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Chang X, Zhang X, Huang X, Yang Z, Zhang F. Transcriptome and metabolome analysis of the developmental changes in Cynanchum thesioides anther. Genomics 2024; 116:110884. [PMID: 38878835 DOI: 10.1016/j.ygeno.2024.110884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/23/2024]
Abstract
Cynanchum thesioides, a xerophytic species utilized both as a medicinal herb and a food source, plays a significant role in arid and desert ecosystem management. Its inflorescence is an umbellate cyme, each carrying nearly a thousand flowers; however, its fruiting rate remains remarkably low. The normal development of the anther is a necessary prerequisite for plants to produce seeds. However, our understanding of the anther development process in Cynanchum thesioides remains limited. To better understand the pollen development process in Cynanchum thesioides, the stages of pollen development were determined through paraffin sectioning, and observations were made on the distribution characteristics of polysaccharides and lipid droplets in the pollen development of Cynanchum thesioides using Periodic Acid-Schiff stain (PAS) and 0.5% Sudan Black B tissue staining. Concurrently, the gene expression patterns and metabolite profiles were delineated across various developmental stages of Cynanchum thesioides anthers (T1: microspore stage, T2: tetrad stage, T3: mononuclear stage, and T4: maturation stage). The findings revealed that Cynanchum thesioides pollen is in an aggregate form. Polysaccharides gradually accumulate during maturation and lipid droplets form a surrounding membrane, thereby preventing pollen dispersion. Furthermore, transcriptomic and metabolomic analyses across distinct developmental phases uncovered a plethora of differentially expressed genes and metabolites associated with the flavonoid biosynthesis pathway. Flavonoid levels exhibited dynamic changes concurrent with anther development, aligning with the gene regulatory patterns of the corresponding biosynthetic pathways. The study identified 63 differentially accumulated flavonoid compounds and 21 differentially expressed genes associated with flavonoid biosynthesis. Weighted gene co-expression network analysis revealed six MYB and ten bHLH transcription factors as key candidates involved in flavonoid biosynthesis, with CtbHLH (Cluster-6587.1050) and CtMYB (Cluster-6587.31743) specifically regulating structural genes within the pathway. These findings underscore the pivotal role of flavonoid biosynthesis in anther development of Cynanchum thesioides. In conclusion, this research offers a comprehensive insight into the anther development process in Cynanchum thesioides.
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Affiliation(s)
- Xiaoyao Chang
- Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia, China
| | - Xiaoyan Zhang
- Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia, China
| | - Xiumei Huang
- Department of Horticulture and Landscape Technology, Inner Mongolia Agricultural University Vocational and technical College, Baotou City, Inner Mongolia, China
| | - Zhongren Yang
- Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia, China.
| | - Fenglan Zhang
- Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia, China.
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Zhou X, Cao J, Liu XM, Wang LN, Zhang WW, Ye JB, Xu F, Cheng S. Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba. THE PLANT GENOME 2024; 17:e20440. [PMID: 38462710 DOI: 10.1002/tpg2.20440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 03/12/2024]
Abstract
4-Coumarate-CoA ligase (4CL) gene plays vital roles in plant growth and development, especially the regulation of lignin metabolism and flavonoid synthesis. To investigate the potential function of 4CL in the lignin biosynthesis of Ginkgo biloba, this study identified two 4CL genes, Gb4CL1 and Gb4CL2, from G. biloba genome. Based on the phylogenetic tree analysis, Gb4CL1 and Gb4CL2 protein were classified into Class I, which has been confirmed to be involved in lignin biosynthesis. Therefore, it can be inferred that these two genes may also participate in lignin metabolism. The tissue-specific expression patterns of these two genes revealed that Gb4CL1 was highly expressed in microstrobilus, whereas Gb4CL2 was abundant in immature leaves. The onion transient expression assay indicated that Gb4CL1 was predominantly localized in the nucleus, indicating its potential involvement in nuclear functions, while Gb4CL2 was observed in the cell wall, suggesting its role in cell wall-related processes. Phytohormone response analysis revealed that the expression of both genes was upregulated in response to indole acetic acid, while methyl jasmonate suppressed it, gibberellin exhibited opposite effects on these genes. Furthermore, Gb4CL1 and Gb4CL2 expressed in all tissues containing lignin that showed a positive correlation with lignin content. Thus, these findings suggest that Gb4CL1 and Gb4CL2 are likely involved in lignin biosynthesis. Gb4CL1 and Gb4CL2 target proteins were successfully induced in Escherichia coli BL21 with molecular weights of 85.5 and 89.2 kDa, proving the integrity of target proteins. Our findings provided a basis for revealing that Gb4CL participated in lignin synthesis in G. biloba.
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Affiliation(s)
- Xian Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Jie Cao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Xiao-Meng Liu
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Li-Na Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Wei-Wei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Jia-Bao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
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Zhang L, Kamitakahara H, Takano T, Morimoto T, Sakamoto S, Mitsuda N, Itai A. Stone cell formation in the pedicel of pears and apples. PLANTA 2023; 258:85. [PMID: 37747516 DOI: 10.1007/s00425-023-04240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
MAIN CONCLUSION For the first time, stone cells in pear and apple pedicel were studied. The lignification of the pedicel outer part was correlated with flesh, and the secondary cell wall biosynthesis genes were activated. Fruit pedicels act as bridges between the fruit and the shoot. They have secondary thickened cell walls that presumably function in mechanical support, water and nutrient transport. Stone cells are cells with a secondary cell wall thickening. In pears, yet not in apples, the stone cells affect the flesh texture. There have been few reports on stone cell formation in pear and apple pedicels; therefore, we studied these cells for the first time. The apple pedicel had few stone cells in the cortex. The formation of stone cells in pear continued until seven weeks after flowering (WAF), and the density was significantly higher than in apple. The stone cell formation degree (SFD) of pear was 3.6-7.1 times higher than that of apple. Total lignin and lignin non-condensed structure (G and S units) content in the pear pedicle outer part was 1.5-2.7 times higher than that of the apple at harvest. The SFD of the pedicel outer part had a positive correlation with the G and S units content of the flesh. The total lignin and G and S units content between flesh and the pedicel outer part were positively correlated. Correlation analysis revealed a positive relationship between fruit and pedicel formation of the stone cells. The WGCNA showed that NST3 was linked to NAC028, MYB46, CESA, POD, LAC, and VSR6. These genes were highly expressed in the outer part of the pear pedicel, while they were suppressed in that issue of the apple at 4 WAF.
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Affiliation(s)
- Lumin Zhang
- Tropical Eco-Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Nancheng Street 150, Yuanmou, 651300, Yunnan, China
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kitaina-Yazuma Oji 74, Seika-Cho, Soraku-Gun, Kyoto, 619-0244, Japan
| | - Hiroshi Kamitakahara
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Toshiyuki Takano
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kitaina-Yazuma Oji 74, Seika-Cho, Soraku-Gun, Kyoto, 619-0244, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Akihiro Itai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kitaina-Yazuma Oji 74, Seika-Cho, Soraku-Gun, Kyoto, 619-0244, Japan.
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Han J, Liu Y, Shen Y, Zhang D, Li W. Transcriptome Dynamics during Spike Differentiation of Wheat Reveal Amazing Changes in Cell Wall Metabolic Regulators. Int J Mol Sci 2023; 24:11666. [PMID: 37511426 PMCID: PMC10380499 DOI: 10.3390/ijms241411666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Coordinated cell proliferation and differentiation result in the complex structure of the inflorescence in wheat. It exhibits unique differentiation patterns and structural changes at different stages, which have attracted the attention of botanists studying the dynamic regulation of its genes. Our research aims to understand the molecular mechanisms underlying the regulation of spike development genes at different growth stages. We conducted RNA-Seq and qRT-PCR evaluations on spikes at three stages. Our findings revealed that genes associated with the cell wall and carbohydrate metabolism showed high expression levels between any two stages throughout the entire process, suggesting their regulatory role in early spike development. Furthermore, through transgenic experiments, we elucidated the role of the cell wall regulator gene in spike development regulation. These research results contribute to identifying essential genes associated with the morphology and development of wheat spike tissue.
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Affiliation(s)
- Junjie Han
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Yichen Liu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Yiting Shen
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Donghai Zhang
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Weihua Li
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
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Cao Y, Chen Y, Zhang L, Cai Y. Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) involved in lignin accumulation in pear fruits. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:791-798. [PMID: 37520811 PMCID: PMC10382451 DOI: 10.1007/s12298-023-01329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 08/01/2023]
Abstract
One of the most important factors impacting the quality of pear fruit is the presence of stone cells and lignin. Lignin is the main component of stone cells in pear fruits. Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) are involved in lignin accumulation in pear fruits. However, the functions of these genes in lignin biosynthesis were excluded in pear. In our study, we isolated and cloned Pb4CL11 (GenBank: KM455955.1) and PbC3H1 (GenBank: KM373790.1) from pear, which contained 1644 bp encoded 54 amino acids (AA), and 1539 bp encoded 513 AA, respectively. The expression of Pb4CL11 and PbC3H1 in Arabidopsis thaliana led to an increase in cell wall thickness for intervascular fibers and xylem cells and lignin content. Overexpression of Pb4CL11 and PbC3H1 in A. thaliana can significantly increase the expression of AtPAL, AtC4H, AtHCT, AtC3H, AtCCOMT, AtCCR, AtF5H, AtCOMT, AtCAD4 and AtCAD5 with promotion of lignin biosynthesis. Taken together, our study's findings not only demonstrated the probable function of Pb4CL11 and PbC3H1 in lignin biosynthesis but also laid the groundwork for future studies using molecular biological methods to control lignin production and the formation of stone cells in pear fruits.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
| | - Yu Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui Zhifei Longcom Biopharmaceutical Co., Ltd., Hefei, China
| | - Lin Zhang
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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LhANS-rr1, LhDFR, and LhMYB114 Regulate Anthocyanin Biosynthesis in Flower Buds of Lilium ‘Siberia’. Genes (Basel) 2023; 14:genes14030559. [PMID: 36980831 PMCID: PMC10048704 DOI: 10.3390/genes14030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
The bulb formation of Lilium is affected by many physiological and biochemical phenomena, including flower bud differentiation, starch and sucrose accumulation, photoperiod, carbon fixation, plant hormone transduction, etc. The transcriptome analysis of flower buds of Lilium hybrid ‘Siberia’ at different maturity stages showed that floral bud formation is associated with the accumulation of anthocyanins. The results of HPLC-MS showed that cyanidin is the major anthocyanin found in Lilium ‘Siberia’. Transcriptome KEGG enrichment analysis and qRT-PCR validation showed that two genes related to flavonoid biosynthesis (LhANS-rr1 and LhDFR) were significantly up-regulated. The functional analysis of differential genes revealed that LhMYB114 was directly related to anthocyanin accumulation among 19 MYB transcription factors. Furthermore, the qRT-PCR results suggested that their expression patterns were very similar at different developmental stages of the lily bulbs. Virus-induced gene silencing (VIGS) revealed that down-regulation of LhANS-rr1, LhDFR, and LhMYB114 could directly lead to a decrease in anthocyanin accumulation, turning the purple phenotype into a white color. Moreover, this is the first report to reveal that LhMYB114 can regulate anthocyanin accumulation at the mature stage of lily bulbs. The accumulation of anthocyanins is an important sign of lily maturity. Therefore, these findings have laid a solid theoretical foundation for further discussion on lily bulb development in the future.
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Cao Y, Fan T, Zhang B, Li Y. Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance to Fusarium wilt in tung tree. PeerJ 2022; 10:e14416. [PMID: 36590451 PMCID: PMC9798904 DOI: 10.7717/peerj.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022] Open
Abstract
The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana's resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.
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Affiliation(s)
- Yunpeng Cao
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China,School of Forestry, Central South University of Forestry and Technology, Changsha, China,Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Tingting Fan
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Bo Zhang
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yanli Li
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
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Rawoof A, Ahmad I, Islam K, Momo J, Kumar A, Jaiswal V, Ramchiary N. Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species. Funct Integr Genomics 2022; 22:1189-1209. [PMID: 36173582 DOI: 10.1007/s10142-022-00902-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/10/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022]
Abstract
To date, several transcriptomic studies during fruit development have been reported; however, no comprehensive integrated study on expression diversity, alternative splicing, and metabolomic profiling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic profiling from early green (EG), mature green (MG), and breaker (Br) fruit stages from two Capsicum species, i.e., C. annuum (Cann) and C. frutescens (Cfrut) from Northeast India. A total of 117,416 and 96,802 alternatively spliced events (AltSpli-events) were identified from Cann and Cfrut, respectively. Among AltSpli-events, intron retention (IR; 32.2% Cann and 25.75% Cfrut) followed by alternative acceptor (AA; 15.4% Cann and 18.9% Cfrut) were the most abundant in Capsicum. Around 7600 genes expressed in at least one fruit stage of Cann and Cfrut were AltSpli. The study identified spliced variants of genes including transcription factors (TFs) potentially involved in fruit development/ripening (Aux/IAA 16-like, ETR, SGR1, ARF, CaGLK2, ETR, CaAGL1, MADS-RIN, FUL1, SEPALLATA1), carotenoid (PDS, CA1, CCD4, NCED3, xanthoxin dehydrogenase, CaERF82, CabHLH100, CaMYB3R-1, SGR1, CaWRKY28, CaWRKY48, CaWRKY54), and capsaicinoids or flavonoid biosynthesis (CaMYB48, CaWRKY51), which were significantly differentially spliced (DS) between consecutive Capsicum fruit stages. Also, this study observed that differentially expressed isoforms (DEiso) from 38 genes with differentially spliced events (DSE) were significantly enriched in various metabolic pathways such as starch and sucrose metabolism, amino acid metabolism, cysteine cutin suberin and wax biosynthesis, and carotenoid biosynthesis. Furthermore, the metabolomic profiling revealed that metabolites from aforementioned pathways such as carbohydrates (mainly sugars such as D-fructose, D-galactose, maltose, and sucrose), organic acids (carboxylic acids), and peptide groups significantly altered during fruit development. Taken together, our findings could help in alternative splicing-based targeted studies of candidate genes involved in fruit development and ripening in Capsicum crop.
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Affiliation(s)
- Abdul Rawoof
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ilyas Ahmad
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khushbu Islam
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - John Momo
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Nirala Ramchiary
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri. Int J Mol Sci 2022; 23:ijms23137054. [PMID: 35806062 PMCID: PMC9266570 DOI: 10.3390/ijms23137054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions.
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Enzyme Activities in the Lignin Metabolism of Chinese Olive (Canarium album) with Different Flesh Characteristics. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Lignin is crucial to the formation of fruit texture quality. Here, we aimed to explore the relationship between lignin metabolism and fruit texture by investigating the lignin content, total phenols and their related enzyme activities among three Chinese olive (Canarium album (Lour.) Raeusch) genotypes. Our results showed that lignin deposition moved from the exocarp to the flesh in Chinese olive fruit. The lignin, total phenols and enzyme activities were all different between the three Chinese olive cultivars at each developmental stage. The lignin content was positively correlated with the PAL, 4CL and POD activities. These results demonstrated that lignin metabolism was regulated through the related enzyme activities. Therefore, our findings may provide insight to facilitate further improvement in fruit texture quality in Chinese olive.
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Systematic Analysis and Expression Profiles of the 4-Coumarate: CoA Ligase (4CL) Gene Family in Pomegranate ( Punica granatum L.). Int J Mol Sci 2022; 23:ijms23073509. [PMID: 35408870 PMCID: PMC8999076 DOI: 10.3390/ijms23073509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
4-Coumarate:CoA ligase (4CL, EC6.2.1.12), located at the end of the phenylpropanoid metabolic pathway, regulates the metabolic direction of phenylpropanoid derivatives and plays a pivotal role in the biosynthesis of flavonoids, lignin, and other secondary metabolites. In order to understand the molecular characteristics and potential biological functions of the 4CL gene family in the pomegranate, a bioinformatics analysis was carried out on the identified 4CLs. In this study, 12 Pg4CLs were identified in the pomegranate genome, which contained two conserved amino acid domains: AMP-binding domain Box I (SSGTTGLPKGV) and Box II (GEICIRG). During the identification, it was found that Pg4CL2 was missing Box II. The gene cloning and sequencing verified that this partial amino acid deletion was caused by genome sequencing and splicing errors, and the gene cloning results corrected the Pg4CL2 sequence information in the ‘Taishanhong’ genome. According to the phylogenetic tree, Pg4CLs were divided into three subfamilies, and each subfamily had 1, 1, and 10 members, respectively. Analysis of cis-acting elements found that all the upstream sequences of Pg4CLs contained at least one phytohormone response element. An RNA-seq and protein interaction network analysis suggested that Pg4CL5 was highly expressed in different tissues and may participate in lignin synthesis of pomegranate. The expression of Pg4CL in developing pomegranate fruits was analyzed by quantitative real-time PCR (qRT-PCR), and the expression level of Pg4CL2 demonstrated a decreasing trend, similar to the trend of flavonoid content, indicating Pg4CL2 may involve in flavonoid synthesis and pigment accumulation. Pg4CL3, Pg4CL7, Pg4CL8, and Pg4CL10 were almost not expressed or lowly expressed, the expression level of Pg4CL4 was higher in the later stage of fruit development, suggesting that Pg4CL4 played a crucial role in fruit ripening. The expression levels of 4CL genes were significantly different in various fruit development stages. The results laid the foundation for an in-depth analysis of pomegranate 4CL gene functions.
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Li J, Zhang M, Li X, Khan A, Kumar S, Allan AC, Lin-Wang K, Espley RV, Wang C, Wang R, Xue C, Yao G, Qin M, Sun M, Tegtmeier R, Liu H, Wei W, Ming M, Zhang S, Zhao K, Song B, Ni J, An J, Korban SS, Wu J. Pear genetics: Recent advances, new prospects, and a roadmap for the future. HORTICULTURE RESEARCH 2022; 9:uhab040. [PMID: 35031796 PMCID: PMC8778596 DOI: 10.1093/hr/uhab040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".
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Affiliation(s)
- Jiaming Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xiaolong Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Awais Khan
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Satish Kumar
- Hawke’s Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand
| | - Andrew Charles Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Richard Victor Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Runze Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Mengfan Qin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Manyi Sun
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Tegtmeier
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Hainan Liu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weilin Wei
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Ming
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kejiao Zhao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiangping Ni
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianping An
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Schuyler S Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Differential Triggering of the Phenylpropanoid Biosynthetic Pathway Key Genes Transcription upon Cold Stress and Viral Infection in Tomato Leaves. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Plants develop a plethora of defense strategies during their acclimation and interactions with various environmental stresses. Secondary metabolites play a pivotal role in the processes during stress acclimation, therefore deciphering their relevant responses exchange the interpretation of the underlying molecular mechanisms that may contribute to improved adaptability and efficacy. In the current study, tomato plants were exposed to short-term cold stress (5 °C for 16 h) or inoculated (20 d) with either Cucumber Mosaic Virus (CMV) or Potato Virus Y (PVY). Responses were recorded via the assessments of leaf total phenolic (TP) content, total flavonoid (TF) levels, and phenylalanine ammonia-lyase (PAL) enzyme activity. The transcription of the gene families regulating the core phenylpropanoid biosynthetic pathway (PBP) at an early (PAL, cinnamic acid 4-hydroxylase, 4-coumarate-CoA ligase) or late (chalcone synthase and flavonol synthase) stage was also evaluated. The results showed that cold stress stimulated an increase in TP and TF contents, while PAL enzyme activity was also elevated compared to viral infection. Besides genes transcription of the enzymes involved in the core PBP was mostly induced by cold stress, whereas transcription of the genes regulating flavonoid biosynthesis was mainly triggered by viral infection. In conclusion, abiotic and biotic stressors induced differential regulation of the core PBP and flavonoid biosynthetic metabolism. Taking the above into consideration, our results highlight the complexity of tomato responses to diverse stimuli allowing for better elucidation of stress tolerance mechanisms at this crop.
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Shi M, Ali MM, He Y, Ma S, Rizwan HM, Yang Q, Li B, Lin Z, Chen F. Flavonoids Accumulation in Fruit Peel and Expression Profiling of Related Genes in Purple ( Passiflora edulis f. edulis) and Yellow ( Passiflora edulis f. flavicarpa) Passion Fruits. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112240. [PMID: 34834602 PMCID: PMC8620868 DOI: 10.3390/plants10112240] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 05/14/2023]
Abstract
Flavonoids play a key role as a secondary antioxidant defense system against different biotic and abiotic stresses, and also act as coloring compounds in various fruiting plants. In this study, fruit samples of purple (Passiflora edulis f. edulis) and yellow (Passiflora edulis f. flavicarpa) passion fruit were collected at five developmental stages (i.e., fruitlet, green, veraison, maturation, and ripening stage) from an orchard located at Nanping, Fujian, China. The contents of flavonoid, anthocyanin, proanthocyanin, and their metabolites were determined using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), activities of key enzymes involved in flavonoid metabolism were measured, and expression profiling of related genes was done using quantitative real-time PCR (qRT-PCR). The results revealed that total flavonoids, anthocyanins, and procyanidins were found to be increased in the fruit peel of both cultivars with fruit maturity. Total flavonoids, anthocyanins, procyanidins, flavonoid metabolites (i.e., rutin, luteolin, and quercetin), and anthocyanin metabolites (i.e., cyanidin-3-O-glucoside chloride, peonidin-3-O-glucoside, and pelargonidin-3-O-glucoside) were found abundant in the peel of purple passion fruit, as compared to yellow passion fruit. Principle component analysis showed that the enzymes, i.e., C4H, 4CL, UFGT, and GST were maybe involved in the regulation of flavonoids metabolism in the peel of passion fruit cultivars. Meanwhile, PePAL4, Pe4CL2,3, PeCHS2, and PeGST7 may play an important role in flavonoid metabolism in fruit peel of the passion fruit. This study provides new insights for future elucidation of key mechanisms regulating flavonoids biosynthesis in passion fruit.
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Affiliation(s)
- Meng Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Yinying He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Songfeng Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Binqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Zhimin Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- Correspondence: (Z.L.); (F.C.)
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
- Correspondence: (Z.L.); (F.C.)
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15
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PbCSE1 promotes lignification during stone cell development in pear (Pyrus bretschneideri) fruit. Sci Rep 2021; 11:9450. [PMID: 33941813 PMCID: PMC8093294 DOI: 10.1038/s41598-021-88825-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Pear [Pyrus bretschneideri cv. Dangshan Su] fruit quality is not always satisfactory owing to the presence of stone cells, and lignin is the main component of stone cells in pear fruits. Caffeoyl shikimate esterase (CSE) is a key enzyme in the lignin biosynthesis. Although CSE-like genes have been isolated from a variety of plant species, their orthologs are not characterized in pear. In this study, the CSE gene family (PbCSE) from P. bretschneideri was identified. According to the physiological data and quantitative RT-PCR (qRT-PCR), PbCSE1 was associated with lignin deposition and stone cell formation. The overexpression of PbCSE1 increased the lignin content in pear fruits. Relative to wild-type (WT) Arabidopsis, the overexpression of PbCSE1 delayed growth, increased the lignin deposition and lignin content in stems. Simultaneously, the expression of lignin biosynthetic genes were also increased in pear fruits and Arabidopsis. These results demonstrated that PbCSE1 plays an important role in cell lignification and will provide a potential molecular strategy to improve the quality of pear fruits.
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Mamat A, Tusong K, Xu J, Yan P, Mei C, Wang J. Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear. Sci Rep 2021; 11:7688. [PMID: 33833305 PMCID: PMC8032765 DOI: 10.1038/s41598-021-87262-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022] Open
Abstract
Korla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.
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Affiliation(s)
- Aisajan Mamat
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China.
| | - Kuerban Tusong
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China
| | - Juan Xu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China
| | - Peng Yan
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China
| | - Chuang Mei
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China
| | - Jixun Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi, 830091, China
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17
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Zhu X, Jiang L, Cai Y, Cao Y. Functional analysis of four Class III peroxidases from Chinese pear fruit: a critical role in lignin polymerization. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:515-522. [PMID: 33854280 PMCID: PMC7981345 DOI: 10.1007/s12298-021-00949-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 06/01/2023]
Abstract
Pear fruit could be used as good medicine to relieve coughs, promote salivation, nourish lungs, and reduce the risk of many diseases for its phytochemical action. Lignin is a major secondary metabolite in Chinese pear fruit. Class III peroxidase (Class III PRX) is an important enzyme in the biosynthesis of lignin in plants. However, we poorly understand the role of PRXs in lignin biosynthesis in Chinese pear fruit. In our study, we cloned five PRXs from Chinese pear (Pyrus bretschneideri), namely PbPRX2, PbPRX22, PbPRX34, PbPRX64, and PbPRX75, which contained 978 bp encoded 326 amino acids (AA), 2607 bp encoded 869 AA, 972 bp encoded 324 AA, 687 bp encoded 229 AA, and 1020 bp encoded 340 AA, respectively. Enzyme activity analysis showed that four recombinant PbPRX proteins had catalytic activities for pyrogallol, guaiacol, ferulic acid, coniferyl alcohol, and sinapyl alcohol. Subcellular localization experiments showed that these genes were located in the cell wall or cell membrane. Enzyme activity and kinetics of PbPRX2 revealed its role in polymerization of lignin in Chinese pear fruit. The present study suggested that PbPRXs played critical roles in lignin biosynthesis in Chinese pear fruit. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00949-9.
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Affiliation(s)
- Xi Zhu
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Lan Jiang
- Yijishan Hospital of Wannan Medical College, Wuhu, 241000 Anhui China
| | - Yongping Cai
- Key Lab of Non-Wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Key Lab of Non-Wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- School of Life Science, Anhui Agricultural University, Hefei, 230036 Anhui China
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18
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Badhan S, Ball AS, Mantri N. First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts. Int J Mol Sci 2021; 22:E396. [PMID: 33401455 PMCID: PMC7795094 DOI: 10.3390/ijms22010396] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
The current genome editing system Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR/Cas9) has already confirmed its proficiency, adaptability, and simplicity in several plant-based applications. Together with the availability of a vast amount of genome data and transcriptome data, CRISPR/Cas9 presents a massive opportunity for plant breeders and researchers. The successful delivery of ribonucleoproteins (RNPs), which are composed of Cas9 enzyme and a synthetically designed single guide RNA (sgRNA) and are used in combination with various transformation methods or lately available novel nanoparticle-based delivery approaches, allows targeted mutagenesis in plants species. Even though this editing technique is limitless, it has still not been employed in many plant species to date. Chickpea is the second most crucial winter grain crop cultivated worldwide; there are currently no reports on CRISPR/Cas9 gene editing in chickpea. Here, we selected the 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes, both associated with drought tolerance for CRISPR/Cas9 editing in chickpea protoplast. The 4CL represents a key enzyme involved in phenylpropanoid metabolism in the lignin biosynthesis pathway. It regulates the accumulation of lignin under stress conditions in several plants. The RVE7 is a MYB transcription factor which is part of regulating circadian rhythm in plants. The knockout of these selected genes in the chickpea protoplast using DNA-free CRISPR/Cas9 editing represents a novel approach for achieving targeted mutagenesis in chickpea. Results showed high-efficiency editing was achieved for RVE7 gene in vivo compared to the 4CL gene. This study will help unravel the role of these genes under drought stress and understand the complex drought stress mechanism pathways. This is the first study in chickpea protoplast utilizing CRISPR/Cas9 DNA free gene editing of drought tolerance associated genes.
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Affiliation(s)
| | | | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne 3000, Australia; (S.B.); (A.S.B.)
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19
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De Luca D, Lauritano C. In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms. BIOLOGY 2020; 9:E110. [PMID: 32456002 PMCID: PMC7284882 DOI: 10.3390/biology9050110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
Abstract
Marine microalgae are photosynthetic microorganisms at the base of the marine food webs. They are characterized by huge taxonomic and metabolic diversity and several species have been shown to have bioactivities useful for the treatment of human pathologies. However, the compounds and the metabolic pathways responsible for bioactive compound synthesis are often still unknown. In this study, we aimed at analysing the microalgal transcriptomes available in the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) database for an in silico search of polyketide synthase type III homologs and, in particular, chalcone synthase (CHS) and stilbene synthase (STS), which are often referred to as the CHS/STS family. These enzymes were selected because they are known to produce compounds with biological properties useful for human health, such as cancer chemopreventive, anti-inflammatory, antioxidant, anti-angiogenic, anti-viral and anti-diabetic. In addition, we also searched for 4-Coumarate: CoA ligase, an upstream enzyme in the synthesis of chalcones and stilbenes. This study reports for the first time the occurrence of these enzymes in specific microalgal taxa, confirming the importance for microalgae of these pathways and giving new insights into microalgal physiology and possible biotechnological applications for the production of bioactive compounds.
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Affiliation(s)
- Daniele De Luca
- Department of Humanities, Università degli Studi Suor Orsola Benincasa, CAP80135 Naples, Italy
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, CAP80121 Naples, Italy
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20
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Gong X, Xie Z, Qi K, Zhao L, Yuan Y, Xu J, Rui W, Shiratake K, Bao J, Khanizadeh S, Zhang S, Tao S. PbMC1a/1b regulates lignification during stone cell development in pear ( Pyrus bretschneideri) fruit. HORTICULTURE RESEARCH 2020; 7:59. [PMID: 32377350 PMCID: PMC7193627 DOI: 10.1038/s41438-020-0280-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 05/16/2023]
Abstract
Programmed cell death (PCD) and secondary cell wall (SCW) thickening in pear fruit are accompanied by the deposition of cellulose and lignin to form stone cells. Metacaspase is an important protease for development, tissue renewal and PCD. The understanding of the molecular mechanism whereby pear (Pyrus) metacaspase promotes PCD and cell wall lignification is still limited. In this study, the Metacaspases gene family (PbMCs) from P. bretschneideri was identified. PbMC1a/1b was associated with lignin deposition and stone cell formation by physiological data, semiquantitative real-time polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR). Relative to wild-type (WT) Arabidopsis, the overexpression of PbMC1a/1b increased lignin deposition and delayed growth, thickened the cell walls of vessels, xylary fibers and interfascicular fibers, and increased the expression of lignin biosynthetic genes. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and GST pull-down assays indicated that the PbMC1a/1b protein physically interacted with PbRD21. Simultaneously, the transient expression of PbMC1a/1b and PbRD21 led to significant changes in the expression of genes and lignin contents in pear fruits and flesh calli. These results indicate that PbMC1a/1b plays an important role in cell wall lignification, possibly by interacting with PbRD21 to increase the mRNA levels of some lignin synthesis-associated genes and promote the formation of stone cells in pear fruit.
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Affiliation(s)
- Xin Gong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihua Xie
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liangyi Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yazhou Yuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiahui Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weikang Rui
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | | | - Jianping Bao
- College of Plant Science, Tarim University, Ala’er City, China
| | - Shahrokh Khanizadeh
- ELM Consulting Inc., St-Lazare, Canada
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shutian Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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21
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Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2. FORESTS 2020. [DOI: 10.3390/f11010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The deposition of lignin in flesh parenchyma cells for pear stone cells, and excessive stone cells reduce the taste and quality of the fruit. The effect of metaxenia on the quality of fruit has been heavily studied, but the effect of metaxenia on stone cell formation has not been fully elucidated to date. This study used P. bretschneideri (Chinese white pear) cv. ‘Yali’ (high-stone cell content) and P. pyrifolia (Sand pear) cv. ‘Cuiguan’ (low-stone cell content) as pollination trees to pollinate P. bretschneideri cv. ‘Lianglizaosu’ separately to fill this gap in the literature. The results of quantitative determination, histochemical staining and electron microscopy indicated that the content of stone cells and lignin in YL fruit (‘Yali’ (pollen parent) × ‘Lianglizaosu’ (seed parent)) was significantly higher than that in CL fruit (‘Cuiguan’ (pollen parent) × ‘Lianglizaosu’ (seed parent)). The transcriptome sequencing results that were obtained from the three developmental stages of the two types of hybrid fruits indicated that a large number of differentially expressed genes (DEGs) related to auxin signal transduction (AUX/IAAs and ARFs), lignin biosynthesis, and lignin metabolism regulation (MYBs, LIMs, and KNOXs) between the CL and YL fruits at the early stage of fruit development. Therefore, metaxenia might change the signal transduction process of auxin in pear fruit, thereby regulating the expression of transcription factors (TFs) related to lignin metabolism, and ultimately affecting lignin deposition and stone cell development. In addition, we performed functional verification of a differentially expressed gene, PbC4H2 (cinnamate 4-hydroxylase). Heterologous expression of PbC4H2 in the c4h mutant not only restored its collapsed cell wall, but also significantly increased the lignin content in the inflorescence stem. The results of our research help to elucidate the metaxenia-mediated regulation of pear stone cell development and clarify the function of PbC4H2 in cell wall development and lignin synthesis, which establishes a foundation for subsequent molecular breeding.
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Wang X, Liu S, Liu C, Liu Y, Lu X, Du G, Lyu D. Biochemical characterization and expression analysis of lignification in two pear (Pyrus ussuriensis Maxim.) varieties with contrasting stone cell content. PROTOPLASMA 2020; 257:261-274. [PMID: 31482203 DOI: 10.1007/s00709-019-01434-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
As lignified stone cells reduce fruit quality, we investigated lignin deposition, phenolic metabolites, and expression of lignin biosynthetic genes during fruit development to elucidate the molecular mechanism of stone cell lignification using histological, biochemical, and transcriptional data from two Ussurian pear varieties (Jianba and Nanguo) with contrasting stone cell content. Lignin content and distribution coincided with stone cell accumulation. As per LC-MS analysis, Jianba exhibited higher levels of lignin monomers and hydroxycinnamates than Nanguo, consistently with lignin amount in each case. However, flavonoid content was much higher in Nanguo. Transcriptional data showed that most monolignol biosynthesis-related genes were particularly upregulated in Jianba during lignin accumulation; especially CCR and LAC, two monolignol biosynthesis-specific genes, were substantially upregulated in Jianba fruits at critical stages. Therefore, differences in stone cell content between "Jianba" and "Nanguo" may result from differential expression of lignin synthase genes located downstream of the lignin biosynthesis pathway. Taken together, our data may provide a deeper understanding of the molecular mechanism for stone cell lignification in pear fruit.
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Affiliation(s)
- Xiaoqian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China
- Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang, People's Republic of China
| | - Siqi Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Chang Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Yang Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Xiaofeng Lu
- Chinese Academy of Agricultural Science, Xingcheng, People's Republic of China
| | - Guodong Du
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China.
- Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang, People's Republic of China.
| | - Deguo Lyu
- College of Horticulture, Shenyang Agricultural University, Shenyang, People's Republic of China.
- Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang, People's Republic of China.
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Cao Y, Meng D, Li X, Wang L, Cai Y, Jiang L. A Chinese White Pear ( Pyrus bretschneideri) BZR Gene PbBZR1 Act as a Transcriptional Repressor of Lignin Biosynthetic Genes in Fruits. FRONTIERS IN PLANT SCIENCE 2020; 11:1087. [PMID: 32765567 PMCID: PMC7379032 DOI: 10.3389/fpls.2020.01087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/01/2020] [Indexed: 05/08/2023]
Abstract
BZR transcription factors play essential roles in plant growth and environmental stimuli, and they are also the positive regulators of Brassinosteroid (BR) signal transduction in diverse plants. In addition, BZR TFs, as crucial regulators of BR synthesis, may have multiple stress-resistance functions and their related regulatory mechanisms have been well illustrated in model plants. Here, we carried out a genome-wide identification of BZR members in Chinese pear (Pyrus bretschneideri) and identified 13 members. By comparative analysis in five Rosaceae genomes, BZR members in the pear genome may have undergone large-scale duplication events during evolution. Purifying selection played an important role in almost all of the orthologous and paralogous gene pairs. According to the expression analysis of the PbBZRs during fruit development, three PbBZRs were selected for detailed analysis. Transcriptional activation assays presented that PbBZR1 repressed the promoters of P. bretschneideri lignin biosynthetic genes, such as PbCES9, PbCOMT3, and PbHCT6. Our study traces the evolution of BZR gene family members in Rosaceae genomes and illustrates that the rates of gene loss and gain are far from equilibrium in different species. At the same time, our results suggest that PbBZR1 may be involved in the negative regulation of lignin biosynthesis.
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Affiliation(s)
- Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoxu Li
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
| | - Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
- *Correspondence: Lihu Wang, ; Yongping Cai, ; Lan Jiang,
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Cao Y, Jiang L, Wang L, Cai Y. Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus. Biomolecules 2019; 9:biom9090490. [PMID: 31527450 PMCID: PMC6770726 DOI: 10.3390/biom9090490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 11/21/2022] Open
Abstract
Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.
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Affiliation(s)
- Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China.
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Lan Jiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China.
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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Cao Y, Meng D, Han Y, Chen T, Jiao C, Chen Y, Jin Q, Cai Y. Comparative analysis of B-BOX genes and their expression pattern analysis under various treatments in Dendrobium officinale. BMC PLANT BIOLOGY 2019; 19:245. [PMID: 31182022 PMCID: PMC6558717 DOI: 10.1186/s12870-019-1851-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 05/28/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in orchids (Orchidaceae) is not well studied. The newly released genome sequences of Dendrobium officinale and Phalaenopsis equestris have allowed a systematic analysis of these important BBX genes in orchids. RESULTS Here we identified 19 (DoBBX01-19) and 16 (PeBBX01-16) BBX genes from D. officinale and P. equestris, respectively, and clustered into five clades (I-V) according to phylogenetic analysis. Thirteen orthologous, two DoBBXs paralogous and two PeBBXs paralogous gene pairs were validated. This gene family mainly underwent purifying selection, but five domains experienced positive selection during evolution. Noteworthy, the expression patterns of root, root_tips, stem, leaf, speal, column, lip, and flower_buds revealed that they might contribution to the formation of these tissues. According to the cis-regulatory elements analysis of BBX genes, qRT-PCR experiments were carried out using D. officinale PLBs (protocorm-like bodies) and displayed that these BBX genes were differentially regulated under AgNO3, MeJA (Methyl Jasmonate), ABA (abscisic acid) and SA (salicylic acid) treatments. CONCLUSIONS Our analysis exposed that DoBBX genes play significant roles in plant growth and development, and response to different environmental stress conditions of D. officinale, which provide aid in the selection of appropriate candidate genes for further functional characterization of BBX genes in plants.
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Affiliation(s)
- Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yahui Han
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tianzhe Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chunyan Jiao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yu Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Su X, Meng T, Zhao Y, Li G, Cheng X, Abdullah M, Sun X, Cai Y, Lin Y. Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2019; 7:e6628. [PMID: 30941270 PMCID: PMC6440465 DOI: 10.7717/peerj.6628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Tiankai Meng
- School of Life Sciences and Technology, TongJi University, Shanghai, China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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Lavhale SG, Kalunke RM, Giri AP. Structural, functional and evolutionary diversity of 4-coumarate-CoA ligase in plants. PLANTA 2018; 248:1063-1078. [PMID: 30078075 DOI: 10.1007/s00425-018-2965-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/30/2018] [Indexed: 05/08/2023]
Abstract
The 4-coumarate-CoA ligases (4CL) contribute in channelizing flux of different phenylpropanoid biosynthetic pathways. Expression of 4CL is optimized at developmental stages and in response to environmental triggers such as biotic and abiotic stresses. The enzyme is valuable in metabolic pathway engineering for curcuminoids, resveratrol, biofuel production and nutritional improvement. Vigorous analysis of regulation at functional and expression level is obligatory to attain efficient commercial production of candidate metabolites using 4CL. Phenylpropanoid pathway provides precursors for numerous secondary metabolites in plants. In this pathway, 4-coumarate-CoA ligase (EC 6.2.1.12, 4CL) is the main branch point enzyme which generates activated thioesters. Being the last enzyme of three shared common steps in general phenylpropanoid pathway, it contributes to channelize precursors for different phenylpropanoids. In plants, 4CL enzymes are present in multiple isoforms and encoded by small gene family. It belongs to adenylate-forming enzyme family and catalyzes the reaction that converts hydroxy or methoxy cinnamic acid derivatives to corresponding thioesters. These thioesters are further utilized for biosynthesis of phenylpropanoids, which are known for having numerous nutritional and medicinal applications. In addition, the 4CL enzymes have been characterized from various plants for their role in plant physiology or in biotic and abiotic stresses. Furthermore, specific isoforms are differentially regulated upon exposure to diverse stimuli leading to flux diversion toward the particular metabolite biosynthesis. Evolutionary studies showed that 4CL separately evolved after monocot and dicot segregation. Here, we provide a comprehensive review on 4CL, which includes evolution, function, gene/protein structure, role in metabolite biosynthesis and cellular partition, and their regulation. Based on the available data, we have explored the scope for pathway engineering by utilizing 4CL enzymes.
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Affiliation(s)
- Santosh G Lavhale
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Raviraj M Kalunke
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
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Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development. Funct Integr Genomics 2018; 18:519-531. [PMID: 29675811 DOI: 10.1007/s10142-018-0609-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 12/16/2022]
Abstract
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes. Thirty-one PbPHD genes were divided into 7 subfamilies based on the phylogenetic analysis, which are consistent with the intron-exon and conserved motif analyses. In addition, we identified five segmental duplication events, implying that the segmental duplications might be a crucial role in the expansion of the PHD-finger gene family in pear. The microsynteny analysis of five Rosaceae species showed that there were independent duplication events in addition to the genome-wide duplication of the pear genome. Subsequently, ten expressed PHD-finger genes of pear fruit were identified using qRT-PCR, and one of these genes, PbPHD10, was identified as an important candidate gene for the regulation of lignin synthesis. Our research provides useful information for the further analysis of the function of PHD-finger gene family in pear.
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Cao Y, Han Y, Meng D, Li D, Jiao C, Jin Q, Lin Y, Cai Y. B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.). BMC PLANT BIOLOGY 2017; 17:156. [PMID: 28927374 PMCID: PMC5606111 DOI: 10.1186/s12870-017-1105-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/08/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear. RESULTS In the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members. The transcript analysis revealed that twelve PbBBX genes (48%) were specifically expressed in pear pollen tubes. Furthermore, qRT-PCR analysis indicated that both PbBBX4 and PbBBX13 have potential role in pear fruit development, while PbBBX5 should be involved in the senescence of pear pollen tube. CONCLUSIONS This study provided a genome-wide survey of BBX gene family in pear, and highlighted its roles in both pear fruits and pollen tubes. The results will be useful in improving our understanding of the complexity of BBX gene family and functional characteristics of its members in future study.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Chunyan Jiao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
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Cao Y, Han Y, Meng D, Li G, Li D, Abdullah M, Jin Q, Lin Y, Cai Y. Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca. Front Genet 2017; 8:78. [PMID: 28663757 PMCID: PMC5471313 DOI: 10.3389/fgene.2017.00078] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Guohui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Muhammad Abdullah
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
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31
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Cao Y, Han Y, Meng D, Li D, Jin Q, Lin Y, Cai Y. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae. PeerJ 2017; 5:e3400. [PMID: 28584725 PMCID: PMC5455322 DOI: 10.7717/peerj.3400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/10/2017] [Indexed: 11/20/2022] Open
Abstract
The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.
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Affiliation(s)
- Yunpeng Cao
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Dahui Li
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei, China
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Cao Y, Han Y, Jin Q, Lin Y, Cai Y. Comparative Genomic Analysis of the GRF Genes in Chinese Pear ( Pyrus bretschneideri Rehd), Poplar ( Populous), Grape ( Vitis vinifera), Arabidopsis and Rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2016; 7:1750. [PMID: 27933074 PMCID: PMC5121280 DOI: 10.3389/fpls.2016.01750] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/07/2016] [Indexed: 05/20/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural UniversityHefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural UniversityHefei, China
- *Correspondence: Yongping Cai,
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Cao Y, Han Y, Meng D, Li D, Jin Q, Lin Y, Cai Y. Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear ( Pyrus bretschneideri). FRONTIERS IN PLANT SCIENCE 2016; 7:1874. [PMID: 28018406 PMCID: PMC5145892 DOI: 10.3389/fpls.2016.01874] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 05/22/2023]
Abstract
Peroxidases (PRXs) are widely existed in various organisms and could be divided into different types according to their structures and functions. Specifically, the Class III Peroxidase, a plant-specific multi-gene family, involves in many physiological processes, such as the metabolism of auxin, the extension and thickening of cell wall, as well as the formation of lignin. By searching the pear genome database, 94 non-redundant PRXs from Pyrus bretschneideri (PbPRXs) were identified. Subsequently, analysis of phylogenetic relationships, gene structures, conserved motifs, and microsynteny was performed. These PbPRXs were unevenly distributed among 17 chromosomes of pear. In addition, 26 segmental duplication events but only one tandem duplication were occurred in these PbPRXs, implying segmental duplication was the main contributor to the expansion of the PbPRX family. By the Ka/Ks analysis, 26 out of 27 duplicated PbPRXs has experienced purifying selection. Twenty motifs were identified in PbPRXs based on the MEME analysis, 11 of which were enriched in pear. A total of 41 expressed genes were identified from ESTs of pear fruit. According to qRT-PCR, the expression trends of five PbPRXs in subgroup C were consistent with the change of lignin content during pear fruit development. So we inferred that the five PbPRXs were candidate genes involved in the lignin synthesis pathway. These results provided useful information for further researches of PRX genes in pear.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Dahui Li
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University Hefei, China
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