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Hu X, Wang M, Cai F, Liu L, Cheng Z, Zhao J, Zhang Q, Long C. A comprehensive review of medicinal Toxicodendron (Anacardiaceae): Botany, traditional uses, phytochemistry and pharmacology. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116829. [PMID: 37429501 DOI: 10.1016/j.jep.2023.116829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/03/2023] [Accepted: 06/20/2023] [Indexed: 07/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Comprising of about 30 species, the genus Toxicodendron (Anacardiaceae) are mainly distributed in East Asia and North America. Among them, 13 species have been traditionally used as folk medicines in Asia and other parts of the world to treat blood diseases, abnormal bleeding, skin diseases, gastrointestinal diseases, liver diseases, bone injury, lung diseases, neurological diseases, cardiovascular diseases, tonic, cancer, eye diseases, menstrual irregularities, inflammation, rheumatism, diabetes mellitus, rattlesnake bite, internal parasites, contraceptive, vomiting and diarrhea. AIM OF THE STUDY To date, no comprehensive review on Toxicodendron has been published and the scientific basis of the traditional medicinal benefits of Toxicodendron have been less reported. Therefore, this review aims to provide a reference for further research and development on medicinal purpose of Toxicodendron by summarizing the works (from 1980 to 2023), and focusing on its botany, traditional uses, phytochemistry and pharmacology. MATERIALS AND METHODS The names of the species were from The Plant List Database (http://www.theplantlist.org), World Flora Online (http://www.worldfloraonline.org), Catalogue of Life Database (https://www.catalogueoflife.org/) and Plants for A Future Database (https://pfaf.org/user/Default.aspx). And the search terms "Toxicodendron" and "the names of 31 species and their synonyms" were used to search for information from electronic databases such as Web of Science, Scopus, Google Scholar, Science Direct, PubMed, Baidu Scholar, Springer, and Wiley Online Library. Moreover, PhD and MSc dissertations were also used to support this work. RESULTS These species on Toxicodendron are widely used in folkloric medicine and modern pharmacological activities. So far, approximately 238 compounds, mainly phenolic acids and their derivatives, urushiols, flavonoids and terpenoids, are extracted and isolated from Toxicodendron plants, commonly, T. trichocarpum, T. vernicifluum, T. succedaneum, and T. radicans. Among them, phenolic acids and flavonoids are the main compound classes that show pharmacological activities in Toxicodendron plants both in vitro and in vivo. Furthermore, the extracts and single compounds of these species show a wide range of activities, such as antioxidant, antibacterial, anti-inflammatory, anti-tumor, liver protection, fat reduction, nerve protection, and treatment of blood diseases. CONCLUSIONS Selected species of Toxicodendron have been used as herbal medicines in the Southeast Asian for a long time. Furthermore, some bioactive constituents have been identified from them, so plants in this genus may be potential new drugs. The existing research on Toxicodendron has been reviewed, and the phytochemistry and pharmacology provide theoretical basis for some of the traditional medicinal uses. Therefore, in this review, the traditional medicinal, phytochemical and modern pharmacology of Toxicodendron plants are summarized to help future researchers to find new drug leads or to get a better understanding of structure-activity relationships.
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Affiliation(s)
- Xian Hu
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Ethnology and Sociology, Minzu University of China, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Miaomiao Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Fei Cai
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Liya Liu
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Zhuo Cheng
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Jiaqi Zhao
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Ethnology and Sociology, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Qing Zhang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
| | - Chunlin Long
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China; Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; Institute of National Security Studies, Minzu University of China, Beijing, 100081, China.
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Huang R, Snedden WA, diCenzo GC. Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PLANT DIRECT 2022; 6:e408. [PMID: 35774624 PMCID: PMC9219011 DOI: 10.1002/pld3.408] [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: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 05/10/2023]
Abstract
Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ∼2-fold more abundant in M. sativa than in M. officinalis, and ∼27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
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Affiliation(s)
- Rui Huang
- Department of BiologyQueen's UniversityKingstonOntarioCanada
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Marx HE, Jorgensen SA, Wisely E, Li Z, Dlugosch KM, Barker MS. Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11409. [PMID: 33680580 PMCID: PMC7910807 DOI: 10.1002/aps3.11409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities. METHODS We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. RESULTS Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. DISCUSSION We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.
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Affiliation(s)
- Hannah E. Marx
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109‐1048USA
| | - Stacy A. Jorgensen
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Eldridge Wisely
- Genetics Graduate Interdisciplinary ProgramUniversity of ArizonaTucsonArizona85721USA
| | - Zheng Li
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
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Adverse Skin Reactions to Plants and Plant Products. Contact Dermatitis 2021. [DOI: 10.1007/978-3-030-36335-2_88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Lott AA, Freed CP, Dickinson CC, Whitehead SR, Collakova E, Jelesko JG. Poison ivy hairy root cultures enable a stable transformation system suitable for detailed investigation of urushiol metabolism. PLANT DIRECT 2020; 4:e00243. [PMID: 32783021 PMCID: PMC7411346 DOI: 10.1002/pld3.243] [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] [Received: 12/10/2019] [Revised: 06/06/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Poison ivy (Toxicodendron radicans) is best known for causing exasperating allergenic delayed-contact dermatitis symptoms that last for weeks on persons who have contacted the plant. Urushiols are alkylcatechols produced by poison ivy responsible for causing this dermatitis. While urushiol chemical structures are well known, the metabolic intermediates and genes responsible for their biosynthesis have not been experimentally validated. A molecular genetic characterization of urushiol biosynthesis in poison ivy will require stable genetic transformation and subsequent regeneration of organs that retain the capacity synthesize urushiol. To this end, Agrobacterium rhizogenes was used to generate hormone-independent poison ivy hairy root cultures. Optimal conditions for hairy root formation were skotomorphic poison ivy hypocotyls prick-inoculated with A. rhizogenes, and preferential propagation of cultures with an atypical clumpy hairy root growth habit. The origin of the poison ivy accession used for A. rhizogenes prick-inoculation did not affect the initial formation of calli/hairy root primordia, but rather significantly influenced the establishment of long-term hormone-independent hairy root growth. A. rhizogenes harboring a recombinant T-DNA binary plasmid with an intron-containing Firefly Luciferase gene produced stable transgenic hairy root lines expressing luciferase activity at high frequency. Poison ivy hairy root lines produced significantly lower steady-state urushiol levels relative to wild-type roots, but higher urushiol levels than a poison ivy undifferentiated callus line with undetectable urushiol levels, suggesting that urushiol biosynthesis requires intact poison ivy organs. The lower urushiol levels in poison ivy hairy root lines facilitated the first identification of anacardic acid metabolites initially in hairy roots, and subsequently in wild-type roots as well. This study establishes a transformation hairy root regeneration protocol for poison ivy that can serve as a platform for future reverse-genetic studies of urushiol biosynthesis in poison ivy hairy roots.
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Affiliation(s)
- Aneirin A. Lott
- Plant Molecular and Cellular BiologyUniversity of FloridaGainesvilleFLUSA
- School of Plant and Environmental ScienceVirginia TechBlacksburgVAUSA
| | | | | | | | - Eva Collakova
- School of Plant and Environmental ScienceVirginia TechBlacksburgVAUSA
| | - John G. Jelesko
- School of Plant and Environmental ScienceVirginia TechBlacksburgVAUSA
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Wang P, Luo Y, Huang J, Gao S, Zhu G, Dang Z, Gai J, Yang M, Zhu M, Zhang H, Ye X, Gao A, Tan X, Wang S, Wu S, Cahoon EB, Bai B, Zhao Z, Li Q, Wei J, Chen H, Luo R, Gong D, Tang K, Zhang B, Ni Z, Huang G, Hu S, Chen Y. The genome evolution and domestication of tropical fruit mango. Genome Biol 2020; 21:60. [PMID: 32143734 PMCID: PMC7059373 DOI: 10.1186/s13059-020-01959-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Background Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.
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Affiliation(s)
- Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jianfeng Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guopeng Zhu
- School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Jiangtao Gai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Huangkai Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Aiping Gao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sen Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shuangyang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Beibei Bai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.,School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China
| | - Zhichang Zhao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Qian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Junya Wei
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Huarui Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Ruixiong Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Deyong Gong
- Guizhou Subtropical Crops Research Institute, Xingyi, Qianxinan, Guzhou, 562400, China
| | - Kexuan Tang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bing Zhang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhangguang Ni
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, 678005, Yunnan, China
| | - Guodi Huang
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, Guangxi, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China. .,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China. .,School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China.
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Lovell C, Paulsen E, Lepoittevin JP. Adverse Skin Reactions to Plants and Plant Products. Contact Dermatitis 2020. [DOI: 10.1007/978-3-319-72451-5_88-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Lovell C, Paulsen E, Lepoittevin JP. Plants and Plant Products. Contact Dermatitis 2020. [DOI: 10.1007/978-3-319-72451-5_88-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado ( Persea americana). Int J Mol Sci 2019; 20:ijms20174117. [PMID: 31450745 PMCID: PMC6747375 DOI: 10.3390/ijms20174117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/17/2022] Open
Abstract
Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.
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Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers. FORESTS 2019. [DOI: 10.3390/f10050411] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.
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Palumbo F, Vannozzi A, Vitulo N, Lucchin M, Barcaccia G. The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants. Sci Rep 2018; 8:10459. [PMID: 29993007 PMCID: PMC6041299 DOI: 10.1038/s41598-018-28775-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 47,775 were annotated using BLASTX analysis performed against the NR protein database subset with 11,853 transcripts representing putative full-length CDS. Bioinformatic analyses revealed 1,011 transcripts encoding transcription factors, mainly from the BHLH, MYB-related, C2H2, MYB, and ERF families, and 6,411 EST-SSR regions. Single-nucleotide variants of SNPs and indels were identified among the 8 samples at a frequency of 0.5 and 0.04 variants per Kb, respectively. Finally, the assembled transcripts were screened to identify genes related to the biosynthesis of t-anethole, a compound well-known for its nutraceutical and medical properties. For each of the 11 genes encoding structural enzymes in the t-anethole biosynthetic pathway, we identified at least one transcript showing a significant match. Overall, our work represents a treasure trove of information exploitable both for marker-assisted breeding and for in-depth studies on thousands of genes, including those involved in t-anethole biosynthesis.
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Affiliation(s)
- Fabio Palumbo
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy.
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