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Zou C, Tan H, Huang K, Zhai R, Yang M, Huang A, Wei X, Mo R, Xiong F. Physiological Characteristic Changes and Transcriptome Analysis of Maize ( Zea mays L.) Roots under Drought Stress. Int J Genomics 2024; 2024:5681174. [PMID: 38269194 PMCID: PMC10807950 DOI: 10.1155/2024/5681174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/08/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Water deficit is a key limiting factor for limiting yield in maize (Zea mays L.). It is crucial to elucidate the molecular regulatory networks of stress tolerance for genetic enhancement of drought tolerance. The mechanism of drought tolerance of maize was explored by comparing physiological and transcriptomic data under normal conditions and drought treatment at polyethylene glycol- (PEG-) induced drought stress (5%, 10%, 15%, and 20%) in the root during the seedling stage. The content of saccharide, SOD, CAT, and MDA showed an upward trend, proteins showed a downward trend, and the levels of POD first showed an upward trend and then decreased. Compared with the control group, a total of 597, 2748, 6588, and 5410 differentially expressed genes were found at 5%, 10%, 15%, and 20% PEG, respectively, and 354 common DEGs were identified in these comparisons. Some differentially expressed genes were remarkably enriched in the MAPK signaling pathway and plant hormone signal transduction. The 50 transcription factors (TFs) divided into 15 categories were screened from the 354 common DEGs during drought stress. Auxin response factor 10 (ARF10), auxin-responsive protein IAA9 (IAA9), auxin response factor 14 (ARF14), auxin-responsive protein IAA1 (IAA1), auxin-responsive protein IAA27 (IAA27), and 1 ethylene response sensor 2 (ERS2) were upregulated. The two TFs, including bHLH 35 and bHLH 96, involved in the MAPK signal pathway and plant hormones pathway, are significantly upregulated in 5%, 10%, 15%, and 20% PEG stress groups. The present study provides greater insight into the fundamental transcriptome reprogramming of grain crops under drought.
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Affiliation(s)
- Chenglin Zou
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Hua Tan
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Ruining Zhai
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Meng Yang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Aihua Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Xinxing Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Runxiu Mo
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
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Dong R, Guo Q, Li H, Li J, Zuo W, Long C. Estimation of morphological variation in seed traits of Sophora moorcroftiana using digital image analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1185393. [PMID: 37313255 PMCID: PMC10258342 DOI: 10.3389/fpls.2023.1185393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Sophora moorcroftiana is a leguminous plant endemic to the Qinghai-Tibet Plateau. It has excellent abiotic stress tolerance and is considered an ideal species for local ecological restoration. However, the lack of genetic diversity in the seed traits of S. moorcroftiana hinders its conservation and utilization on the plateau. Therefore, in this study, genotypic variation and phenotypic correlations were estimated for nine seed traits among 15 accessions of S. moorcroftiana over two years, 2014 and 2019, respectively from 15 sample points. All traits evaluated showed significant (P< 0.05) genotypic variation. In 2014, accession mean repeatability was high for seed perimeter, length, width, and thickness, and 100-seed weight. In 2019, mean repeatability for seed perimeter and thickness, and 100-seed weight were high. The estimates of mean repeatability for seed traits across the two years ranged from 0.382 for seed length to 0.781 for seed thickness. Pattern analysis showed that 100-seed weight was significantly positively correlated with traits such as seed perimeter, length, width, and thickness, and identified populations with breeding pool potential. In the biplot, principal components 1 and 2 explained 55.22% and 26.72% of the total variation in seed traits, respectively. These accessions could produce breeding populations for recurrent selection to develop S. moorcroftiana varieties suitable for restoring the fragile ecological environment of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Rui Dong
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
| | - Qiqiang Guo
- Institute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang, China
| | - Huie Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jiangrong Li
- Key Lab Forest Ecology Tibet Plateau, Ministry Education, Tibet Agriculture & Animal Husbandry University, Nyingchi, China
| | - Weiwei Zuo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, China
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Zhang J, Liang Q, Li Y, Deng Z, Song G, Wang H, Yan M, Wang X. Integrated transcriptome and metabolome analyses shed light on the defense mechanisms in tomato plants after (E)-2-hexenal fumigation. Genomics 2023; 115:110592. [PMID: 36854356 DOI: 10.1016/j.ygeno.2023.110592] [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: 11/14/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Tomato is a widely cultivated fruit and vegetable and is valued for its flavor, colour, and nutritional value. C6-aldehydes, such as (E)-2-hexenal, not only have antibacterial and antifungal properties but also function as signaling molecules that control the defense mechanisms of plants, including tomatoes. In this study, we used liquid chromatography-mass spectrometry (LC-MS) and RNA sequencing techniques to generate metabolome and transcriptome datasets that elucidate the molecular mechanisms regulating defense responses in tomato leaves exposed to (E)-2-hexenal. A total of 28.27 Gb of clean data were sequenced and assembled into 23,720 unigenes. In addition, a non-targeted metabolomics approach detected 739 metabolites. There were 233 significant differentially expressed genes (DEGs) (158 up-regulated, 75 down-regulated) and 154 differentially expressed metabolites (DEMs) (86 up-regulated, 69 down-regulated). Most nucleotides and amino acids (L-Phenylalanine, L-Asparagine, L-Histidine, L-Arginine, and L-Tyrosine) and their derivatives were enriched. The analyses revealed that mitogen-activated protein kinase (MPK), pathogenesis-related protein (PR), and endochitinase (CHIB) were primarily responsible for the adaptation of plant defense responses. Therefore, the extensive upregulation of these genes may be associated with the increased plant defense response. These findings help us comprehend the defense response of plants to (E)-2-hexenal and improve the resistance of horticultural plants.
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Affiliation(s)
- Jihong Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Quanwu Liang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuqiong Li
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Ge Song
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Haihua Wang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens GA30602, USA
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Transcriptomic insights into the effects of abscisic acid on the germination of Magnolia sieboldii K. Koch seed. Gene 2023; 853:147066. [PMID: 36455787 DOI: 10.1016/j.gene.2022.147066] [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: 08/12/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022]
Abstract
Magnolia sieboldii K. Koch is a deciduous tree species. However, the wild resource of M. sieboldii has been declining due to excessive utilization and seed dormancy. In our previous research, M. sieboldii seeds have morphophysiological dormancy and low germination rates under natural conditions. The aim of the present study was to identify the genes involved in dormancy maintenance. In this study, the germination percentage of M. sieboldii seeds negatively correlated with the content of endogenous abscisic acid (ABA). The hydration of seeds for germination showed three distinct phases. Five key time points were identified: 0 h imbibition (dry seed, GZ), 0 day after imbibition (DAI), 16 DAI, 40 DAI, and 56 DAI. The comprehensive transcript profiles of M. sieboldii seeds treated with ABA and water at the five key germinating stages were obtained. A total of 9641 differentially expressed genes (DEGs) were identified, and 208 and 197 common DEGs were found throughout the ABA and water treatments, respectively. Compared with that in the GZ, 518, 696, 2133, and 1535 DEGs were identified in the SH group at 0, 16, 40 and 56 DAI, respectively. 666, 1725, 1560 and 1415 DEGs were identified in the ABA group at 0, 16, 40, and 56 DAI, respectively. Among the identified DEGs, 12 722 were annotated with GO terms, the top three enriched GO terms were different among the DEGs at 56 DAI in the ABA vs. SH treatments. KEGG pathway enrichment analysis for DEGs indicated that oxidative phosphorylation, protein processing in endoplasmic reticulum, starch and sucrose metabolism play an important role in seed response to ABA. 1926 TFs are obtained and classified into 72 families from the M. sieboldii transcriptome. Results of differential gene expression analysis together with qRT-PCR indicated that phase II is crucial for rapid and successful seed germination. This study is the first to present the global expression patterns of ABA-regulated transcripts in M. sieboldii seeds at different germinating phases.
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Yin X, Yang D, Liu Y, Yang S, Zhang R, Sun X, Liu H, Duan Y, Yang Y, Yang Y. Sophora moorcroftiana genome analysis suggests association between sucrose metabolism and drought adaptation. PLANT PHYSIOLOGY 2023; 191:844-848. [PMID: 36472533 PMCID: PMC9922414 DOI: 10.1093/plphys/kiac558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
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Yuan Y, Zuo J, Zhang H, Zu M, Liu S. Analysis of the different growth years accumulation of flavonoids in Dendrobium moniliforme (L.) Sw. by the integration of metabolomic and transcriptomic approaches. Front Nutr 2022; 9:928074. [PMID: 36225877 PMCID: PMC9549206 DOI: 10.3389/fnut.2022.928074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022] Open
Abstract
Dendrobium moniliforme (L.) Sw. is a valuable herbal crop, and flavonoids are primarily distributed as active ingredients in the stem, but the composition and synthesis mechanisms of flavonoids in different growth years are not clear. The accumulation of flavonoids in D. moniliforme from four different years was investigated, using a combined metabolomics and transcriptomics approach in this study. The phenylpropanoid and flavonoid biosynthetic pathways were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). The widely targeted metabolomics technique revealed a total of 173 kinds of flavonoid metabolites. The metabolomics data confirmed the trend of total flavonoids (TF) content in stems of D. moniliforme, with chalcone, naringenin, eriodictyol, dihydroquercetin, and other flavonoids considerably up-accumulating in the third year. Twenty DEGs were detected that regulate flavonoid synthesis and the expression of these genes in different growth years was verified using real-time quantitative PCR (qRT-PCR). Furthermore, a comprehensive regulatory network was built for flavonoid biosynthesis and it was discovered that there is one FLS gene, one CCR gene and two MYB transcription factors (TFs) with a high connection with flavonoid biosynthesis by weighted gene co-expression network analysis (WGCNA). In this study, the correlation between genes involved in flavonoid biosynthesis and metabolites was revealed, and a new regulatory mechanism related to flavonoid biosynthesis in D. moniliforme was proposed. These results provide an important reference for the farmers involved in the cultivation of D. moniliforme.
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Tang D, Quan C, Lin Y, Wei K, Qin S, Liang Y, Wei F, Miao J. Physio-Morphological, Biochemical and Transcriptomic Analyses Provide Insights Into Drought Stress Responses in Mesona chinensis Benth. FRONTIERS IN PLANT SCIENCE 2022; 13:809723. [PMID: 35222473 PMCID: PMC8866654 DOI: 10.3389/fpls.2022.809723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/18/2022] [Indexed: 05/04/2023]
Abstract
Drought stress affects the normal growth and development of Mesona chinensis Benth (MCB), which is an important medicinal and edible plant in China. To investigate the physiological and molecular mechanisms of drought resistance in MCB, different concentrations of polyethylene glycol 6000 (PEG6000) (0, 5, 10, and 15%) were used to simulate drought conditions in this study. Results showed that the growth of MCB was significantly limited under drought stress conditions. Drought stress induced the increases in the contents of Chla, Chlb, Chla + b, soluble protein, soluble sugar, and soluble pectin and the activities of superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (TAC), hydrogen peroxide (H2O2), and malondialdehyde (MDA). Transcriptome analysis revealed 3,494 differentially expressed genes (DEGs) (1,961 up-regulated and 1,533 down-regulated) between the control and 15% PEG6000 treatments. These DEGs were identified to be involved in the 10 metabolic pathways, including "plant hormone signal transduction," "brassinosteroid biosynthesis," "plant-pathogen interaction," "MAPK signaling pathway-plant," "starch and sucrose metabolism," "pentose and glucuronate interconversions," "phenylpropanoid biosynthesis," "galactose metabolism," "monoterpenoid biosynthesis," and "ribosome." In addition, transcription factors (TFs) analysis showed 8 out of 204 TFs, TRINITY_DN3232_c0_g1 [ABA-responsive element (ABRE)-binding transcription factor1, AREB1], TRINITY_DN4161_c0_g1 (auxin response factor, ARF), TRINITY_DN3183_c0_g2 (abscisic acid-insensitive 5-like protein, ABI5), TRINITY_DN28414_c0_g2 (ethylene-responsive transcription factor ERF1b, ERF1b), TRINITY_DN9557_c0_g1 (phytochrome-interacting factor, PIF3), TRINITY_DN11435_c1_g1, TRINITY_DN2608_c0_g1, and TRINITY_DN6742_c0_g1, were closely related to the "plant hormone signal transduction" pathway. Taken together, it was inferred that these pathways and TFs might play important roles in response to drought stress in MCB. The current study provided important information for MCB drought resistance breeding in the future.
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Affiliation(s)
- Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Changqian Quan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yang Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Shuangshuang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Lei L, Zhao Y, Shi K, Liu Y, Hu Y, Shao H. Phytotoxic Activity of Alkaloids in the Desert Plant Sophora alopecuroides. Toxins (Basel) 2021; 13:toxins13100706. [PMID: 34678999 PMCID: PMC8540331 DOI: 10.3390/toxins13100706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Sophora alopecuroides is known to produce relatively large amounts of alkaloids; however, their ecological consequences remain unclear. In this study, we evaluated the allelopathic potential of the main alkaloids, including aloperine, matrine, oxymatrine, oxysophocarpine, sophocarpine, sophoridine, as well as their mixture both in distilled H2O and in the soil matrix. Our results revealed that all the alkaloids possessed inhibitory activity on four receiver species, i.e., Amaranthus retroflexus, Medicago sativa, Lolium perenne and Setaria viridis. The strength of the phytotoxicity of the alkaloids was in the following order: sophocarpine > aloperine > mixture > sophoridine > matrine > oxysophocarpine > oxymatrine (in Petri dish assays), and matrine > mixture > sophocarpine > oxymatrine > oxysophocarpine > sophoridine > aloperine (in pot experiments). In addition, the mixture of the alkaloids was found to significantly increase the IAA content, MDA content and POD activity of M. sativa seedlings, whereas CTK content, ABA content, SOD activity and CAT activity of M. sativa seedlings decreased markedly. Our results suggest S. alopecuroides might produce allelopathic alkaloids to improve its competitiveness and thus facilitate the establishment of its dominance; the potential value of these alkaloids as environmentally friendly herbicides is also discussed.
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Affiliation(s)
- Lijing Lei
- Chemistry and Environment Science School, Yili Normal University, Yining 835000, China;
| | - Yu Zhao
- Bioscience and Geosciences School, Yili Normal University, Yining 835000, China; (Y.Z.); (Y.L.)
- Historical Geography and Tourism School, Shangrao Normal University, Jiangxi 334001, China
| | - Kai Shi
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Liu
- Bioscience and Geosciences School, Yili Normal University, Yining 835000, China; (Y.Z.); (Y.L.)
- Chemistry and Environment Science School, Shangrao Normal University, Jiangxi 334001, China
| | - Yunxia Hu
- Chemistry and Environment Science School, Yili Normal University, Yining 835000, China;
- Correspondence: (Y.H.); (H.S.); Tel.: +86-991-7823-155 (H.S.)
| | - Hua Shao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.H.); (H.S.); Tel.: +86-991-7823-155 (H.S.)
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Selection and Evaluation of Potential Reference Genes for Quantitative Real-Time PCR in Agaricus blazei Based on Transcriptome Sequencing Data. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6661842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely used to detect gene expression due to its high sensitivity, high throughput, and convenience. The accurate choice of reference genes is required for normalization of gene expression in qRT-PCR analysis. In order to identify the optimal candidates for gene expression analysis using qRT-PCR in Agaricus blazei, we studied the potential reference genes in this economically important edible fungus. In this study, transcriptome datasets were used as source for identification of candidate reference genes. And 27 potential reference genes including 21 newly stable genes, three classical housekeeping genes, and homologous genes of three ideal reference genes in Volvariella volvacea, were screened based on transcriptome datasets of A. blazei and previous studies. The expression stability of these genes was investigated by qRT-PCR analysis and further evaluated by four software packages, geNorm, NormFinder, BestKeeper, and RefFinder. Among these candidates, α-TUB (Tubulin alpha) and Cox5a (COX5A subunit VA of cytochrome c oxidase) were revealed as the most stable in fruit body, and suitable for 5 different developmental stages. α-TUB and ATP3 (ATP3 gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase) showed the most stable expression in stipe tissues and, Uqcrc (core subunit of the ubiquinol-cytochrome c reductase complex) and PUP3 (20S proteasome subunit beta 3) performed well in pileus tissues during the process of A. blazei development, while GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was among the least stable genes in all sample sets. Finally, the Ableln3 (homology of eln3 gene of Coprinus cinereus) was adopted to validate the reliability of these stable and unstable reference genes, indicating that the use of unsuitable reference genes as internal controls could change the target gene’s expression pattern. This study can provide guidance for choosing reference genes for analyzing the expression pattern of target genes and facilitate the functional genomic investigation on fruit body formation and development, as well as stipe elongation and pileus expansion in A. blazei.
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Lu X, Liu S, Zhi S, Chen J, Ye G. Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:375-390. [PMID: 33296551 DOI: 10.1111/plb.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.
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Affiliation(s)
- X Lu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - S Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
| | - S Zhi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, China
| | - J Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - G Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Liu Y, Yi F, Yang G, Wang Y, Pubu C, He R, Xiao Y, Wang J, Lu N, Wang J, Ma W. Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS). PeerJ 2020; 8:e9609. [PMID: 33240581 PMCID: PMC7676378 DOI: 10.7717/peerj.9609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/05/2020] [Indexed: 11/20/2022] Open
Abstract
Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Wang
- Forest Science Research Institute of Tibet Municipality, Lhasa, Tibet, China
| | - Ciren Pubu
- Forest Science Research Institute of Tibet Municipality, Lhasa, Tibet, China
| | - Runhua He
- College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junchen Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Mitra T, Mahanty A, Ganguly S, Mohanty BP. Transcriptomic responses to pollution in natural riverine environment in Rita rita. ENVIRONMENTAL RESEARCH 2020; 186:109508. [PMID: 32325295 DOI: 10.1016/j.envres.2020.109508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Aquatic pollution is one of the most common threats to the ecological health of aquatic ecosystems and its biota. Fish as lower vertebrates are excellent model to study the impact and responses of aquatic pollution. In fish, gill is the main organ indicator of whole animal health as it comes in contact with the surrounding water and absorbs many pollutants and contaminants; therefore, investigations on alterations in fish gill at transcriptome level could provide newer insights to the stress response mechanism(s) and pathways. For comprehensive evaluation of the impacts of pollutants (joint toxicity) prevalent in the riverine environment, comparative transcriptome analysis, by Next Generation Sequencing under Illumina HiSeq 2500 platform, was carried out in gill tissues of Rita rita collected from two stretches of river Ganga (Kanpur and Farakka) and results were validated by RT-qPCR. Out of 154,077 unigenes (Accession SRR548008), a total of 2024 differentially expressed genes (DEGs) including 942 up-regulated and 1082 down-regulated genes were identified by DESeq program. Further, Gene Ontology (GO) of DEGs showed that ribosomal large subunit biogenesis, mitochondrial ribosome and box H/ACA SnoRNA binding categories are highly affected by pollution. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed the involvement of the DEGs in energy metabolism, translational and transcriptional machinery, protein folding and degradation suggesting that these signalling pathways are highly affected by aquatic pollution. Among the DEGs, up-regulation of cytochrome c oxidase subunit (cox) 7a2 (69.47 fold), hsp70 subunit 14 (hsp70-14, 5.27 fold), muscle related coiled-coil protein (MURC, 21.55 fold), lysozyme G (40.14 fold), cox17 (29.36 fold) were the conspicuous ones which showed similar trends in expression when analysed by RT-qPCR. Based on fold change, perturbation values, correlation analysis by PCA and RT-qPCR validation, up-regulation of cox7a2, MURC and hsp70-14 appeared to be the most promising biomarker responses and could be useful in the evaluation of gill health and possibly be extended towards aquatic ecosystem health assessment.
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Affiliation(s)
- Tandrima Mitra
- ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; School of Biotechnology, KIIT-Deemed to be University, Patia, Bhubaneswar, 751024, India
| | - Arabinda Mahanty
- ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; ICAR-National Rice Research Institute, Crop Protection Division, Cuttack, 753006, India
| | - Satabdi Ganguly
- ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India
| | - Bimal Prasanna Mohanty
- ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; ICAR-Fisheries Science Division, Krishi Anusandhan Bhawan II, Pusa, New Delhi, 110 012, India.
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Chen Y, Pan W, Jin S, Lin S. Combined metabolomic and transcriptomic analysis reveals key candidate genes involved in the regulation of flavonoid accumulation in Anoectochilus roxburghii. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Mohanty BP, Mahanty A, Mitra T, Mohanty S, Naik AK, Parija SC. Proteomic and transcriptomic changes in rat liver following oral feeding of formaldehyde. CHEMOSPHERE 2020; 245:125599. [PMID: 31855752 DOI: 10.1016/j.chemosphere.2019.125599] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 11/25/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
Formaldehyde (FA), a ubiquitous volatile organic compound present in a wide range of resources, is a hazardous chemical and human carcinogen. Contamination of FA in food, especially perishable commodities like fish and meat, is a major source of exposure, although it is not recommended for use in food and food products owing to its carcinogenicity. Effects of oral feeding of FA have been studied by evaluating general health, haematology and clinical chemistry in rat. Recent studies have shown that FA exposure leads to detrimental cardiovascular effects. It regulates vascular tensions through nitric oxide-cGMP signalling pathway and ion channels in rats. Although FA is an established carcinogen, molecular studies on carcinogenic potential with dose dependency are meagre. In this context, the present study was undertaken to investigate the toxicogenomic and proteomic alterations in liver of rats fed FA through drinking water. By proteomic analysis, 621 proteins/protein-subunits showed differential abundance (proteome data available via ProteomeXchange with identifier PXD010534), whereas 536 differentially-expressed-genes were identified by transcriptome analysis (data available via Sequence Read Archive with identifier SRR7974113). Gene ontology analysis showed that binding, catalysis, signal transduction were affected in formaldehyde-fed rats. Pathway analysis revealed that formaldehyde-exposure activated PI3K-AKT pathway that leads to inhibition of caspase activity thereby assisting cells to survive against apoptosis. Decreased abundance/down-regulation of ANGPT, eNOS, STAT3 proteins/transcripts and increased abundance of EDN1 indicated decrease in angiogenesis and vasodilatation that restricted hepatic cells from becoming tumorigenic; thus, indicating FA could be less toxic and non-tumorigenic at low concentrations.
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Affiliation(s)
- Bimal Prasanna Mohanty
- ICAR-Central Inland Fisheries Research Institute, FREM Division, Biochemistry Laboratory- Proteomics Unit, Barrackpore, Kolkata, 700120, West Bengal, India.
| | - Arabinda Mahanty
- ICAR-Central Inland Fisheries Research Institute, FREM Division, Biochemistry Laboratory- Proteomics Unit, Barrackpore, Kolkata, 700120, West Bengal, India; ICAR-National Rice Research Institute, Crop Protection Division, Cuttack, 753006, India
| | - Tandrima Mitra
- ICAR-Central Inland Fisheries Research Institute, FREM Division, Biochemistry Laboratory- Proteomics Unit, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Sasmita Mohanty
- Department of Biotechnology, Faculty of Science and Technology, Rama Devi Women's' University, Bhubabeswar, 751022, India
| | - Ajit Kumar Naik
- Department of Pharmacology & Toxicology, Faculty of Veterinary Science, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Subas Chandra Parija
- Department of Pharmacology & Toxicology, Faculty of Veterinary Science, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
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The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome. PLoS One 2019; 14:e0226100. [PMID: 31805153 PMCID: PMC6894834 DOI: 10.1371/journal.pone.0226100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.
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Li H, Yang L, Li Q, Li J. Completed plastome sequence of Sophora moorcroftiana, an endemic shrub to the Qinghai-Tibet Plateau, China. Mitochondrial DNA B Resour 2019; 4:4182-4183. [PMID: 33366373 PMCID: PMC7707758 DOI: 10.1080/23802359.2019.1692713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sophora moorcroftiana, an endemic Fabaceae species occurred in the Qinghai-Tibet plateau, China, has important economic value in local. Its completed plastome sequence is 148,930 bp in size, and comprises a pair of inverted repeat (IR) regions of 23,787 bp each, a large single-copy region of 83,342 bp and a small single-copy region of 18,014 bp. The GC content of the plastome was 30.2%. A total of 124 genes were identified, comprising 80 protein-coding genes, 36 tRNA genes and eight rRNA genes. There are 94 unique genes, with 15 genes duplicated in the IR regions. Phylogenetic tree shows that plastome of S. moorcroftiana is most related to that of S. alopecuroides. This plastome would be helpful for the study of molecular mechanism of photosynthesis, sustainable conservation, genetic improvement of S. moorcroftiana.
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Affiliation(s)
- Huie Li
- College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Lan Yang
- College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Qian Li
- College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Jiangrong Li
- Key laboratory of Forest Ecology in Tibet Plateau of Ministry of Education, Tibet Agriculture & Animal Husbandry University, Nyingchi, China
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Cai YF, Wang JH, Zhang L, Song J, Peng LC, Zhang SB. Physiological and transcriptomic analysis highlight key metabolic pathways in relation to drought tolerance in Rhododendron delavayi. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:991-1008. [PMID: 31402822 PMCID: PMC6656850 DOI: 10.1007/s12298-019-00685-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/25/2019] [Accepted: 05/13/2019] [Indexed: 05/05/2023]
Abstract
Rhododendron delavayi is an alpine evergreen ornamental plant, but water shortage limits its growth and development in urban gardens. However, the adaptive mechanism of alpine evergreen rhododendrons to drought remains unclear. Here, a water control experiment was conducted to study the physiological and transcriptomic response of R. delavayi to drought. The drought treatment for 9 days decreased photosynthetic rate, induced accumulation of reactive oxygen species (ROS), and damaged chloroplast ultrastructure of R. delavayi. However, the photosynthetic rate quickly recovered to the level before treatment when the plants were re-watered. De novo assembly of RNA-Seq data generated 86,855 unigenes with an average length of 1870 bp. A total of 22,728 differentially expressed genes (DEGs) were identified between the control and drought plants. The expression of most DEGs related to photosynthesis were down-regulated during drought stress, and were up-regulated when the plants were re-watered, including the DEGs encoding subunits of light-harvesting chlorophyll-protein complex, photosystem II and photosystem I reaction center pigment-protein complexes, and photosynthetic electron transport. The expressions of many DEGs related to signal transduction, flavonoid biosynthesis and antioxidant activity were also significantly affected by drought stress. The results indicated that the response of R. delavayi to drought involved multiple physiological processes and metabolic pathways. Photosynthetic adjustment, ROS-scavenging system, abscisic acid and brassinosteroid signal transduction pathway may play important roles to improve drought tolerance of R. delavayi. Our findings provided valuable information for understanding the mechanisms of drought tolerance employed by Rhododendron species.
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Affiliation(s)
- Yan-Fei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205 China
- National Engineering Research Center for Ornamental Horticulture, Kunming, Yunnan 650205 China
| | - Ji-Hua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205 China
- National Engineering Research Center for Ornamental Horticulture, Kunming, Yunnan 650205 China
| | - Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205 China
- National Engineering Research Center for Ornamental Horticulture, Kunming, Yunnan 650205 China
| | - Jie Song
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205 China
- National Engineering Research Center for Ornamental Horticulture, Kunming, Yunnan 650205 China
| | - Lv-Chun Peng
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205 China
- National Engineering Research Center for Ornamental Horticulture, Kunming, Yunnan 650205 China
| | - Shi-Bao Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
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Song Q, Cheng S, Chen Z, Nie G, Xu F, Zhang J, Zhou M, Zhang W, Liao Y, Ye J. Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis. BMC PLANT BIOLOGY 2019; 19:199. [PMID: 31092208 PMCID: PMC6521437 DOI: 10.1186/s12870-019-1801-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/25/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA3) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA3 on F. hupehensis seed germination. RESULTS We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA3 (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA3 treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA3 contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA3 (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA3 signal transduction were also observed in the G group. GA3-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA3-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes. CONCLUSION Exogenous GA3 increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA3 on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.
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Affiliation(s)
- Qiling Song
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023 China
| | - Zexiong Chen
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160 China
| | - Gongping Nie
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
- Engineering Research Center of Ecology and Agricultural Use of Wetland (Ministry of Education), Yangtze University, Jingzhou, 434025 Hubei China
| | - Jian Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Mingqin Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
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Sarwar MB, Ahmad Z, Rashid B, Hassan S, Gregersen PL, Leyva MDLO, Nagy I, Asp T, Husnain T. De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms. Sci Rep 2019; 9:396. [PMID: 30674899 PMCID: PMC6344536 DOI: 10.1038/s41598-018-35891-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/29/2018] [Indexed: 11/30/2022] Open
Abstract
Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance to their xeric environments. They employ various strategies to overcome environmental constraints, such as crassulacean acid metabolism, wax depositions, and protective leaf morphology. Genomic resources of Agave species have received little attention irrespective of their cultural, economic and ecological importance, which so far prevented the understanding of the molecular bases underlying their adaptations to the arid environment. In this study, we aimed to elucidate molecular mechanism(s) using transcriptome sequencing of A. sisalana. A de novo approach was applied to assemble paired-end reads. The expression study unveiled 3,095 differentially expressed unigenes between well-irrigated and drought-stressed leaf samples. Gene ontology and KEGG analysis specified a significant number of abiotic stress responsive genes and pathways involved in processes like hormonal responses, antioxidant activity, response to stress stimuli, wax biosynthesis, and ROS metabolism. We also identified transcripts belonging to several families harboring important drought-responsive genes. Our study provides the first insight into the genomic structure of A. sisalana underlying adaptations to drought stress, thus providing diverse genetic resources for drought tolerance breeding research.
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Affiliation(s)
- Muhammad Bilal Sarwar
- Plant Genomics Lab, Center of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, 53700, Pakistan
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Zarnab Ahmad
- Plant Genomics Lab, Center of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Bushra Rashid
- Plant Genomics Lab, Center of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, 53700, Pakistan.
| | - Sameera Hassan
- Plant Genomics Lab, Center of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Maria De la O Leyva
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Tayyab Husnain
- Plant Genomics Lab, Center of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, 53700, Pakistan
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De Novo Assembly and Discovery of Genes That Involved in Drought Tolerance in the Common Vetch. Int J Mol Sci 2019; 20:ijms20020328. [PMID: 30650531 PMCID: PMC6359484 DOI: 10.3390/ijms20020328] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
The common vetch (Vicia sativa) is often used as feed for livestock because of its high nutritional value. However, drought stress reduces forage production through plant damage. Here, we studied the transcriptional profiles of common vetch exposed to drought in order to understand the molecular mechanisms of drought tolerance in this species. The genome of the common vetch has not been sequenced, therefore we used Illumina sequencing to generate de novo transcriptomes. Nearly 500 million clean reads were used to generate 174,636 transcripts, including 122,299 unigenes. In addition, 5313 transcription factors were identified and these transcription factors were classified into 79 different gene families. We also identified 11,181 SSR loci from di- to hexa-nucleotides whose repeat number was greater than five. On the basis of differentially expressed genes, Gene Ontology analysis identified many drought-relevant categories, including “oxidation-reduction process”, “lipid metabolic process” and “oxidoreductase activity”. In addition to these, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified pathways, such as “Plant hormone signal transduction”, “Glycolysis/Gluconeogenesis” and “Phenylpropanoid biosynthesis”, as differentially expressed in the plants exposed to drought. The expression results in this study will be useful for further extending our knowledge on the drought tolerance of common vetch.
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Zhao D, Shi Y, Senthilkumar HA, Qiao Q, Wang Q, Shen Y, Hu G. Enriched networks 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' potentially conferred to drought adaptation of the epiphytic orchid Dendrobium wangliangii. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:31-45. [PMID: 30804628 PMCID: PMC6352522 DOI: 10.1007/s12298-018-0607-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 08/12/2018] [Accepted: 09/24/2018] [Indexed: 05/17/2023]
Abstract
Dendrobium wangliangii is an endangered and epiphytic orchid with tolerance to seasonally extreme arid conditions and occurs exclusively in the hot-dry valley area of southwestern China. To reveal its molecular basis responsible for ecological adaptation, large-scale transcriptome sequencing was performed using Illumina sequencing with pooled mRNA extracted from whole plants and pseudobulbs during drought and rainy seasons. Based on the target transcript selection, the differentially expressed genes were related to 8 well-known drought-tolerant categories, and to morphological traits in resistance to water stress including pseudobulbs and roots. Further gene ontology enrichment analysis revealed that 'nucleoside/nucleotide and ribonucleoside/ribonucleotide metabolic processes' and 'response to stimulus' were the two most important aspects in resistance to drought stress with respect to the whole plant. In addition, the difference in the number and category of differentially expressed genes in whole plant and stem suggested the involvement of genes specifically localized in the stem, such as GTP-binding protein, lipases, signaling related transcripts and those involved in the ATP metabolic process. The comprehensive analysis of the epiphytic orchid in response to water deprivation indicates that integral tactics lead to active adaptation as a basal defense response to drought stress by the endangered epiphyte, including the collaboration of metabolic processes, responses to a various stimulus and other candidate genes contribute to its extreme drought tolerance. Insights from this study can be further utilized to understand stress-responsive genes in other medicinally important species and to improve the drought tolerance of food crops.
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Affiliation(s)
- Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
| | - Yana Shi
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
| | - Qiuxia Wang
- Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province, Kunming University, Kunming, China
| | - Yong Shen
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guangwan Hu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Moon KB, Ahn DJ, Park JS, Jung WY, Cho HS, Kim HR, Jeon JH, Park YI, Kim HS. Transcriptome Profiling and Characterization of Drought-Tolerant Potato Plant ( Solanum tuberosum L.). Mol Cells 2018; 41:979-992. [PMID: 30396236 PMCID: PMC6277564 DOI: 10.14348/molcells.2018.0312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 01/25/2023] Open
Abstract
Potato (Solanum tuberosum L.) is the third most important food crop, and breeding drought-tolerant varieties is vital research goal. However, detailed molecular mechanisms in response to drought stress in potatoes are not well known. In this study, we developed EMS-mutagenized potatoes that showed significant tolerance to drought stress compared to the wild-type (WT) 'Desiree' cultivar. In addition, changes to transcripts as a result of drought stress in WT and drought-tolerant (DR) plants were investigated by de novo assembly using the Illumina platform. One-week-old WT and DR plants were treated with -1.8 Mpa polyethylene glycol-8000, and total RNA was prepared from plants harvested at 0, 6, 12, 24, and 48 h for subsequent RNA sequencing. In total, 61,100 transcripts and 5,118 differentially expressed genes (DEGs) displaying up- or down-regulation were identified in pairwise comparisons of WT and DR plants following drought conditions. Transcriptome profiling showed the number of DEGs with up-regulation and down-regulation at 909, 977, 1181, 1225 and 826 between WT and DR plants at 0, 6, 12, 24, and 48 h, respectively. Results of KEGG enrichment showed that the drought tolerance mechanism of the DR plant can mainly be explained by two aspects, the 'photosynthetic-antenna protein' and 'protein processing of the endoplasmic reticulum'. We also divided eight expression patterns in four pairwise comparisons of DR plants (DR0 vs DR6, DR12, DR24, DR48) under PEG treatment. Our comprehensive transcriptome data will further enhance our understanding of the mechanisms regulating drought tolerance in tetraploid potato cultivars.
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
- Department of Biological Sciences, Chungnam National University, Daejeon,
Korea
| | - Dong-Joo Ahn
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Hye-Ran Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
| | - Youn-il Park
- Department of Biological Sciences, Chungnam National University, Daejeon,
Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon,
Korea
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24
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Meng HL, Zhang W, Zhang GH, Wang JJ, Meng ZG, Long GQ, Yang SC. Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima. PLoS One 2018; 13:e0202848. [PMID: 30500823 PMCID: PMC6268015 DOI: 10.1371/journal.pone.0202848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022] Open
Abstract
Marsdenia tenacissima is a well-known anti-cancer medicinal plant used in traditional Chinese medicine, which often grows on the karst landform and the water conservation capacity of land is very poorly and drought occurrences frequently. We found M. tenacissima has strong drought resistance because of continuousdrought16 d, the leaves of M. tenacissima were fully curly and dying. But the leaves were fully almost recovering after re-watering 24h. The activity of SOD and POD were almost doubled under drought stress. The content of osmotic regulating substance proline and soluble sugar were three times than control group. But after re-watering, these indexes were declined rapidly. Three cDNA libraries of control, drought stress, and re-watering treatments were constructed. There were 43,129,228, 47,116,844, and 42,815,454 clean reads with Q20 values of 98.06, 98.04, and 97.88respectively.SRA accession number of raw data was PRJNA498187 on NCBI. A total of 8672, 6043, and 6537 differentially expressed genes (DEGs) were identified in control vs drought stress, control vs re-watering, and drought stress vs re-watering, respectively. In addition, 1039, 1016, and 980 transcription factors (TFs) were identified, respectively. Among them, 363, 267, and 299 TFs were identified as DEGs in drought stress, re-watering, and drought stress and re-watering, respectively. These differentially expressed TFs mainly belonged to the bHLH, bZIP, C2H2, ERF, MYB, MYB-related, and NAC families. A comparative analysis found that 1174 genes were up-regulated and 2344 were down-regulated under drought stress and this pattern was the opposite to that found after re-watering. Among the up-regulated genes, 64 genes were homologous to known functional genes that directly protect plants against drought stress. Furthermore, 44 protein kinases and 38 TFs with opposite expression patterns under drought stress and re-watering were identified, which are possibly candidate regulators for drought stress resistance in M. tenacissima. Our study is the first to characterize the M. tenacissima transcriptome in response to drought stress, and will serve as a useful resource for future studies on the functions of candidate protein kinases and TFs involved in M. tenacissima drought stress resistance.
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Affiliation(s)
- Heng-Ling Meng
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Wei Zhang
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Jian-Jun Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Zhen-Gui Meng
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Guang-Qiang Long
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
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Ma X, Lin H, Zhang J, She Y, Zhou X, Li X, Cui Y, Wang J, Rabah T, Shao Y. Extraction and identification of matrine-type alkaloids fromSophora moorcroftianausing double-templated molecularly imprinted polymers with HPLC-MS/MS. J Sep Sci 2018; 41:1691-1703. [DOI: 10.1002/jssc.201701133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Xingbin Ma
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou Gansu China
- Key Lab of Veterinary Pharmaceutics Development; Ministry of Agriculture; Key Lab of New Animal Drug Project; Gansu Province; Lanzhou Institute of Husbandry Science and Veterinary Pharmaceutical Sciences; Chinese Academy of Agricultural Sciences; Lanzhou China
- Institute of Veterinary and Animal husbandries; Tibet Academy of Agricultural and Animal Husbandry Sciences; Lhasa China
| | - Hongling Lin
- Zhanjiang Experimental Station of Chinese Academy of Tropical Sciences; Zhanjiang China
| | - Jiyu Zhang
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou Gansu China
- Key Lab of Veterinary Pharmaceutics Development; Ministry of Agriculture; Key Lab of New Animal Drug Project; Gansu Province; Lanzhou Institute of Husbandry Science and Veterinary Pharmaceutical Sciences; Chinese Academy of Agricultural Sciences; Lanzhou China
| | - Yongxin She
- Institute of Quality Standards and Testing Technology for Agri-Products; Chinese Academy of Agricultural Sciences; Beijing China
| | - Xuzheng Zhou
- Key Lab of Veterinary Pharmaceutics Development; Ministry of Agriculture; Key Lab of New Animal Drug Project; Gansu Province; Lanzhou Institute of Husbandry Science and Veterinary Pharmaceutical Sciences; Chinese Academy of Agricultural Sciences; Lanzhou China
| | - Xiaozhong Li
- Institute of Veterinary and Animal husbandries; Tibet Academy of Agricultural and Animal Husbandry Sciences; Lhasa China
| | - Yan Cui
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou Gansu China
| | - Jing Wang
- Institute of Quality Standards and Testing Technology for Agri-Products; Chinese Academy of Agricultural Sciences; Beijing China
| | - Tsdan Rabah
- Institute of Veterinary and Animal husbandries; Tibet Academy of Agricultural and Animal Husbandry Sciences; Lhasa China
| | - Yong Shao
- Institute of Quality Standards and Testing Technology for Agri-Products; Chinese Academy of Agricultural Sciences; Beijing China
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Zhao X, Li C, Wan S, Zhang T, Yan C, Shan S. Transcriptomic analysis and discovery of genes in the response of Arachis hypogaea to drought stress. Mol Biol Rep 2018; 45:119-131. [PMID: 29330721 DOI: 10.1007/s11033-018-4145-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 01/05/2018] [Indexed: 12/17/2022]
Abstract
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11. Pooled samples obtained at 6, 12, 18, 24, and 48 h were compared with control samples at 0 h. In total, 51,554 genes were found, including 49,289 known genes and 2265 unknown genes. We identified 224 differentially expressed transcription factors, 296,335 SNPs and 28,391 InDELs. In addition, we detected significant differences in the gene expression profiles of the treatment and control groups. After comparing the two groups, 4648 genes were identified. An in-depth analysis of the data revealed that a large number of genes were associated with drought stress, including transcription factors and genes involved in photosynthesis-antenna proteins, carbon metabolism and the citrate cycle. The results of this study provide insights into the diverse mechanisms that underlie the successful establishment of drought resistance in the peanut, thereby facilitating the identification of important genes in the peanut related to drought management. Transcriptome analysis based on RNA-Seq is a powerful approach for gene discovery and molecular marker development for this species.
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Affiliation(s)
- Xiaobo Zhao
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Chunjuan Li
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Shubo Wan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, People's Republic of China
| | - Tingting Zhang
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Caixia Yan
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Shihua Shan
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China.
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Gu L, Zhang ZY, Quan H, Li MJ, Zhao FY, Xu YJ, Liu J, Sai M, Zheng WL, Lan XZ. Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in rotenoid biosynthesis in the medicinal plant Mirabilis himalaica. Mol Genet Genomics 2017; 293:635-647. [PMID: 29285563 PMCID: PMC5948277 DOI: 10.1007/s00438-017-1409-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/14/2017] [Indexed: 02/04/2023]
Abstract
Mirabilis himalaica (Edgew.) Heimerl is among the most important genuine medicinal plants in Tibet. However, the biosynthesis mechanisms of the active compounds in this species are unclear, severely limiting its application. To clarify the molecular biosynthesis mechanism of the key representative active compounds, specifically rotenoid, which is of special medicinal value for M. himalaica, RNA sequencing and TOF-MS technologies were used to construct transcriptomic and metabolomic libraries from the roots, stems, and leaves of M. himalaica plants collected from their natural habitat. As a result, each of the transcriptomic libraries from the different tissues was sequenced, generating more than 10 Gb of clean data ultimately assembled into 147,142 unigenes. In the three tissues, metabolomic analysis identified 522 candidate compounds, of which 170 metabolites involved in 114 metabolic pathways were mapped to the KEGG. Of these genes, 61 encoding enzymes were identified to function at key steps of the pathways related to rotenoid biosynthesis, where 14 intermediate metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to rotenoid biosynthesis were synthesized in the roots, stems and leaves of M. himalaica, which suggested that the use of non-medicinal tissues to extract compounds was feasible. In addition, the CHS and CHI genes were found to play important roles in rotenoid biosynthesis, especially, since CHS might be an important rate-limiting enzyme. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of rotenoid in M. himalaica.
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Affiliation(s)
- Li Gu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.,Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhong-Yi Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Hong Quan
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Ming-Jie Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Fang-Yu Zhao
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Yuan-Jiang Xu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Jiang Liu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Man Sai
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Wei-Lie Zheng
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.
| | - Xiao-Zhong Lan
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.
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29
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Chen J, Li R, Xia Y, Bai G, Guo P, Wang Z, Zhang H, Siddique KHM. Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomic assemblies. PLoS One 2017; 12:e0184736. [PMID: 28902884 PMCID: PMC5597223 DOI: 10.1371/journal.pone.0184736] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs). From the unigenes, 8,165 EST-SSR loci were identified and 98.57% of them were 1-3 nucleotide repeats with 14.32%, 41.08% and 43.17% of mono-, di- and tri-nucleotide repeats, respectively. Fifty-eight types of motifs were identified with A/T, AG/CT, AT/AT, AC/GT, AAG/CTT and AGG/CCT the most abundant. The lengths of repeated nucleotide sequences in all SSR loci ranged from 12 to 60 bp, with most (88.51%) under 20 bp. Among 170 primer pairs were randomly selected from a total of 4,912 SSR primers we designed, 48 yielded unambiguously polymorphic bands with high reproducibility. Cluster analysis using 48 SSRs classified 34 flowering Chinese cabbage cultivars into three groups. A large number of EST-SSR markers identified in this study will facilitate marker-assisted selection in the breeding programs of flowering Chinese cabbage.
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Affiliation(s)
- Jingfang Chen
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture–Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- * E-mail:
| | - Zhiliang Wang
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, China
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth WA, Australia
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Li H, Zhang Y, Guo Q, Yao W. Molecular characterisation of a DREB gene from Sophora moorcroftiana, an endemic species of plateau. PROTOPLASMA 2017; 254:1735-1741. [PMID: 28050661 DOI: 10.1007/s00709-016-1065-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
Various plant species in the Qinghai-Tibet Plateau exposed to harsh conditions, such as low oxygen, drought, extremely low temperatures and salinity, have evolved both molecular and physiological adaptation strategies to deal with these multiple stresses. Sophora moorcroftiana (Benth.) Baker (Fabaceae) is a highly drought-resistant endemic Sophora shrub species in the Qinghai-Tibet Plateau. In our previous study, a drought-induced DREB transcription factor gene was identified and was designated as SmDREB1. SmDREB1-GFP fusion construct was introduced into Arabidopsis protoplast to characterise the function of SmDREB1 in drought resistance. The results showed that SmDREB1 targets the nucleus of Arabidopsis protoplast. Ectopic expression of SmDREB1 in model plant species Arabidopsis was performed. The transgenic lines showed increasing expressions of drought marker genes including AtDHN, AtLEA, AtPIP2 ;2, AtPIP2;3 and AtRD29, increasing activities of antioxidant enzymes and proline contents and increasing light-use efficiency under drought stress as compared with the wild-type plants; SmDREB1 transgenic lines are more resistant to drought than wild-type plants. Therefore, the SmDREB1 is a drought-resistant transcription factor gene of S. moorcroftiana and could be a candidate in genetic engineering to improve drought resistance of plateau plant species.
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Affiliation(s)
- Huie Li
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, 860000, People's Republic of China.
| | - Yanfu Zhang
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, 860000, People's Republic of China
| | - Qiqiang Guo
- College of Forestry, Guizhou University, Guiyang, 550025, People's Republic of China
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, 860000, People's Republic of China
| | - Weijie Yao
- Agricultural and Animal Husbandry College, Tibet University, Nyingchi, 860000, People's Republic of China
- Forest Inventory and Planning Institute of Tibet Autonomous Region, Lhasa, 850000, People's Republic of China
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Li H, Fu Y, Sun H, Zhang Y, Lan X. Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum. Sci Rep 2017; 7:74. [PMID: 28250432 PMCID: PMC5428373 DOI: 10.1038/s41598-017-00078-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/30/2017] [Indexed: 11/23/2022] Open
Abstract
Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum, as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.
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Affiliation(s)
- Huie Li
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yaru Fu
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Hao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yanfu Zhang
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Xiaozhong Lan
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China.
- TAAHC-SWU Medicinal Plants Joint Research and Development Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China.
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32
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Han BC, Wei W, Mi XC, Ma KP. De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress. PLoS One 2016; 11:e0166975. [PMID: 27930677 PMCID: PMC5145176 DOI: 10.1371/journal.pone.0166975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/07/2016] [Indexed: 12/01/2022] Open
Abstract
Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress. More than 320 million clean reads were generated and 72218 unique transcripts were obtained through de novo assembly. These unigenes were further annotated by blasting with different public databases and a total of 53300 unique transcripts were annotated. A total of 31586 simple sequence repeat (SSR) loci were presented. Through gene expression profiling analysis between drought treatment and control, 11038 genes were found to be significantly enriched in drought-stressed seedlings. Based on these differentially expressed genes (DEGs), Gene Ontology (GO) terms enrichment and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis indicated that drought stress caused a number of changes in the types of sugars, enzymes, secondary mechanisms, and light responses, and induced some potential physical protection mechanisms. In addition, the expression patterns of 18 transcripts induced by drought, as determined by quantitative real-time PCR, were consistent with their transcript abundance changes, as identified by RNA-seq. This transcriptome study provides a rapid method for understanding the response of S. superba seedlings to drought stress and provides a number of gene sequences available for further functional genomics studies.
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Affiliation(s)
- Bao-cai Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany Chinese Academy of Sciences (IBCAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany Chinese Academy of Sciences (IBCAS), Beijing, China
| | - Xiang-cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany Chinese Academy of Sciences (IBCAS), Beijing, China
| | - Ke-ping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany Chinese Academy of Sciences (IBCAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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RETRACTED ARTICLE: Cadmium permeates through calcium channels and activates transcriptomic complexity in wheat roots in response to cadmium stress. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0488-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wang Y, Dong C, Xue Z, Jin Q, Xu Y. De novo transcriptome sequencing and discovery of genes related to copper tolerance in Paeonia ostii. Gene 2016; 576:126-35. [PMID: 26435192 DOI: 10.1016/j.gene.2015.09.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/08/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022]
Abstract
Paeonia ostii, an important ornamental and medicinal plant, grows normally on copper (Cu) mines with widespread Cu contamination of soils, and it has the ability to lower Cu contents in the Cu-contaminated soils. However, very little molecular information concerned with Cu resistance of P. ostii is available. In this study, high-throughput de novo transcriptome sequencing was carried out for P. ostii with and without Cu treatment using Illumina HiSeq 2000 platform. A total of 77,704 All-unigenes were obtained with a mean length of 710 bp. Of these unigenes, 47,461 were annotated with public databases based on sequence similarities. Comparative transcript profiling allowed the discovery of 4324 differentially expressed genes (DEGs), with 2207 up-regulated and 2117 down-regulated unigenes in Cu-treated library as compared to the control counterpart. Based on these DEGs, Gene Ontology (GO) enrichment analysis indicated Cu stress-relevant terms, such as 'membrane' and 'antioxidant activity'. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis uncovered some important pathways, including 'biosynthesis of secondary metabolites' and 'metabolic pathways'. In addition, expression patterns of 12 selected DEGs derived from quantitative real-time polymerase chain reaction (qRT-PCR) were consistent with their transcript abundance changes obtained by transcriptomic analyses, suggesting that all the 12 genes were authentically involved in Cu tolerance in P. ostii. This is the first report to identify genes related to Cu stress responses in P. ostii, which could offer valuable information on the molecular mechanisms of Cu resistance, and provide a basis for further genomics research on this and related ornamental species for phytoremediation.
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Affiliation(s)
- Yanjie Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Chunlan Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zeyun Xue
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Qijiang Jin
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yingchun Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Liu SC, Jin JQ, Ma JQ, Yao MZ, Ma CL, Li CF, Ding ZT, Chen L. Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery. PLoS One 2016; 11:e0147306. [PMID: 26788738 PMCID: PMC4720391 DOI: 10.1371/journal.pone.0147306] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/01/2016] [Indexed: 11/18/2022] Open
Abstract
Tea plant (Camellia sinensis) is an economically important beverage crop. Drought stress (DS) seriously limits the growth and development of tea plant, thus affecting crop yield and quality. To elucidate the molecular mechanisms of tea plant responding to DS, we performed transcriptomic analysis of tea plant during the three stages [control (CK) and during DS, and recovery (RC) after DS] using RNA sequencing (RNA-Seq). Totally 378.08 million high-quality trimmed reads were obtained and assembled into 59,674 unigenes, which were extensively annotated. There were 5,955 differentially expressed genes (DEGs) among the three stages. Among them, 3,948 and 1,673 DEGs were up-regulated under DS and RC, respectively. RNA-Seq data were further confirmed by qRT-PCR analysis. Genes involved in abscisic acid (ABA), ethylene, and jasmonic acid biosynthesis and signaling were generally up-regulated under DS and down-regulated during RC. Tea plant potentially used an exchange pathway for biosynthesis of indole-3-acetic acid (IAA) and salicylic acid under DS. IAA signaling was possibly decreased under DS but increased after RC. Genes encoding enzymes involved in cytokinin synthesis were up-regulated under DS, but down-regulated during RC. It seemed probable that cytokinin signaling was slightly enhanced under DS. In total, 762 and 950 protein kinases belonging to 26 families were differentially expressed during DS and RC, respectively. Overall, 547 and 604 transcription factor (TF) genes belonging to 58 families were induced in the DS vs. CK and RC vs. DS libraries, respectively. Most members of the 12 TF families were up-regulated under DS. Under DS, genes related to starch synthesis were down-regulated, while those related to starch decomposition were up-regulated. Mannitol, trehalose and sucrose synthesis-related genes were up-regulated under DS. Proline was probably mainly biosynthesized from glutamate under DS and RC. The mechanism by which ABA regulated stomatal movement under DS and RC was partly clarified. These results document the global and novel responses of tea plant during DS and RC. These data will serve as a valuable resource for drought-tolerance research and will be useful for breeding drought-resistant tea cultivars.
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Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
- Guizhou Tea Research Institute, Guiyang, Guizhou, China
| | - Ji-Qiang Jin
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Ming-Zhe Yao
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Lei Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Fang Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Zhao-Tang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
- * E-mail: ;
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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Zhang L, Long Y, Fu C, Xiang J, Gan J, Wu G, Jia H, Yu L, Li M. Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:637. [PMID: 27242839 PMCID: PMC4861853 DOI: 10.3389/fpls.2016.00637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp. All the unigenes were annotated using Nr, SwissProt, COGs (Clusters of Orthologous Groups), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. A total of 35,327 differentially expressed genes (DEGs, P ≤ 0.05) between leaves and flowers were detected. Among them, a total of 6602 DEGs were assigned with important biological processes including "Metabolic process," "Response to stimulus," "Cellular process," and etc. KEGG analysis showed that three possible enzymes involved in the biosynthesis of chlorogenic acid were up-regulated in flowers. Furthermore, the TF-based regulation network in L. japonica identified three differentially expressed transcription factors between leaves and flowers, suggesting distinct regulatory roles in L. japonica. Taken together, this study has provided a global picture of differential gene expression patterns between leaves and flowers in L japonica, providing a useful genomic resource that can also be used for functional genomics research on L. japonica in the future.
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Affiliation(s)
- Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Gang Wu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Haibo Jia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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Wu Q, Chen Z, Sun W, Deng T, Chen M. De novo Sequencing of the Leaf Transcriptome Reveals Complex Light-Responsive Regulatory Networks in Camellia sinensis cv. Baijiguan. FRONTIERS IN PLANT SCIENCE 2016; 7:332. [PMID: 27047513 PMCID: PMC4801010 DOI: 10.3389/fpls.2016.00332] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 03/04/2016] [Indexed: 05/08/2023]
Abstract
Tea plants (Camellia sinensis L.) possess high genetic diversity that is important for breeding. One cultivar, Baijiguan, exhibits a yellow leaf phenotype, reduced chlorophyll (Chl) content, and aberrant chloroplast structures under high light intensity. In contrast, under low light intensity, the flush shoot from Baijiguan becomes green, the Chl content increases significantly, and the chloroplasts exhibit normal structures. To understand the underlying molecular mechanisms for these observations, we performed de novo transcriptome sequencing and digital gene expression (DGE) profiling using Illumina sequencing technology. De novo transcriptome assembly identified 88,788 unigenes, including 1652 transcription factors from 25 families. In total, 1993 and 2576 differentially expressed genes (DEGs) were identified in Baijiguan plants treated with 3 and 6 days of shade, respectively. Gene Ontology (GO) and pathway enrichment analyses indicated that the DEGs are predominantly involved in the ROS scavenging system, chloroplast development, photosynthetic pigment synthesis, secondary metabolism, and circadian systems. The light-responsive gene POR (protochlorophyllide oxidoreductase) and transcription factor HY5 were identified. Quantitative real-time PCR (qRT-PCR) analysis of 20 selected DEGs confirmed the RNA-sequencing (RNA-Seq) results. Overall, these findings suggest that high light intensity inhibits the expression of photosystem II 10-kDa protein (PsbR) in Baijiguan, thus affecting PSII stability, chloroplast development and chlorophyll biosynthesis.
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Affiliation(s)
- Quanjin Wu
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhidan Chen
- Department of Tea Science, Anxi College of Tea Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weijiang Sun
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Tea Science, Anxi College of Tea Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Weijiang Sun
| | - Tingting Deng
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Mingjie Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
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Deep Sequencing Reveals the Effect of MeJA on Scutellarin Biosynthesis in Erigeron breviscapus. PLoS One 2015; 10:e0143881. [PMID: 26656917 PMCID: PMC4687647 DOI: 10.1371/journal.pone.0143881] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/10/2015] [Indexed: 01/10/2023] Open
Abstract
Background Erigeron breviscapus, a well-known traditional Chinese medicinal herb, is broadly used in the treatment of cerebrovascular disease. Scutellarin, a kind of flavonoids, is considered as the material base of the pharmaceutical activities in E. breviscapus. The stable and high content of scutellarin is critical for the quality and efficiency of E. breviscapus in the clinical use. Therefore, understanding the molecular mechanism of scutellarin biosynthesis is crucial for metabolic engineering to increase the content of the active compound. However, there is virtually no study available yet concerning the genetic research of scutellarin biosynthesis in E. breviscapus. Results Using Illumina sequencing technology, we obtained over three billion bases of high-quality sequence data and conducted de novo assembly and annotation without prior genome information. A total of 182,527 unigenes (mean length = 738 bp) were found. 63,059 unigenes were functionally annotated with a cut-off E-value of 10−5. Next, a total of 238 (200 up-regulated and 38 down-regulated genes) and 513 (375 up-regulated and 138 down-regulated genes) differentially expressed genes were identified at different time points after methyl jasmonate (MeJA) treatment, which fell into categories of ‘metabolic process’ and ‘cellular process’ using GO database, suggesting that MeJA-induced activities of signal pathway in plant mainly led to re-programming of metabolism and cell activity. In addition, 13 predicted genes that might participate in the metabolism of flavonoids were found by two co-expression analyses in E. breviscapus. Conclusions Our study is the first to provide a transcriptome sequence resource for E. breviscapus plants after MeJA treatment and it reveals transcriptome re-programming upon elicitation. As the result, several putative unknown genes involved in the metabolism of flavonoids were predicted. These data provide a valuable resource for the genetic and genomic studies of special flavonoids metabolism and further metabolic engineering in E. breviscapus.
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Transcriptome analysis of genes involved in defence response in Polyporus umbellatus with Armillaria mellea infection. Sci Rep 2015; 5:16075. [PMID: 26526032 PMCID: PMC4630638 DOI: 10.1038/srep16075] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022] Open
Abstract
Polyporus umbellatus, a species symbiotic with Armillaria mellea and it also exhibits substantial defence response to Armillaria mellea infection. There are no genomics resources databases for understanding the molecular mechanism underlying the infection stress of P. umbellatus. Therefore, we performed a large-scale transcriptome sequencing of this fungus with A. mellea infection using Illumina sequencing technology. The assembly of the clean reads resulted in 120,576 transcripts, including 38,444 unigenes. Additionally, we performed a gene expression profiling analysis upon infection treatment. The results indicated significant differences in the gene expression profiles between the control and the infection group. In total, 10933 genes were identified between the two groups. Based on the differentially expressed genes, a Gene Ontology annotation analysis showed many defence-relevant categories. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways. Furthermore, the expression patterns of 13 putative genes that are involved in defence response resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The sequenced genes covered a considerable proportion of the P. umbellatus transcriptome, and the expression results may be useful to strengthen the knowledge on the defence response of this fungus defend against Armillaria mellea invasion.
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Mao Y, Zhang Y, Xu C, Qiu Y. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae. Mol Ecol Resour 2015; 16:228-41. [PMID: 25879377 DOI: 10.1111/1755-0998.12415] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 12/13/2022]
Abstract
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
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Affiliation(s)
- Yunrui Mao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Zhuang H, Fu Y, He W, Wang L, Wei Y. Selection of appropriate reference genes for quantitative real-time PCR in Oxytropis ochrocephala Bunge using transcriptome datasets under abiotic stress treatments. FRONTIERS IN PLANT SCIENCE 2015; 6:475. [PMID: 26175743 PMCID: PMC4484982 DOI: 10.3389/fpls.2015.00475] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/15/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Oxytropis ochrocephala Bunge, an indigenous locoweed species in China, poses great threats to livestock on grasslands. There is a need for further genetic study in the plants per se, for understanding the basis of its acclimation mechanism in various unfavorable environmental conditions and to implement effective control measures. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is the most commonly used method for gene expression analysis. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable reference genes is required. The aim of this study was to select the most stable reference genes for transcriptional analysis in O. ochrocephala. RESULTS We selected 12 candidate reference genes, 18S ribosomal RNA (18S RNA), actin2/7 (ACT7), β-actin (ACTB), actin101 (ACT101), actin11 (ACT11), β-tubulin (TUB), α-tubulin (TUA), glyceraldehyde-3-phosphate dehydrogenase-1 (GAPDH1), GAPDH2, metallothionein-like protein (MET), fructose-bisphosphate aldolase (FBA) and histone H3 (HIS), from the transcriptome datasets of O. ochrocephala and determined the suitability by analyzing their expression levels when exposed to a range of abiotic stress conditions. By employing software packages including geNorm, NormFinder and BestKeeper, HIS, ACT7, and ACT101 were assessed as the most suitable set for normalization in all samples. When normalized with the most stable reference genes, the expression patterns of the three target genes were in accordance with those in the transcriptome data, indicating that the reference genes selected in this study are suitable. CONCLUSIONS The study provided appropriate reference genes for accurate normalization in qRT-PCR analysis in O. ochrocephala and emphasized the importance of validating reference genes for gene expression analysis under specific experimental condition. The usage of inappropriate reference gene would cause misinterpretation.
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Affiliation(s)
| | | | | | | | - Yahui Wei
- *Correspondence: Yahui Wei, Key Laboratory of Resource Biology and Biotechnology in Western China, Department of Life Science, Northwest University, No. 229 Tai Bai North Road, Xi'an 710069, China
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