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Tataru D, Leon MD, Dutton S, Perez FM, Rendahl A, Ferris KG. Fluctuating selection in a Monkeyflower hybrid zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599085. [PMID: 38948721 PMCID: PMC11212913 DOI: 10.1101/2024.06.14.599085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus , we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus- like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus , specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species. Lay Summary Early evolutionary biologists understood hybridization, or interbreeding between species, as limiting to adaptation. While recent studies have shown that hybridization is important for adaptation, much remains to be learned about the role of natural selection in maintaining hybridization. We use a repeated transplant experiment in dry and wet years with two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus , and experimental hybrids, to identify how hybridization is maintained. By measuring environmental variables, we found that the hybrid zone is more similar to M. laciniatus's habitat than M. guttatus's in some years. We found that hybrids do equally well as parental species in hybrid zones. Additionally, the drought adapted species, M. laciniatus, performed better than M. guttatus in both parental habitats, and there was selection for more M. laciniatus- like traits in the hybrid habitat. These results suggest that hybridization might introduce drought-adapted traits and genes from M. laciniatus in a dry year. In a wet year, first generation hybrids performed better than advanced generation hybrids, possibly due to negative genetic interactions. In summary, we find that hybridization is beneficial and costly, and variation in environmental factors likely determines patterns of hybridization.
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Zare T, Paril JF, Barnett EM, Kaur P, Appels R, Ebert B, Roessner U, Fournier-Level A. Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds. THE PLANT GENOME 2024; 17:e20430. [PMID: 38339968 DOI: 10.1002/tpg2.20430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/28/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein-coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3-PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω-3 content in oil crops.
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Affiliation(s)
- Tannaz Zare
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jeff F Paril
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Emma M Barnett
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Rudi Appels
- School of Agriculture, Food and Ecosystem Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Berit Ebert
- School of Biology and Biotechnology, Ruhr-Universitat Bochum, Bochum, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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Omar SM, Zahran NN, Alhotan RA, Hussein EO, Galik B, Saleh AA. Evaluation of Salvia hispanica as a Therapeutic Agent against Sodium Arsenic-Induced Testicular Toxicity in a Male Rats Model. Life (Basel) 2024; 14:109. [PMID: 38255724 PMCID: PMC10817305 DOI: 10.3390/life14010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Chia seeds offer therapeutic properties that aid in the prevention of a variety of ailments, including cardiovascular disease, diabetes, obesity, and other risk factors. Arsenite, a common environmental chemical, has been identified as a reproductive toxin owing to its negative effects on male reproductive health. It has been shown to inhibit spermatogenesis and generate androgenic effects in men. The primary goal of this research was to look into the effect of Salvia hispanica on testicular toxicity caused by sodium arsenite in male rats. A set of 36 male albino rats was allocated to a negative control cohort. The individuals in this group were given a basic meal and orally given distilled water for a duration of 28 days. The other five groups were given a regular meal and received intra-peritoneal injections of sodium arsenite (NaAsO2) at a concentration of 4 mg/kg body weight that was diluted in a 0.9% NaCl solution. The injections were administered consecutively, with two doses given within a two-day period. Subsequently, the rats were categorized into several groups using the following classification: Group 2 consisted of a positive control cohort, in which the rats were given a typical baseline diet. Groups 3, 4, 5, and 6 were given a basic diet that included varying proportions of ground chia seeds, namely 5%, 10%, 15%, and 20% per 100 g of the diet. After the trial was completed, the rats were euthanized, and further biological examination was conducted. The measurements of the reproductive organs were documented and reported. The research assessed the following characteristics: sperm count, motility, progressive motility, and normal morphology. The research included examining serum sex hormones, namely luteinizing hormone (LH), follicle-stimulating hormone (FSH), and testosterone. An evaluation of the activity of antioxidant enzymes was performed in the tissue of the testicles. There were statistically significant improvements in the sperm parameters, serum sex hormone levels, and the activity of antioxidant enzymes, such as GPX, SOD, and CAT, in the therapy groups. The levels of malondialdehyde (MDA) exhibited a noteworthy decrease (p ≤ 0.05) when compared to the positive control group. Salvia hispanica seeds have demonstrated a significant level of effectiveness in reducing sodium arsenite-induced testicular toxicity, which leads to the conclusion. The flavonoid content and antioxidant properties of Salvia hispanica seeds may be to blame for the observed behavior. These indicated characteristics may have therapeutic significance in treating testicular harm induced by arsenite exposure.
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Affiliation(s)
- Sara Mahmoud Omar
- Nutrition and Food Science Department, Faculty of Home Economics, AL-Azhar University, Tanta 31732, Egypt;
| | - Nasser Nesim Zahran
- Department of Therapeutic Nutrition, Menoufia University Hospitals, Shebin El-Kom 11352, Egypt;
| | - Rashed A. Alhotan
- Department of Animal Production, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (R.A.A.); (E.O.H.)
| | - Elsayed Osman Hussein
- Department of Animal Production, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (R.A.A.); (E.O.H.)
| | - Branislav Galik
- Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Slovakia. Trieda A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Ahmed Ali Saleh
- Department of Poultry Production, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 333516, Egypt
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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [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: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Verbeecke V, Custódio L, Strobbe S, Van Der Straeten D. The role of orphan crops in the transition to nutritional quality-oriented crop improvement. Biotechnol Adv 2023; 68:108242. [PMID: 37640278 DOI: 10.1016/j.biotechadv.2023.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.
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Affiliation(s)
- Vincent Verbeecke
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Laura Custódio
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Alejo-Jacuinde G, Nájera-González HR, Chávez Montes RA, Gutierrez Reyes CD, Barragán-Rosillo AC, Perez Sanchez B, Mechref Y, López-Arredondo D, Yong-Villalobos L, Herrera-Estrella L. Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism. Commun Biol 2023; 6:820. [PMID: 37550387 PMCID: PMC10406817 DOI: 10.1038/s42003-023-05192-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
Chia (Salvia hispanica) is an emerging crop considered a functional food containing important substances with multiple potential applications. However, the molecular basis of some relevant chia traits, such as seed mucilage and polyphenol content, remains to be discovered. This study generates an improved chromosome-level reference of the chia genome, resolving some highly repetitive regions, describing methylation patterns, and refining genome annotation. Transcriptomic analysis shows that seeds exhibit a unique expression pattern compared to other organs and tissues. Thus, a metabolic and proteomic approach is implemented to study seed composition and seed-produced mucilage. The chia genome exhibits a significant expansion in mucilage synthesis genes (compared to Arabidopsis), and gene network analysis reveals potential regulators controlling seed mucilage production. Rosmarinic acid, a compound with enormous therapeutic potential, was classified as the most abundant polyphenol in seeds, and candidate genes for its complex pathway are described. Overall, this study provides important insights into the molecular basis for the unique characteristics of chia seeds.
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Affiliation(s)
- Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Ricardo A Chávez Montes
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Alfonso Carlos Barragán-Rosillo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Benjamin Perez Sanchez
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Lenin Yong-Villalobos
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
| | - Luis Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto., 36821, Mexico.
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Lee M, Wang L, Yue GH. Transcriptomic Responses of Salvia hispanica to the Infestation of Red Spider Mites ( Tetranychus neocaledonicus). Int J Mol Sci 2023; 24:12261. [PMID: 37569636 PMCID: PMC10418447 DOI: 10.3390/ijms241512261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Salvia hispanica (chia) is a highly nutritious food source and has gained popularity due to its high omega-3 fatty acid content. Red spider mites are a serious problem in the production of S. hispanica. However, no study has been conducted to analyze the defensive response to the infestation of red spider mites in S. hispanica. To elucidate the molecular mechanisms of the defensive response of S. hispanica to red spider mites, we performed a transcriptomic analysis of S. hispanica when infested by red spider mites. In the comparative assessment of leaf transcriptomes, a total of 1743 differentially expressed genes (DEGs) were identified between control and mite-infested S. hispanica. From these, 1208 (69%) transcripts were upregulated and 535 (31%) were downregulated. The DEGs included transcription factors, defense hormones, and secondary metabolites that were either suppressed or activated in response to spider mite herbivory. Gene Ontology (GO) enrichment analysis revealed that plant secondary metabolites, such as glucosinolates, and signaling pathways, including the jasmonic acid signaling pathway, may play an important role in the defense against red spider mites. This study provides novel insights into the defense response of S. hispanica to insect herbivory and could be a resource for the improvement of pest resistance in the chia.
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Affiliation(s)
- May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore (L.W.)
| | - Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore (L.W.)
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore (L.W.)
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
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8
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Health-promoting approaches of the use of chia seeds. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
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Oltehua-López O, Arteaga-Vázquez MA, Sosa V. Stem transcriptome screen for selection in wild and cultivated pitahaya ( Selenicereus undatus): an epiphytic cactus with edible fruit. PeerJ 2023; 11:e14581. [PMID: 36632141 PMCID: PMC9828283 DOI: 10.7717/peerj.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
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Affiliation(s)
| | | | - Victoria Sosa
- Biologia Evolutiva, Instituto de Ecologia AC, Xalapa, Veracruz, Mexico
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Salgado VDSCN, Zago L, Antunes AEC, Miyahira RF. Chia (Salvia hispanica L.) Seed Germination: a Brief Review. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2022; 77:485-494. [PMID: 36083408 DOI: 10.1007/s11130-022-01011-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Chia (Salvia hispanica L.) is a seed native to northern Mexico and southern Guatemala that has started to be consumed in recent years in other regions of the world owing to its nutritional and functional properties. Germination of chia seeds seems to be able to further improve these properties, and it has been the subject of some studies. In general, germination has proven to be a simple and inexpensive process capable of improving the content of phenolic compounds and the antioxidant capacity of foods, as well as reducing antinutritional factors that interfere with nutrient absorption. A particular characteristic of chia seeds is that they produce mucilage when they are hydrated. For this reason, the germination conditions of the seed need to be adapted. The nutritional guidelines of some countries, such as Brazil, Germany and Sweden, recommend that the diet of the population should be more plant-based, thus encouraging the consumption of foods with a high content of bioactive compounds and nutrients, e.g., germinated seeds. This review briefly explored the germination conditions of chia seeds as well as the changes in phytonutrient content and antinutritional factors after their germination process. The main information available in the literature is that germination of chia seeds can increase the contents of protein, fiber, and total phenolic compounds. As a conclusion, germination of chia seeds is favorable for increasing their health benefits and nutritional value. However, chia germination parameters should be adjusted and microbiological risks should be properly evaluated.
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Affiliation(s)
| | - Lilia Zago
- Institute of Nutrition, State University of Rio de Janeiro, Rua São Francisco Xavier, 524, 12° andar, sala 12006 D - Maracanã, Rio de Janeiro, RJ, CEP: 20550-013, Brazil
| | | | - Roberta Fontanive Miyahira
- Institute of Nutrition, State University of Rio de Janeiro, Rua São Francisco Xavier, 524, 12° andar, sala 12006 D - Maracanã, Rio de Janeiro, RJ, CEP: 20550-013, Brazil.
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11
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Wang L, Lee M, Sun F, Song Z, Yang Z, Yue GH. A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds. PLANT COMMUNICATIONS 2022; 3:100326. [PMID: 35605203 PMCID: PMC9284293 DOI: 10.1016/j.xplc.2022.100326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/14/2022] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
Chia (Salvia hispanica) is a functional food crop for humans. Although its seeds contain high omega-3 fatty acids, the seed yield of chia is still low. Genomic resources available for this plant are limited. We report the first high-quality chromosome-level genome sequence of chia. The assembled genome size was 347.6 Mb and covered 98.1% of the estimated genome size. A total of 31 069 protein-coding genes were predicted. The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size. Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds. The white seed coat color is determined by a single locus on chromosome 4. This study provides novel insights into the evolution of Salvia species and high omega-3 content, as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Fei Sun
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zhuojun Song
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zituo Yang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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Klimova A, Ruiz Mondragón KY, Molina Freaner F, Aguirre-Planter E, Eguiarte LE. Genomic Analyses of Wild and Cultivated Bacanora Agave (Agave angustifolia var. pacifica) Reveal Inbreeding, Few Signs of Cultivation History and Shallow Population Structure. PLANTS 2022; 11:plants11111426. [PMID: 35684199 PMCID: PMC9183054 DOI: 10.3390/plants11111426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 01/12/2023]
Abstract
Due to the recent increase in demand for agave-based beverages, many wild agave populations have experienced rapid decline and fragmentation, whereas cultivated plants are now managed at monocultural plantations, in some cases involving clonal propagation. We examined the relative effect of migration, genetic drift, natural selection and human activities on the genetic repertoire of Agave angustifolia var. pacifica, an agave used for bacanora (an alcoholic spirit similar to tequila) production in northwestern Mexico. We sampled 34 wild and cultivated sites and used over eleven thousand genome-wide SNPs. We found shallow genetic structure among wild samples, although we detected differentiation between coastal and inland sites. Surprisingly, no differentiation was found between cultivated and wild populations. Moreover, we detected moderate inbreeding (FIS ~ 0.13) and similar levels of genomic diversity in wild and cultivated agaves. Nevertheless, the cultivated plants had almost no private alleles and presented evidence of clonality. The overall low genetic structure in A. angustifolia var. pacifica is apparently the result of high dispersibility promoted by pollinators and the possibility of clonal reproduction. Incipient cultivation history and reliance on wild seeds and plants are probably responsible for the observed patterns of high genetic connectivity and considerable diversity in cultivated samples.
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Affiliation(s)
- Anastasia Klimova
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
- Correspondence: (A.K.); (L.E.E.); Tel.: +052-6121716113 (A.K.); +052-5556229006 (L.E.E.)
| | - Karen Y. Ruiz Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
| | - Francisco Molina Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Hermosillo, Sonora 83250, Mexico;
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
- Correspondence: (A.K.); (L.E.E.); Tel.: +052-6121716113 (A.K.); +052-5556229006 (L.E.E.)
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13
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Paredes-Lopez O. Meet the Editorial Board Member. CURRENT NUTRITION & FOOD SCIENCE 2022. [DOI: 10.2174/157340131803220318120529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Octavio Paredes-Lopez
- Department Biotechnology and Biochemistry Irapuato Unit
Centre for Research and Advanced Studies
Irapuato
Mexico
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14
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Motyka S, Koc K, Ekiert H, Blicharska E, Czarnek K, Szopa A. The Current State of Knowledge on Salvia hispanica and Salviae hispanicae semen (Chia Seeds). Molecules 2022; 27:molecules27041207. [PMID: 35208997 PMCID: PMC8877361 DOI: 10.3390/molecules27041207] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 01/11/2023] Open
Abstract
Chia seeds (Salviae hispanicae semen) are obtained from Salvia hispanica L. This raw material is distinguished by its rich chemical composition and valuable nutritional properties. It is currently referred to as “health food”. The purpose of the present work was to perform a literature review on S. hispanica and chia seeds, focusing on their chemical composition, biological properties, dietary importance, and medicinal uses. The valuable biological properties of chia seeds are related to their rich chemical composition, with particularly high content of polyunsaturated fatty acids, essential amino acids, polyphenols, as well as vitamins and bioelements. The available scientific literature indicates the cardioprotective, hypotensive, antidiabetic, and antiatherosclerotic effects of this raw material. In addition, studies based on in vitro assays and animal and human models have proven that chia seeds are characterized by neuroprotective, hepatoprotective, anti-inflammatory, and antioxidant properties. These properties indicate a valuable role of chia in the prevention of civilization diseases. Chia seeds are increasingly popular in functional food and cosmetic and pharmaceutical industries. That is attributed not only to their desirable chemical composition and biological activity but also to their high availability. Nevertheless, S. hispanica is also the object of specific biotechnological studies aimed at elaboration of micropropagation protocols of this plant species.
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Affiliation(s)
- Sara Motyka
- Chair and Department of Pharmaceutical Botany, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (S.M.); (K.K.); (H.E.)
| | - Katarzyna Koc
- Chair and Department of Pharmaceutical Botany, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (S.M.); (K.K.); (H.E.)
| | - Halina Ekiert
- Chair and Department of Pharmaceutical Botany, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (S.M.); (K.K.); (H.E.)
| | - Eliza Blicharska
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4a St., 20-093 Lublin, Poland
- Correspondence: (E.B.); (A.S.); Tel.: +48-814487182 (E.B.); +48-126205430 (A.S.)
| | - Katarzyna Czarnek
- Institute of Health Sciences, Faculty of Science and Health Sciences in Lublin, The John Paul II Catholic University of Lublin, ul. Konstantynów 1 H, 20-708 Lublin, Poland;
| | - Agnieszka Szopa
- Chair and Department of Pharmaceutical Botany, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (S.M.); (K.K.); (H.E.)
- Correspondence: (E.B.); (A.S.); Tel.: +48-814487182 (E.B.); +48-126205430 (A.S.)
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15
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Yue Y, Chen C, Zhong K, Wu Y, Gao H. Purification, Fermentation Optimization, and Antibacterial Activity of Pyrrole-2-carboxylic Acid Produced by an Endophytic Bacterium, Bacillus cereus ZBE, Isolated from Zanthoxylum bungeanum. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c04164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuxi Yue
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, P. R. China
| | - Chong Chen
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, P. R. China
| | - Kai Zhong
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, P. R. China
| | - Yanping Wu
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, P. R. China
| | - Hong Gao
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, P. R. China
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16
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Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int J Mol Sci 2021; 22:8093. [PMID: 34360856 PMCID: PMC8348985 DOI: 10.3390/ijms22158093] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Thattantavide Anju
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sushil Kumar
- Department of Botany, Govt. Degree College, Kishtwar 182204, Jammu and Kashmir, India;
| | - Sushil Satish Chhapekar
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Sajana Sreedharan
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sonam Singh
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Su Ryun Choi
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Yong Pyo Lim
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
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Gupta P, Geniza M, Naithani S, Phillips JL, Haq E, Jaiswal P. Chia ( Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:667678. [PMID: 34354718 PMCID: PMC8330693 DOI: 10.3389/fpls.2021.667678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy L. Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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18
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Klein A, Husselmann LHH, Williams A, Bell L, Cooper B, Ragar B, Tabb DL. Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies. PLANTS (BASEL, SWITZERLAND) 2021; 10:765. [PMID: 33919777 PMCID: PMC8070742 DOI: 10.3390/plants10040765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/24/2022]
Abstract
While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.
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Affiliation(s)
- Ashwil Klein
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Lizex H. H. Husselmann
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Achmat Williams
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
| | - Bret Cooper
- USDA Agricultural Research Service, Beltsville, MD 20705, USA;
| | - Brent Ragar
- Departments of Internal Medicine and Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02150, USA;
| | - David L. Tabb
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa
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19
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Molecular Cloning and Characterization of FAD6 Gene from Chia (Salvia hispanica L.). Biochem Genet 2021; 59:1295-1310. [PMID: 33797013 DOI: 10.1007/s10528-021-10063-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
Plastidial Δ12 fatty acid desaturase (FAD6) is a key enzyme for linoleic acid (LA) and α-linolenic acid (ALA) biosynthesis. Chia (Salvia hispanica L.) is a revived omega-3 plant source that is richest in ALA level. In this study, based on the RACE method, one full-length cDNA sequence encoding FAD6, named ShFAD6, was isolated from chia. There exist three alternative transcription start sites and five alternative poly(A) tailing sites in ShFAD6. The 5'UTR of ShFAD6 contains a purine-stretch of 44 bp. ShFAD6 has an ORF of 1335 bp encoding a 444 aa protein of 51.33 kDa. ShFAD6 contains a conserved Delta12-FADS-like domain together with three strong trans-membrane helices and three histidine motifs. There also exists a chloroplast transmit peptide in ShFAD6 N-terminal. Phylogenetic analyses validated its identity of dicot FAD6 protein and suggested some critical evolutionary features of plant FAD6 genes. Heterologous yeast expression confirmed the catalytic activity of ShFAD6. The qRT-PCR assay showed that ShFAD6 is mainly expressed in leaves, stems, flowers, buds and early-stage seeds, and also responded to various stresses and hormone treatments. Under Sclerotinia infection, qRT-PCR and fluorescence imaging illustrated the possible correlation of ShFAD6 expression and photosynthesis. This study provides insight for further function study of ShFAD6 in oil quality improvement in staple oilseed crops as well as stress response and adaptation in plants.
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Abdel-Salam EM, Faisal M, Alatar AA, Saquib Q, Alwathnani HA. Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process. PLANTS (BASEL, SWITZERLAND) 2020; 9:E63. [PMID: 31947725 PMCID: PMC7020419 DOI: 10.3390/plants9010063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/29/2019] [Accepted: 12/30/2019] [Indexed: 12/01/2022]
Abstract
The cultivated cucumber (Cucumis sativus L.) was reported to have been developed from a wild cucumber (Cucumis hystrix Chakrav.), nevertheless, these two organisms exhibit noteworthy differences. For example, the wild cucumber is known for its high resistance to different biotic and abiotic stresses. Moreover, the leaves and fruits of the wild cucumber have a bitter taste compared to the cultivated cucumber. These differences could be attributed mainly to the differences in gene expression levels. In the present investigation, we analyzed the RNA-sequencing data to show the differentially expressed genes (DEGs) between the wild and cultivated cucumbers. The identified DEGs were further utilized for Gene Ontology (GO) and pathway enrichment analysis and for identification of transcription factors and regulators. In the results, several enriched GO terms in the biological process, cellular component, and molecular functions categories were identified and various enriched pathways, especially the biosynthesis pathways of secondary products were recognized. Plant-specific transcription factor families were differentially expressed between the wild and cultivated cucumbers. The results obtained provide preliminary evidence for the transcriptional differences between the wild and cultivated cucumbers which developed during the domestication process as a result of natural and/or artificial selection, and they formulate the basis for future genetic research and improvement of the cultivated cucumber.
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Affiliation(s)
- Eslam M. Abdel-Salam
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Mohammad Faisal
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Abdulrahman A. Alatar
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Quaiser Saquib
- Zoology Department, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia;
| | - Hend A. Alwathnani
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
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