factor to construct overexpression tobacco plants; overexpression of this factor promoted anthocyanin accumulation, turning the leaves purple and increasing their malvidin 3-o-glucoside and petunidin 3-o-glucoside content. CONCLUSIONS This study elucidates the effects of anthocyanin-related metabolites on potato leaves and identifies anthocyanin metabolic network candidate genes.
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Affiliation(s)
- Yanru Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Tengkun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, Shaanxi, China.
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China.
| | - Qin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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Zhuang Y, Manzitto-Tripp EA. Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae). BMC Ecol Evol 2022; 22:27. [PMID: 35260074 PMCID: PMC8905905 DOI: 10.1186/s12862-021-01955-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
Abstract
Background Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data. Results Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled. Analysis of non-synonymous/synonymous (dn/ds) mutation rates indicated all identified loci are under purifying selection, suggesting overall selection to prevent the accumulation of deleterious mutations. Additionally, upstream enzymes have lower rates of molecular evolution compared to downstream enzymes. However, site-specific tests of selection yielded evidence for positive selection at several sites, including four in F3'H2 and five in DFR3, and these sites are located in protein binding regions. A species-level phylogenetic tree constructed using a newly implemented hybrid transcriptome–RADseq approach implicates several flower color transitions among the 10 species. We found evidence of both regulatory and structural mutations to F3′5'H in helping to explain the evolution of red flowers from purple-flowered ancestors. Conclusions Sequence comparisons and co-expression analyses of ABP loci revealed that mutations in regulatory loci are likely to play a greater role in flower color transitions in Ruellia compared to mutations in underlying structural genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01955-x.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA.,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Erin A Manzitto-Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA. .,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.
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Srideepthi R, Krishna MSR, Suneetha P, Krishna RS, Karthikeyan S. Genome-wide identification, characterization and expression analysis of non-RD receptor like kinase gene family under Colletotrichum truncatum stress conditions in hot pepper. Genetica 2020; 148:283-296. [PMID: 32918190 DOI: 10.1007/s10709-020-00104-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 09/08/2020] [Indexed: 11/24/2022]
Abstract
Receptor like kinases (RLKs) are preserved upstream signaling molecules which regulate several biological processes from plant development to various stress adaptation programs. Non arginine aspartate (non-RD) a prominent class of RLKs plays a significant role in disease resistance and apoptosis in plants. In present investigation, a comprehensive in silico analysis for non-RD Kinase gene family as well as identification of gene structures, sequence similarity, chromosomal localization, gene duplication analysis, promoter analysis, transcript expression profiles and phylogenic studies were done. In this study, twenty-six genes were observed on nine out of twelve chromosomes. All these genes were clustered into five subfamilies under large monophyletic group termed as Interleukin-1 Receptor-Associated Kinase (IRAK) family. Some of the important physiochemical properties of twenty-six proteins are determined and ranged in the following order: (a) Amino acids size ranged from (620 to 1781) (b) Molecular weight ranged as of (70.11 to 197.11 KDa) and (c) Theoretical PI ranged from (5.69 to 8.63) respectively. Structural diversity in genomic structure among non-RD kinase gene family was identified and presence of pathogen induced cis regulatory elements including STRE, MYC, MYB, and W box were found. Expression profiles revealed the potential ability of three genes CaRLK1 from LRRXII and CaRLK15,16 from stress antifung subfamily were pointedly upregulated beyond the severe stress time period (9 DAI) in anthracnose resistant genotype PBC-80 in response to Colletotrichum truncatum infection. Subsequently, in silico studies from the available genome sequencing data helped us to identify candidate genes tangled in inducing disease resistance.
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Affiliation(s)
- R Srideepthi
- Koneru Lakshmaiah Education Foundation, Guntur, India
| | - M S R Krishna
- Koneru Lakshmaiah Education Foundation, Guntur, India.
| | - P Suneetha
- Professor Jaya Shanker Telangana State Agricultural University, Hyderabad, India
| | - R Sai Krishna
- ICAR- National Rice Research Institute, Cuttack, India
| | - S Karthikeyan
- Koneru Lakshmaiah Education Foundation, Guntur, India
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Gao J, Huang BH, Wan YT, Chang J, Li JQ, Liao PC. Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes. Sci Rep 2017; 7:14830. [PMID: 29093470 PMCID: PMC5666015 DOI: 10.1038/s41598-017-13645-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/29/2017] [Indexed: 12/29/2022] Open
Abstract
The protein encoded by the TERMINAL FLOWER1 (TFL1) gene maintains indeterminacy in inflorescence meristem to repress flowering, and has undergone multiple duplications. However, basal angiosperms have one copy of a TFL1-like gene, which clusters with eudicot TFL1/CEN paralogs. Functional conservation has been reported in the paralogs CENTRORADIALIS (CEN) in eudicots, and ROOTS CURL IN NPA (RCNs) genes in monocots. In this study, long-term functional conservation and selective constraints were found between angiosperms, while the relaxation of selective constraints led to subfunctionalisation between paralogs. Long intron lengths of magnoliid TFL1-like gene contain more conserved motifs that potentially regulate TFL1/CEN/RCNs expression. These might be relevant to the functional flexibility of the non-duplicate TFL1-like gene in the basal angiosperms in comparison with the short, lower frequency intron lengths in eudicot and monocot TFL1/CEN/RCNs paralogs. The functionally conserved duplicates of eudicots and monocots evolved according to the duplication-degeneration-complementation model, avoiding redundancy by relaxation of selective constraints on exon 1 and exon 4. These data suggest that strong purifying selection has maintained the relevant functions of TFL1/CEN/RCNs paralogs on flowering regulation throughout the evolution of angiosperms, and the shorter introns with radical amino acid changes are important for the retention of paralogous duplicates.
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Affiliation(s)
- Jian Gao
- College of Forestry, Beijing Forestry University, No.35, Tsinghua East Rd., Haidian Dist., Beijing, 100083, People's Republic of China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China
| | - Yu-Ting Wan
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China
| | - JenYu Chang
- Department of Horticulture, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute No. 1, Nung-Kai-Chang, Lutsao township, Chiayi, 611, Taiwan, Republic of China
| | - Jun-Qing Li
- College of Forestry, Beijing Forestry University, No.35, Tsinghua East Rd., Haidian Dist., Beijing, 100083, People's Republic of China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China.
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Huang BH, Huang CW, Huang CL, Liao PC. Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants. Sci Rep 2017; 7:5465. [PMID: 28710389 PMCID: PMC5511155 DOI: 10.1038/s41598-017-05900-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/06/2017] [Indexed: 01/11/2023] Open
Abstract
Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson's metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan.
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