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Zhu Y, Liu Y, Wang W, Li H, Liu C, Dou L, Wei L, Cheng W, Bao M, Yi Q, He Y. Identification and characterization of CYC2-like genes related to floral symmetric development in Tagetes erecta (Asteraceae). Gene 2023; 889:147804. [PMID: 37716585 DOI: 10.1016/j.gene.2023.147804] [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: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Marigold (Tagetes erecta) is an annual herbaceous flower belonging to Asteraceae, whose capitulum is composed of bilateral symmetry ray florets on the outer periphery and radial symmetry disk florets on the inside. The flower symmetry evolution from radial symmetry to bilateral symmetry has changed the morphology, inflorescence architecture and function of florets among several lineages in Asteraceae. Several studies have identified that CYC2 genes in TCP transcription factor family are the key genes regulating the flower morphogenesis, such as corolla symmetry and stamen development. Here, seven TeCYC2 genes were cloned and phylogenetically grouped into the CYC2 branch of TCP transcription family. TeCYC2c and TeCYC2d were found to be expressed specifically in ray florets, TeCYC2b was strongly expressed in both ray and disk florets, TeCYC2g was significantly higher expressed in ray florets than in disk florets, while TeCYC2a, TeCYC2e1 and TeCYC2e2 were significantly expressed in disk florets, according to an examination of the expression profile. Among the ectopic expression lines of seven TeCYC2 genes in Arabidopsis thaliana, the flower symmetry of all transgenic lines was changed from radial symmetry to bilateral symmetry, and only the reproductive growth of TeCYC2c lines was affected. In TeCYC2c transgenic Arabidopsis, the pollen sac was difficult to crack, and the filaments were shorter than the pistils, resulting in a significant decrease in the seed setting rate. All TeCYC2 proteins were localized in the nucleus. Eight pairs of interactions between TeCYC2 proteins were validated by Y2H and BiFC assays, indicating the possibility of TeCYC2 proteins forming homodimers or heterodimers to improve functional specificity. Our findings verified the main regulatory role of TeCYC2c on the development of corollas and stamen in marigold, and analyzed the interaction network of the formation mechanism of floral symmetry in two florets, which provided more insights into the expansion of CYC2 genes in the evolution of Asteraceae inflorescence and contributed to elucidate the complex regulatory network, as well as the molecular breeding concerning flower form diversity in marigold.
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Affiliation(s)
- Yu Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuhan Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuicui Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Linlin Dou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ludan Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhan Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingping Yi
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen 448000, Hubei, China.
| | - Yanhong He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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Mahmoud A, Qi R, Chi X, Liao N, Malangisha GK, Ali A, Moustafa-Farag M, Yang J, Zhang M, Hu Z. Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon. Int J Mol Sci 2023; 25:65. [PMID: 38203237 PMCID: PMC10779233 DOI: 10.3390/ijms25010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.
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Affiliation(s)
- Ahmed Mahmoud
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Rui Qi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Xiaolu Chi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Guy Kateta Malangisha
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Abid Ali
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Mohamed Moustafa-Farag
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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Tyagi P, Singh D, Mathur S, Singh A, Ranjan R. Upcoming progress of transcriptomics studies on plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:1030890. [PMID: 36589087 PMCID: PMC9798009 DOI: 10.3389/fpls.2022.1030890] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.
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Hua YP, Chen JF, Zhou T, Zhang TY, Shen DD, Feng YN, Guan PF, Huang SM, Zhou ZF, Huang JY, Yue CP. Multiomics reveals an essential role of long-distance translocation in regulating plant cadmium resistance and grain accumulation in allohexaploid wheat (Triticum aestivum). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7516-7537. [PMID: 36063365 DOI: 10.1093/jxb/erac364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) is a highly toxic heavy metal that readily enters cereals, such as wheat, via the roots and is translocated to the shoots and grains, thereby posing high risks to human health. However, the vast and complex genome of allohexaploid wheat makes it challenging to understand Cd resistance and accumulation. In this study, a Cd-resistant cultivar of wheat, 'ZM1860', and a Cd-sensitive cultivar, 'ZM32', selected from a panel of 442 accessions, exhibited significantly different plant resistance and grain accumulation. We performed an integrated comparative analysis of the morpho-physiological traits, ionomic and phytohormone profiles, genomic variations, transcriptomic landscapes, and gene functionality in order to identify the mechanisms underlying these differences. Under Cd toxicity, 'ZM1860' outperformed 'ZM32', which showed more severe leaf chlorosis, poorer root architecture, higher accumulation of reactive oxygen species, and disordered phytohormone homeostasis. Ionomics showed that 'ZM32' had a higher root-to-shoot translocation coefficient of Cd and accumulated more Cd in the grains than 'ZM1860'. Whole-genome re-sequencing (WGS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport between the two genotypes. Combined ionomics, transcriptomics, and functional gene analysis identified the plasma membrane-localized heavy metal ATPase TaHMA2b-7A as a crucial Cd exporter regulating long-distance Cd translocation in wheat. WGS- and PCR-based analysis of sequence polymorphisms revealed a 25-bp InDel site in the promoter region of TaHMA2b-7A, and this was probably responsible for the differential expression. Our multiomics approach thus enabled the identification of a core transporter involved in long-distance Cd translocation in wheat, and it may provide an elite genetic resource for improving plant Cd resistance and reducing grain Cd accumulation in wheat and other cereal crops.
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Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Dan-Dan Shen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pan-Feng Guan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shao-Min Huang
- Institute of Plant Nutrient and Environmental Resources, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Zheng-Fu Zhou
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Wang F, Liu J, Zeng Q, Zhuoga D. Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep. Sci Rep 2022; 12:6597. [PMID: 35449433 PMCID: PMC9023463 DOI: 10.1038/s41598-022-08625-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/03/2022] [Indexed: 01/21/2023] Open
Abstract
Tibetan sheep have lived on the Qinghai-Tibetan Plateau for thousands of years and have good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism by which Tibetan sheep adapt to this extreme environment, especially the role of genetic regulation, is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in the adaptation to high-altitude hypoxia of Tibetan sheep, we analysed the expression profile of lncRNAs and mRNAs in the liver and lung tissues of sheep using comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and one Hu sheep population (low altitude). The results showed a total of 7848 differentially expressed (DE) lncRNA transcripts, and 22,971 DE mRNA transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR, and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA–mRNA and lncRNA–mRNA interaction networks further revealed transcripts potentially involved in adaptation to high-altitude hypoxia, and the hub genes DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, and TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1, were also identified as candidate genes associated with high-altitude hypoxia adaptation. In conclusion, a collection of novel expressed lncRNAs, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results are the first to identify the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provide insights into the genetic regulation mechanisms by which Tibetan sheep adapt to high-altitude hypoxic environments.
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Affiliation(s)
- Fan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.,China Agricultural Veterinary Biological Science and Technology Co., Ltd., Lanzhou, 730046, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qiaoying Zeng
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Deqing Zhuoga
- Institute of Livestock Research, Tibet Academy of Agriculture and Animal Science, Lhasa, 850000, China.
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Zhang C, Wei L, Yu X, Li H, Wang W, Wu S, Duan F, Bao M, Chan Z, He Y. Functional conservation and divergence of SEPALLATA-like genes in the development of two-type florets in marigold. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110938. [PMID: 34134845 DOI: 10.1016/j.plantsci.2021.110938] [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: 01/06/2021] [Revised: 03/06/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Marigold (Tagetes erecta), as one member of Asteraceae family, bears a typical capitulum with two morphologically distinct florets. The SEPALLATA genes are involved in regulating the floral meristem determinacy, organ identity, fruit maturation, seed formation, and plant architecture. Here, five SEP-like genes were cloned and identified from marigold. Sequence alignment and phylogenetic analysis demonstrated that TeSEP3-1, TeSEP3-2, and TeSEP3-3 proteins were grouped into SEP3 clade, and TeSEP1 and TeSEP4 proteins were clustered into SEP1/2/4 clade. Quantitative real-time PCR analysis revealed that TeSEP1 and TeSEP3-3 were broadly expressed in floral organs, and that TeSEP3-2 and TeSEP4 were mainly expressed in pappus and corollas, while TeSEP3-1 was mainly expressed in two inner whorls. Ectopic expression of TeSEP1, TeSEP3-2, TeSEP3-3, and TeSEP4 in arabidopsis and tobacco resulted in early flowering. However, overexpression of TeSEP3-1 in arabidopsis and tobacco caused no visible phenotypic changes. Notably, overexpression of TeSEP4 in tobacco decreased the number of petals and stamens. Overexpression of TeSEP1 in tobacco led to longer sepals and simpler inflorescence architecture. The comprehensive pairwise interaction analysis suggested that TeSEP proteins had a broad interaction with class A, C, D, E proteins to form dimers. The yeast three-hybrid analysis suggested that in ternary complexes, class B proteins interacted with TeSEP3 by forming heterodimer TePI-TeAP3-2. The regulatory network analysis of MADS-box genes in marigold further indicated that TeSEP proteins played a "glue" role in regulating floral organ development, implying functional conservation and divergence of MADS box genes in regulating two-type floret developments. This study provides an insight into the formation mechanism of floral organs of two-type florets, thus broadening our knowledge of the genetic basis of flower evolution.
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Affiliation(s)
- Chunling Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Ludan Wei
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Xiaomin Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Hang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Wenjing Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Shenzhong Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Feng Duan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Zhulong Chan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
| | - Yanhong He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China; Key Laboratory of Urban Agriculture in Central China (Pilot Run), Ministry of Agriculture, Wuhan, 430070, China.
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Wang J, Tang F, Gao C, Gao X, Xu B, Shi F. Comparative transcriptome between male fertile and male sterile alfalfa ( Medicago varia). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1487-1498. [PMID: 34366591 PMCID: PMC8295440 DOI: 10.1007/s12298-021-01026-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Male sterility is an important factor in improving crop quality and yield through heterosis breeding. In this study, we analyzed the transcriptomes of male fertile (MF) and male sterile (MS) alfalfa flower buds using the Illumina HiSeq™ 4000 platform. A total of 54.05 million clean reads were generated and assembled into 65,777 unigenes with an average length of 874 bp. The differentially expressed genes (DEGs) between the MF and MS flowers at three stages of pollen development were identified, and there were 3832, 5678 and 5925 DEGs respectively in stages 1, 2 and 3. GO and KEGG functional enrichment analysis revealed 12, 12, 6 and 12 key branch-point genes involved in circadian rhythm, transcription factors, pollen development and flavonoid biosynthesis. Our findings provide novel insights into the mechanism of male sterility in alfalfa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01026-x.
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Affiliation(s)
- Jia Wang
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
- Department of Pharmacy, Baotou Medical College, Baotou, 014040 Inner Mongolia China
| | - Fang Tang
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
| | - Cuiping Gao
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
| | - Xia Gao
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
| | - Bo Xu
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
| | - Fengling Shi
- Key Laboratory of Grassland Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, No.29 Erdos Street, Saihan District, Hohhot, 010011 Inner Mongolia China
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Tang N, Liu W, Zhang W, Tang D. Integrative analysis of transcriptomic and proteomic changes related to male sterility in Tagetes erecta. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2061-2074. [PMID: 33088050 PMCID: PMC7548268 DOI: 10.1007/s12298-020-00886-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/24/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Male sterile and male fertile two-type lines are important in heterosis utilization and breeding in Tagetes erecta, but the genes and pathways involved in male sterility are poorly understood. To explore these topics, transcriptome data (by RNA-seq) and proteome data (by iTRAQ) were gathered from flower buds of the male sterile line 'MS2-2' and male fertile line 'MF2-2' and integrated for a better understanding of the underlying molecular mechanisms of male sterility in T. erecta. The RNA-seq procedure generated 285,139,740 clean reads and 63359 unigenes and 6640 differentially expressed genes (DEGs) were identified, of which 4136 were downregulated and 2504 were upregulated in 'MS2-2'. DEGs related to flower development, pollen development, pollen wall assembly, endogenous hormones and transcription factors were identified. The iTRAQ analysis identified 3950 proteins in total; 789 were differentially expressed proteins (381 upregulated, 408 downregulated), which were mainly annotated to the Ribosome, Carbon metabolism and Biosynthesis of amino acids pathways. An association analysis revealed strong correlation (r Pearson = 0.6019) between the transcriptomic and proteomic data, and 256 and 34 proteins showed the same and opposite expression patterns with regard to their transcripts, respectively. Pathways such as photosynthesis, fatty acid biosynthesis and phenylpropanoid biosynthesis which influence tapetum and pollen development in male sterile plants, were significantly enriched at the transcript and protein levels. Most genes involved in these pathways were downregulated in 'MS2-2'. The low expression of these genes or functional loss of proteins could be associated with flower development, pollen development and related to changes in fertility in T. erecta. This study provided transcriptomic and proteomic information for T. erecta that could illuminate the mechanism of male sterility.
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Affiliation(s)
- Nan Tang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 People’s Republic of China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001 People’s Republic of China
| | - Wei Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471003 People’s Republic of China
| | - Wuhua Zhang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
| | - Daocheng Tang
- Plateau Flower Research Centre, Department of Agriculture and Husbandry, Qinghai University, Xining, 810016 People’s Republic of China
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Jiang M, Xu Y, Wang L, Liu J, Yu J, Chen H. High level of intraspecific divergence and low frequency of RNA editing in the chloroplast genome sequence of Tagetes erecta. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2948-2953. [PMID: 33458014 PMCID: PMC7782230 DOI: 10.1080/23802359.2020.1791001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tagetes erecta L. is an important commercial and medicinal plant. In this study, we reported the complete chloroplast genome sequence of T. erecta. The genome has a circular structure of 152,076 bp containing a large single-copy region (LSC) of 83,914 bp, a small copy region (SSC) of 18,064 bp, and two inverted repeats (IR) of 25,049 bp by each. It harbors 111 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 28 transfer RNA genes. A total of 41 microsatellite, 20 tandem, and 37 interspersed repeats were detected in the genome. The phylogenomic analysis shows that T. erecta is a single phylogenetic cluster. The complete chloroplast genome of T. erecta lays the foundation for the phylogenetic, evolutionary, and conservation studies of the genus Tagetes. Furthermore, the intergenic region of atpB-rbcL was variable among the species T. erecta. This suggests that this region might be a mutation hotspot and will be useful for phylogenetic study and the development of molecular markers. At last, we systematically identified the RNA editing sites in the chloroplast genome of T. erecta based on the transcriptome downloaded from the SRA database. This study identified the characteristics of the T. erecta chloroplast genome, SNPs, and RNA editing sites, which will facilitate species identification and phylogenetic analysis within T. erecta.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yicen Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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Transcriptome and digital gene expression analysis unravels the novel mechanism of early flowering in Angelica sinensis. Sci Rep 2019; 9:10035. [PMID: 31296928 PMCID: PMC6624268 DOI: 10.1038/s41598-019-46414-2] [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: 11/23/2017] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Angelica sinensis (Oliv.) Diels is a widely used medicinal plant mainly originated in Gansu, China. Angelica sinensis is greatly demanded in the clinical practice of Chinese medicine due to its broad pharmacological activities of hematopoietic and anti-inflammatory properties. But, the percentage of early flowering in Angelica sinensis arrives to 20%~30%, which severely affects its quality and quantity. Here, transcriptome profiling and digital gene expression analysis were applied to study the mechanism of early flowering in Angelica sinensis. A total of 49,183,534 clean reads were obtained and assembled into 68,262 unigenes, and 49,477 unigenes (72.5%) could be annotated to a minimum of one database in the Nr, Nt, Swiss-Pro, GO, COG and KEGG. Taking the above transcriptome data as a reference, digital gene expression result showed that 5,094 genes expression level were significant changed during early flowering. These annotated genes offered much information promoting that the biosynthesis of secondary metabolites pathway, the hormone signal transduction pathway, and the transcription regulation system may be closely related to the early flowering phenomenon of Angelica sinensis. Further expression patterns of key genes contribute to early flowering were analyzed using quantitative real-time PCR. The transcriptome result offered important gene expression information about early flowering in Angelica sinensis.
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Mudumbi JBN, Daso AP, Okonkwo OJ, Ntwampe SKO, Matsha TE, Mekuto L, Itoba-Tombo EF, Adetunji AT, Sibali LL. Propensity of Tagetes erecta L., a Medicinal Plant Commonly Used in Diabetes Management, to Accumulate Perfluoroalkyl Substances. TOXICS 2019; 7:toxics7010018. [PMID: 30934572 PMCID: PMC6468628 DOI: 10.3390/toxics7010018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/16/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023]
Abstract
It has been extensively demonstrated that plants accumulate organic substances emanating from various sources, including soil and water. This fact suggests the potentiality of contamination of certain vital bioresources, such as medicinal plants, by persistent contaminants, such as perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), and perfluorobutane sulfonate (PFBS). Hence, in this study, the propensity of Tagetes erecta L. (a commonly used medicinal plant) to accumulate PFOA, PFOS, and PFBS was determined using liquid chromatography/tandem mass spectrometry (LC⁻MS/MS-8030). From the results, PFOA, PFOS, and PFBS were detected in all the plant samples and concentration levels were found to be 94.83 ng/g, 5.03 ng/g, and 1.44 ng/g, respectively, with bioconcentration factor (BCF) ranges of 1.30 to 2.57, 13.67 to 72.33, and 0.16 to 0.31, respectively. Little evidence exists on the bioaccumulative susceptibility of medicinal plants to these persistent organic pollutants (POPs). These results suggest that these medicinal plants (in particular, Tagetes erecta L., used for the management of diabetes) are also potential conduits of PFOA, PFOS, and PFBS into humans.
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Affiliation(s)
- John Baptist Nzukizi Mudumbi
- Bioresource Engineering Research Group (BioERG), Department of Biotechnology and Consumer Sciences, Cape Peninsula University of Technology, PO Box 652, Cape Town 8000, Western Cape, South Africa.
| | - Adegbenro Peter Daso
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Pretoria 0083, South Africa.
| | - Okechukwu Jonathan Okonkwo
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Pretoria 0083, South Africa.
| | - Seteno Karabo Obed Ntwampe
- Bioresource Engineering Research Group (BioERG), Department of Biotechnology and Consumer Sciences, Cape Peninsula University of Technology, PO Box 652, Cape Town 8000, Western Cape, South Africa.
| | - Tandi E Matsha
- Department of Bio-Medical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, Western Cape, South Africa.
| | - Lukhanyo Mekuto
- Department of Chemical Engineering, University of Johannesburg, PO Box 17011, Johannesburg 2028, Gauteng, South Africa.
| | - Elie Fereche Itoba-Tombo
- Bioresource Engineering Research Group (BioERG), Department of Biotechnology and Consumer Sciences, Cape Peninsula University of Technology, PO Box 652, Cape Town 8000, Western Cape, South Africa.
| | - Adewole T Adetunji
- Department of Agriculture, Cape Peninsula University of Technology, Wellington Campus, Wellington 7655, Western Cape, South Africa.
| | - Linda L Sibali
- Research Management Unit, Faculty of Applied Sciences, Cape Peninsula University of Technology, PO Box 652, Cape Town 8000, Western Cape, South Africa.
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The transcriptome analyses of Tagetes erecta provides novel insights into secondary metabolite biosynthesis during flower development. Gene 2018; 660:18-27. [PMID: 29574190 DOI: 10.1016/j.gene.2018.03.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 03/13/2018] [Accepted: 03/16/2018] [Indexed: 11/21/2022]
Abstract
Genomic and transcriptomic sequences of Tagetes erecta are very limited in public databases, despite its nutritional and economical value. In this study, nine cDNA libraries were constructed from leaves, immature and mature flowers and sequenced using Illumina Hiseq 2000. Over 45.66 Gb nucleotides were generated and a total of 72,499 unigenes were assembled, 34,892 (48.13%) of which were annotated in NR, Swiss-prot, COG, GO, KOG, KEGG and Pfam. 11,721 differentially expressed genes were identified in leaves, immature flowers and mature flowers. The differentially expressed genes between immature flowers and mature flowers were mainly involved in photosynthesis and secondary metabolite biosynthesis. Additionally, the catalysis-related unigenes and their expression involved in carotenoids biosynthesis were determined. Using our newly identified reference genes as internal control, the expression profiles of carotenoids biosynthetic genes were verified by real-time qRT-PCR, and four of the unigenes were cloned for full length sequences confirmation. Furthermore, gene expansions occurred among the catalytic gene families in carotenoids biosynthesis pathway, which might explain the high pigment content in T. erecta.
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Yang W, Lou X, Li J, Pu M, Mirbahar AA, Liu D, Sun J, Zhan K, He L, Zhang A. Cloning and Functional Analysis of MADS-box Genes, TaAG-A and TaAG-B, from a Wheat K-type Cytoplasmic Male Sterile Line. FRONTIERS IN PLANT SCIENCE 2017; 8:1081. [PMID: 28676817 PMCID: PMC5476771 DOI: 10.3389/fpls.2017.01081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/06/2017] [Indexed: 05/30/2023]
Abstract
Wheat (Triticum aestivum L.) is a major crop worldwide. The utilization of heterosis is a promising approach to improve the yield and quality of wheat. Although there have been many studies on wheat cytoplasmic male sterility, its mechanism remains unclear. In this study, we identified two MADS-box genes from a wheat K-type cytoplasmic male sterile (CMS) line using homology-based cloning. These genes were localized on wheat chromosomes 3A and 3B and named TaAG-A and TaAG-B, respectively. Analysis of TaAG-A and TaAG-B expression patterns in leaves, spikes, roots, and stems of Chinese Spring wheat determined using quantitative RT-PCR revealed different expression levels in different tissues. TaAG-A had relatively high expression levels in leaves and spikes, but low levels in roots, while TaAG-B had relatively high expression levels in spikes and lower expression in roots, stems, and leaves. Both genes showed downregulation during the mononucleate to trinucleate stages of pollen development in the maintainer line. In contrast, upregulation of TaAG-B was observed in the CMS line. The transcript levels of the two genes were clearly higher in the CMS line compared to the maintainer line at the trinucleate stage. Overexpression of TaAG-A and TaAG-B in Arabidopsis resulted in phenotypes with earlier reproductive development, premature mortality, and abnormal buds, stamens, and stigmas. Overexpression of TaAG-A and TaAG-B gives rise to mutants with many deformities. Silencing TaAG-A and TaAG-B in a fertile wheat line using the virus-induced gene silencing (VIGS) method resulted in plants with green and yellow striped leaves, emaciated spikes, and decreased selfing seed set rates. These results demonstrate that TaAG-A and TaAG-B may play a role in male sterility in the wheat CMS line.
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Affiliation(s)
- Wenlong Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Xueyuan Lou
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Juan Li
- College of Life Sciences, Hunan Agricultural UniversityChangsha, China
| | - Mingyu Pu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Ameer A. Mirbahar
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- Department of Botany, Shah Abdul Latif UniversityKhairpur, Pakistan
| | - Dongcheng Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Jiazhu Sun
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Kehui Zhan
- The Collaborative Center for Grain Crops in Henan, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Lixiong He
- College of Life Sciences, Hunan Agricultural UniversityChangsha, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- The Collaborative Center for Grain Crops in Henan, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
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Ai Y, Zhang C, Sun Y, Wang W, He Y, Bao M. Characterization and Functional Analysis of Five MADS-Box B Class Genes Related to Floral Organ Identification in Tagetes erecta. PLoS One 2017; 12:e0169777. [PMID: 28081202 PMCID: PMC5231280 DOI: 10.1371/journal.pone.0169777] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/21/2016] [Indexed: 11/23/2022] Open
Abstract
According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs. Yeast hybrid experiments of the B class proteins showed that TePI protein could form a homodimer and heterodimers with all the other four B class proteins TeAP3-1, TeAP3-2, TeTM6-1 and TeTM6-2. No homodimer or interaction was observed between the euAP3 and TM6 clade members. Over-expression of five B class genes of T. erecta in Nicotiana rotundifolia showed that only the transgenic plants of 35S::TePI showed altered floral morphology compared with the non-transgenic line. This study could contribute to the understanding of the function of B class genes in flower development of T. erecta, and provide a theoretical basis for further research to change floral organ structures and create new materials for plant breeding.
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Affiliation(s)
- Ye Ai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou, Fujian, China
| | - Chunling Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yalin Sun
- Institute of Vegetable Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weining Wang
- Gulf Coast Research and Education Center, Department of Environmental Horticulture, University of Florida, Wimauma, Florida, United States of America
| | - Yanhong He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
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Yang M, Zhu L, Li L, Li J, Xu L, Feng J, Liu Y. Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus ( Nelumbo nucifera). FRONTIERS IN PLANT SCIENCE 2017; 8:80. [PMID: 28197160 PMCID: PMC5281601 DOI: 10.3389/fpls.2017.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/13/2017] [Indexed: 05/21/2023]
Abstract
The predominant alkaloids in lotus leaves are aporphine alkaloids. These are the most important active components and have many pharmacological properties, but little is known about their biosynthesis. We used digital gene expression (DGE) technology to identify differentially-expressed genes (DEGs) between two lotus cultivars with different alkaloid contents at four leaf development stages. We also predicted potential genes involved in aporphine alkaloid biosynthesis by weighted gene co-expression network analysis (WGCNA). Approximately 335 billion nucleotides were generated; and 94% of which were aligned against the reference genome. Of 22 thousand expressed genes, 19,000 were differentially expressed between the two cultivars at the four stages. Gene Ontology (GO) enrichment analysis revealed that catalytic activity and oxidoreductase activity were enriched significantly in most pairwise comparisons. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, dozens of DEGs were assigned to the categories of biosynthesis of secondary metabolites, isoquinoline alkaloid biosynthesis, and flavonoid biosynthesis. The genes encoding norcoclaurine synthase (NCS), norcoclaurine 6-O-methyltransferase (6OMT), coclaurine N-methyltransferase (CNMT), N-methylcoclaurine 3'-hydroxylase (NMCH), and 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (4'OMT) in the common pathways of benzylisoquinoline alkaloid biosynthesis and the ones encoding corytuberine synthase (CTS) in aporphine alkaloid biosynthetic pathway, which have been characterized in other plants, were identified in lotus. These genes had positive effects on alkaloid content, albeit with phenotypic lag. The WGCNA of DEGs revealed that one network module was associated with the dynamic change of alkaloid content. Eleven genes encoding proteins with methyltransferase, oxidoreductase and CYP450 activities were identified. These were surmised to be genes involved in aporphine alkaloid biosynthesis. This transcriptomic database provides new directions for future studies on clarifying the aporphine alkaloid pathway.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Lingping Zhu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- Department of Agricultural Sciences, Viikki Plant Science Center, University of HelsinkiHelsinki, Finland
| | - Ling Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Juanjuan Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Liming Xu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Ji Feng
- Tobacco Research Institute of Hubei ProvinceWuhan, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- *Correspondence: Yanling Liu
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Khosa JS, Lee R, Bräuning S, Lord J, Pither-Joyce M, McCallum J, Macknight RC. Doubled Haploid 'CUDH2107' as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility. PLoS One 2016; 11:e0166568. [PMID: 27861615 PMCID: PMC5115759 DOI: 10.1371/journal.pone.0166568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/31/2016] [Indexed: 11/21/2022] Open
Abstract
Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line ‘CUDH2107’ by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits.
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Affiliation(s)
| | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sophia Bräuning
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Department of Botany, University of Otago, Dunedin, New Zealand
| | - Janice Lord
- Department of Botany, University of Otago, Dunedin, New Zealand
| | | | - John McCallum
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
- * E-mail:
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