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Liu B, Zhu J, Lin L, Yang Q, Hu B, Wang Q, Zou XX, Zou SQ. Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis. Front Genet 2022; 12:737293. [PMID: 35069676 PMCID: PMC8766721 DOI: 10.3389/fgene.2021.737293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.
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Affiliation(s)
- Bobin Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Juanli Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Lina Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qixin Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Bangping Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qingying Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Xiao-Xing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
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Liang D, Deng H, Deng Q, Lin L, Lv X, Wang J, Wang Z, Xiong B, Zhao X, Xia H. Dynamic Changes of Phenolic Compounds and Their Associated Gene Expression Profiles Occurring during Fruit Development and Ripening of the Donghong Kiwifruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11421-11433. [PMID: 32936614 DOI: 10.1021/acs.jafc.0c04438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The newly released Donghong kiwifruit is a promising commercial cultivar. The dynamic changes of major phenolic compounds (flavonols, flavanols, phenolic acids, and anthocyanins) during the representative stages of fruit development and ripening of the Donghong kiwifruit were determined by high-performance liquid chromatography. The corresponding time-course transcriptional changes were evaluated using the combined analysis of RNA-Seq and qRT-PCR. The most predominant phenolic compound in the Donghong kiwifruit was epicatechin. Cyanidin 3-O-[2-O-(β-xylosyl)-β-galactoside] and cyanidin 3-O-β-galactoside were two essential anthocyanins detected. Candidate genes and pathways involved in phenolic compounds biosynthesis were highlighted. The structural genes (AcLDOX2, Ac5GGT1, and Ac5AT2) and the transcription factor (bHLH74-2) were strongly associated with anthocyanin biosynthesis. AcMYB4-1 may be a novel transcription factor that reduces anthocyanin accumulation. Results from the study may be a very useful supplement to current knowledge of molecular mechanisms to elucidate coloration in the red-fleshed kiwifruit and could help breeders modify the kiwifruit germplasm.
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Affiliation(s)
- Dong Liang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Honghong Deng
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Qunxian Deng
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Lijin Lin
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Xiulan Lv
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Jin Wang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Zhihui Wang
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Bo Xiong
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Xuewen Zhao
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Hui Xia
- Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
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Yang CL, Yuan XY, Zhang J, Sun WH, Liu ZJ, Zou SQ. Comprehensive transcriptome analysis of reference genes for fruit development of Euscaphis konishii. PeerJ 2020; 8:e8474. [PMID: 32095336 PMCID: PMC7020815 DOI: 10.7717/peerj.8474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022] Open
Abstract
Background Quantitativereal-time reverse transcriptase polymerase chain reaction is the common method to quantify relative gene expression. Normalizating using reliable genes is critical in correctly interpreting expression data from qRT-PCR. Euscaphis konishii is a medicinal plant with a long history in China, which has various chemical compounds in fruit. However, there is no report describing the selection of reference genes in fruit development of Euscaphis konishii. Methods We selected eight candidate reference genes based on RNA-seq database analysis, and ranked expression stability using statistical algorithms GeNorm, NormFinder, BestKeeper and ReFinder. Finally, The nine genes related to the anthocyanin synthesis pathway of Euscaphis konishii were used to verify the suitability of reference gene. Results The results showed that the stability of EkUBC23, EkCYP38 and EkGAPDH2 was better, and the low expression reference genes (EkUBC23 and EkCYP38) were favourable for quantifying low expression target genes, while the high expression reference gene (EkGAPDH2) was beneficial for quantifying high expression genes. In this study, we present the suitable reference genes for fruit development of Euscaphis konishii based on transcriptome data, our study will contribute to further studies in molecular biology and gene function on Euscaphis konishii and other closely related species.
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Affiliation(s)
- Cheng-Long Yang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Xue-Yan Yuan
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources at College of Forestry, Fujian Agriculture and Forestry University, Fujian, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Zhang
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Wei-Hong Sun
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources at College of Forestry, Fujian Agriculture and Forestry University, Fujian, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhong-Jian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources at College of Forestry, Fujian Agriculture and Forestry University, Fujian, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuang-Quan Zou
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources at College of Forestry, Fujian Agriculture and Forestry University, Fujian, Fuzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado ( Persea americana). Int J Mol Sci 2019; 20:ijms20174117. [PMID: 31450745 PMCID: PMC6747375 DOI: 10.3390/ijms20174117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/17/2022] Open
Abstract
Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.
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Sun W, Yuan X, Liu ZJ, Lan S, Tsai WC, Zou SQ. Multivariate analysis reveals phenotypic diversity of Euscaphis japonica population. PLoS One 2019; 14:e0219046. [PMID: 31310621 PMCID: PMC6634381 DOI: 10.1371/journal.pone.0219046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/16/2019] [Indexed: 11/21/2022] Open
Abstract
Fruit traits affect population genetic diversity by affecting seed protection and dispersal strategies, thereby comprising important components of phenotypic variation. Understanding of the phenotypic variation is an indispensable first step for developing breeding strategies. However, little information is known about the genetic variation in E. japonica-a monotypic species with abundant phenotypes that is mainly distributed in southern China. In this study, we evaluated the phenotypic diversity of 67 E. japonica using 23 phenotypic traits. Our results showed that the Shannon-Wiener (I) index of qualitative traits ranged from 0.55 to 1.26, and the color traits had a relatively high I. The average coefficient of variation of compound leaf traits (14.74%) was higher than that of fruit and seed traits (12.77% and 11.47%, respectively). Principal component analysis also showed that compound leaf and fruit traits were important components of total variation. Furthermore, correlation analysis revealed a significant difference in elevation and fruit color, irregular ribs, leaf margin and texture. The F value within populations was smaller than among populations, indicating the variation in phenotypic traits among populations was much greater than within populations. Dehua and Zunyi populations had the highest coefficients of variation, whereas Wenzhou population had the smallest-which may be attributed to habitat destruction. According to Q-type clustering, 67 samples clustered into four groups, with those having similar phenotypes clustering into the same group. In general, leaf and fruit traits had abundant phenotypic diversity, representing the main sources of phenotypic variation. Combined with clustering results and field surveys, this study suggests that the phenotypes of E. japonica are classified into two main categories: The deciduous E. japonica present at high altitudes; and the evergreen E. japonica present at low altitudes. Excavating E. japonica variations provides a theoretical reference for its classification and diversity, and is of great significance for planning genetic resources and establishing conservation strategies.
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Affiliation(s)
- Weihong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueyan Yuan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen-chieh Tsai
- Department of Biological Sciences and Technology, National University of Tainan, Tainan, Taiwan, China
| | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ornamental Plant Germplasm Resources Innovation and Engineering Application Research Center, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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