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Huang X, Hu X, Liu Q, Xie Z, Tan S, Qin X, Chen T, Wu W, Saud S, Nawaz T, El-Kahtany K, Fahad S, Yi K. Full-length agave transcriptome reveals candidate glycosyltransferase genes involved in hemicellulose biosynthesis. Int J Biol Macromol 2024; 274:133508. [PMID: 38944067 DOI: 10.1016/j.ijbiomac.2024.133508] [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: 01/27/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Agave species are typical crassulacean acid metabolism (CAM) plants commonly cultivated to produce beverages, fibers, and medicines. To date, few studies have examined hemicellulose biosynthesis in Agave H11648, which is the primary cultivar used for fiber production. We conducted PacBio sequencing to obtain full-length transcriptome of five agave tissues: leaves, shoots, roots, flowers, and fruits. A total of 41,807 genes were generated, with a mean length of 2394 bp and an annotation rate of 97.12 % using public databases. We identified 42 glycosyltransferase genes related to hemicellulose biosynthesis, including mixed-linkage glucan (1), glucomannan (5), xyloglucan (16), and xylan (20). Their expression patterns were examined during leaf development and fungal infection, together with hemicellulose content. The results revealed four candidate glycosyltransferase genes involved in xyloglucan and xylan biosynthesis, including glucan synthase (CSLC), xylosyl transferase (XXT), xylan glucuronyltransferase (GUX), and xylan α-1,3-arabinosyltransferase (XAT). These genes can be potential targets for manipulating xyloglucan and xylan traits in agaves, and can also be used as candidate enzymatic tools for enzyme engineering. We have provided the first full-length transcriptome of agave, which will be a useful resource for gene identification and characterization in agave species. We also elucidated the hemicellulose biosynthesis machinery, which will benefit future studies on hemicellulose traits in agave.
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Affiliation(s)
- Xing Huang
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoli Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Zhouli Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shibei Tan
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Weihuai Wu
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shah Saud
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Taufiq Nawaz
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Khaled El-Kahtany
- Geology and Geophysics Department, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Shah Fahad
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakh-tunkhwa, 23200, Pakistan.
| | - Kexian Yi
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China; Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China.
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Wang X, Huang X, Chen L, Xie Z, Tan S, Qin X, Chen T, Huang Y, Xi J, Chen H, Yi K. Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave. PLANTS (BASEL, SWITZERLAND) 2023; 12:2020. [PMID: 37653937 PMCID: PMC10222593 DOI: 10.3390/plants12102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/06/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.
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Affiliation(s)
- Xuxia Wang
- Urban Construction College, Wuchang Shouyi University, Wuhan 430064, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lisha Chen
- Quality Supervision, Inspection and Testing Center of Sisal and Products, Ministry of Agriculture and Rural Affairs, Zhanjiang 524022, China
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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Ramos LC, Báez M, Fuchs J, Houben A, Carvalho R, Pedrosa-Harand A. Differential Repeat Accumulation in the Bimodal Karyotype of Agave L. Genes (Basel) 2023; 14:491. [PMID: 36833420 PMCID: PMC9956584 DOI: 10.3390/genes14020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The genus Agave presents a bimodal karyotype with x = 30 (5L, large, +25S, small chromosomes). Bimodality within this genus is generally attributed to allopolyploidy in the ancestral form of Agavoideae. However, alternative mechanisms, such as the preferential accumulation of repetitive elements at the macrochromosomes, could also be important. Aiming to understand the role of repetitive DNA within the bimodal karyotype of Agave, genomic DNA from the commercial hybrid 11648 (2n = 2x = 60, 6.31 Gbp) was sequenced at low coverage, and the repetitive fraction was characterized. In silico analysis showed that ~67.6% of the genome is mainly composed of different LTR retrotransposon lineages and one satellite DNA family (AgSAT171). The satellite DNA localized at the centromeric regions of all chromosomes; however, stronger signals were observed for 20 of the macro- and microchromosomes. All transposable elements showed a dispersed distribution, but not uniform across the length of the chromosomes. Different distribution patterns were observed for different TE lineages, with larger accumulation at the macrochromosomes. The data indicate the differential accumulation of LTR retrotransposon lineages at the macrochromosomes, probably contributing to the bimodality. Nevertheless, the differential accumulation of the satDNA in one group of macro- and microchromosomes possibly reflects the hybrid origin of this Agave accession.
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Affiliation(s)
- Lamonier Chaves Ramos
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
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Zhang Y, Li Y, Yang J, Yang X, Chen S, Xie Z, Zhang M, Huang Y, Zhang J, Huang X. Genome-Wide Analysis and Expression of Cyclic Nucleotide-Gated Ion Channel ( CNGC) Family Genes under Cold Stress in Mango ( Mangifera indica). PLANTS (BASEL, SWITZERLAND) 2023; 12:592. [PMID: 36771676 PMCID: PMC9920709 DOI: 10.3390/plants12030592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The 'king of fruits' mango (Mangifera indica) is widely cultivated in tropical areas and has been threatened by frequent extreme cold weather. Cyclic nucleotide-gated ion channel (CNGC) genes have an important function in the calcium-mediated development and cold response of plants. However, few CNGC-related studies are reported in mango, regardless of the mango cold stress response. In this study, we identified 43 CNGC genes in mango showing tissue-specific expression patterns. Five MiCNGCs display more than 3-fold gene expression induction in the fruit peel and leaf under cold stress. Among these, MiCNGC9 and MiCNGC13 are significantly upregulated below 6 °C, suggesting their candidate functions under cold stress. Furthermore, cell membrane integrity was damaged at 2 °C in the mango leaf, as shown by the content of malondialdehyde (MDA), and eight MiCNGCs are positively correlated with MDA contents. The high correlation between MiCNGCs and MDA implies MiCNGCs might regulate cell membrane integrity by regulating MDA content. Together, these findings provide a valuable guideline for the functional characterization of CNGC genes and will benefit future studies related to cold stress and calcium transport in mango.
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Affiliation(s)
| | - Yubo Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jing Yang
- Hainan Climate Center, Haikou 570203, China
| | - Xinli Yang
- Guilinyang Campus, Qiongtai Normal University, Haikou 571127, China
| | - Shengbei Chen
- Hainan Meteorological Service Center, Haikou 570203, China
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China
| | | | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghong Zhang
- Hainan Climate Center, Haikou 570203, China
- Key Laboratory of South China Sea Meteorological Disaster Prevention and Mitigation of Hainan Province, Haikou 570203, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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5
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Davis SC. Agave americana: Characteristics and Potential Breeding Priorities. PLANTS 2022; 11:plants11172305. [PMID: 36079687 PMCID: PMC9460544 DOI: 10.3390/plants11172305] [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: 06/28/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022]
Abstract
Agave americana L. is one of many Agave species that could be developed for the production of valuable agricultural products. Although all species in this genus use Crassulacean Acid Metabolism (CAM) and most have drought and heat tolerance, Agave americana also has the combined traits of high yield and cold tolerance. This review highlights key characteristics of Agave americana that make it an exceptional novel crop for fiber, sweeteners, bioproducts, and bioethanol with resilient traits for changing climate conditions. Then, it proposes potential directions for breeding that will support production in semi-arid climates. With selection and breeding, yields of 16 Mg ha−1 y−1 may be achieved. Current field observations, with no crop improvement, indicate ~9 Mg ha−1 is the maximum yield, and in arid regions, a yield of ~3 Mg ha−1 y−1 is observed. It may be beneficial to breed for a shorter time to flowering, as has been successful for Agave tequilana Weber var. azul, so that further breeding goals are achievable in a decadal timespan. Specific trait selection during breeding will depend on whether fiber or sugar yields are the desired products at a given location. Even without breeding, varieties of Agave americana are climate resilient alternatives for some current commodity crops.
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Affiliation(s)
- Sarah C Davis
- Voinovich School of Leadership and Public Service, Ohio University, Athens, OH 45701, USA
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Xu B, Tan S, Qin X, Huang X, Xi J, Chen H, Qin J, Chen T, Yi K. The complete chloroplast genome of Agave amaniensis (Asparagales: Asparagaceae: Agavoideae). Mitochondrial DNA B Resour 2022; 7:1519-1521. [PMID: 36034534 PMCID: PMC9415635 DOI: 10.1080/23802359.2022.2109440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Bochao Xu
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Jianfeng Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Integrated Pest Management on Tropical Crops, Haikou, PR China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
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7
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Maceda-López LF, Góngora-Castillo EB, Ibarra-Laclette E, Morán-Velázquez DC, Girón Ramírez A, Bourdon M, Villalpando-Aguilar JL, Toomer G, Tang JZ, Azadi P, Santamaría JM, López-Rosas I, López MG, Simpson J, Alatorre-Cobos F. Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111496. [PMID: 35684270 PMCID: PMC9182668 DOI: 10.3390/plants11111496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 05/08/2023]
Abstract
Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.
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Affiliation(s)
- Luis F. Maceda-López
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Elsa B. Góngora-Castillo
- CONACYT-Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico;
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico;
| | - Dalia C. Morán-Velázquez
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Amaranta Girón Ramírez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - José L. Villalpando-Aguilar
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Gabriela Toomer
- Division of Microbiology and Molecular Biology, IIT Research Institute, Chicago, IL 60616, USA;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Itzel López-Rosas
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Mercedes G. López
- Departmento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - Fulgencio Alatorre-Cobos
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence:
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Tan S, Liang Y, Huang Y, Xi J, Huang X, Yang X, Yi K. Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111434. [PMID: 35684207 PMCID: PMC9182991 DOI: 10.3390/plants11111434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 05/08/2023]
Abstract
Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.
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Affiliation(s)
- Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Yanqiong Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
- Correspondence: (X.H.); (X.Y.); (K.Y.)
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (X.H.); (X.Y.); (K.Y.)
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.T.); (Y.L.); (J.X.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
- Correspondence: (X.H.); (X.Y.); (K.Y.)
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Marone MP, Campanari MFZ, Raya FT, Pereira GAG, Carazzolle MF. Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PeerJ 2022; 10:e13252. [PMID: 35529479 PMCID: PMC9070324 DOI: 10.7717/peerj.13252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves' fungi as biotechnological tools.
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Affiliation(s)
- Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Fabio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
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10
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Enríquez-González C, Garcidueñas-Piña C, Castellanos-Hernández OA, Enríquez-Aranda S, Loera-Muro A, Ocampo G, Pérez-Molphe Balch E, Morales-Domínguez JF. De Novo Transcriptome of Mammillaria bombycina (Cactaceae) under In Vitro Conditions and Identification of Glyoxalase Genes. PLANTS 2022; 11:plants11030399. [PMID: 35161380 PMCID: PMC8838482 DOI: 10.3390/plants11030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
Mammillaria bombycina is a cactus distributed in the central region of Mexico. Cactaceae have the particularity of surviving drought and high temperatures, which is why in vitro propagation studies have been carried out successfully to preserve this species and use it as a study model in cacti. In this contribution, a de novo transcriptome of M. bombycina was produced under in vitro conditions for the identification and expression of genes related to abiotic stress. Samples were sequenced using an Illumina platform, averaging 24 million clean readings. From assembly and annotation, 84,975 transcripts were generated, 55% of which were unigenes. Among these, the presence of 13 isoforms of genes belonging to glyoxalase I, II and III were identified. An analysis of the qRT-PCR expression of these genes was performed under in vitro and ex vitro conditions and dehydration at 6 and 24 h. The highest expression was observed under greenhouse conditions and dehydration at 24 h, according to the control. The de novo assembly of the M. bombycina transcriptome remains a study model for future work in cacti.
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Affiliation(s)
- Carolina Enríquez-González
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Cristina Garcidueñas-Piña
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Osvaldo Adrián Castellanos-Hernández
- Centro de Investigación en Biología Molecular Vegetal, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad, 1115, Linda Vista, Ocotlán 47810, Mexico
| | - Sergio Enríquez-Aranda
- Centro de Ciencias Básicas, Departamento de Sistemas de la Información, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Abraham Loera-Muro
- CONACyT Centro de Investigaciones Biológicas del Noroeste S.C., Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz 23096, Mexico
| | - Gilberto Ocampo
- Centro de Ciencias Básicas, Departamento de Biología, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - Eugenio Pérez-Molphe Balch
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
| | - José Francisco Morales-Domínguez
- Centro de Ciencias Básicas, Departamento de Química, Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20100, Mexico
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11
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Transcriptome profiling and differential gene expression analysis provides insights into Lr24-based resistance in wheat against Puccinia triticina. 3 Biotech 2021; 11:455. [PMID: 34631354 DOI: 10.1007/s13205-021-02972-9] [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: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022] Open
Abstract
Leaf rust caused by Puccinia triticina is an important disease of wheat and Lr24 gene confers resistance to all known pathotypes of P. triticina in India. Transcripts associated with the Lr24 mediated resistance were identified through transcriptome sequencing and further expression analysis of differentially regulated genes was performed using qPCR technique. De novo transcriptome assembly showed 66,415 and 68,688 transcripts in resistant and susceptible genotypes, respectively. The study revealed that 5873 genes unique to resistant; 6782 genes unique to susceptible, while 10,841 genes were common to both. Gene Ontology distribution statistics showed 1030 and 1068 CDS in biological processes; 1234 and 1326 CDS in cellular processes; 1321 and 1352 CDS in molecular functions, respectively. A total of 659 genes were found to be differentially expressed, of which 349 were upregulated and 310 were downregulated in resistant genotype. Pathway analysis of transcripts appeared in resistant genotype revealed that 279 transcripts had homology with genes involved in signal transduction, 18 transcripts in membrane transport, one transcript in signaling molecules. Real-time PCR study showed that most of the up-regulated defense related genes expressed in early hours indicating that a cascade of defense starts early in Lr24 mediated resistance, which successfully inhibited pathogen establishment. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02972-9.
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12
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Yang X, Huang X, Tan S, Chen T, Qin X, Chen H, Xi J, Yi K. The complete chloroplast genome of Agave sisalana. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1855-1856. [PMID: 34124368 PMCID: PMC8183535 DOI: 10.1080/23802359.2021.1935345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Agave sisalana is one of the Agave cultivars for sisal fiber production around the tropical areas of the world. In the present study, we successfully sequenced and assembled its chloroplast genome. The full size of the genome is 157,268 bp with a GC content at 37.85%. The genome is constructed with a large single copy region (LSC, 85,894 bp), a pair of inverted repeat regions (IR, 26,573 bp) and a small single copy region (SSC, 18,228 bp). Besides, 86 protein-coding genes, 38 tRNAs and 8 rRNAs are annotated on the chloroplast genome. Phylogenetic result reveals that A. sisalana is closely related with A. americana and A. H11648.
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Affiliation(s)
- Xinli Yang
- College of Tropical Crops, Hainan University, Haikou, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
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13
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Morreeuw ZP, Escobedo-Fregoso C, Ríos-González LJ, Castillo-Quiroz D, Reyes AG. Transcriptome-based metabolic profiling of flavonoids in Agave lechuguilla waste biomass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110748. [PMID: 33691954 DOI: 10.1016/j.plantsci.2020.110748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 05/23/2023]
Abstract
Agave lechuguilla is one of the most abundant species in arid and semiarid regions of Mexico, and is used to extract fiber. However, 85 % of the harvested plant material is discarded. Previous bioprospecting studies of the waste biomass suggest the presence of bioactive compounds, although the extraction process limited metabolite characterization. This work achieved flavonoid profiling of A. lechuguilla in both processed and non-processed leaf tissues using transcriptomic analysis. Functional annotation of the first de novo transcriptome of A. lechuguilla (255.7 Mbp) allowed identifying genes coding for 33 enzymes and 8 transcription factors involved in flavonoid biosynthesis. The flavonoid metabolic pathway was mostly elucidated by HPLC-MS/MS screening of alcoholic extracts. Key genes of flavonoid synthesis were higher expressed in processed leaf tissues than in non-processed leaves, suggesting a high content of flavonoids and glycoside derivatives in the waste biomass. Targeted HPLC-UV-MS analyses confirmed the concentration of isorhamnetin (1251.96 μg), flavanone (291.51 μg), hesperidin (34.23 μg), delphinidin (24.23 μg), quercetin (15.57 μg), kaempferol (13.71 μg), cyanidin (12.32 μg), apigenin (9.70 μg) and catechin (7.91 μg) per gram of dry residue. Transcriptomic and biochemical profiling concur in the potential of lechuguilla by-products with a wide range of applications in agriculture, feed, food, cosmetics, and pharmaceutical industries.
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Affiliation(s)
- Zoé P Morreeuw
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico
| | - Cristina Escobedo-Fregoso
- CONACYT-CIBNOR, Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico
| | - Leopoldo J Ríos-González
- Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila (UAdeC), Blvd. V. Carranza, Col. Republica Oriente, C.P. 25280, Saltillo, Coahuila, Mexico
| | - David Castillo-Quiroz
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Saltillo, Carretera Saltillo-Zacatecas 9515, Col. Hacienda Buenavista, C.P. 25315, Saltillo, Coahuila, Mexico
| | - Ana G Reyes
- CONACYT-CIBNOR, Av. Instituto Politécnico Nacional 195, Col. Playa Palo Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico.
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14
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Maceda-López LF, Villalpando-Aguilar JL, García-Hernández E, Ávila de Dios E, Andrade-Canto SB, Morán-Velázquez DC, Rodríguez-López L, Hernández-Díaz D, Chablé-Vega MA, Trejo L, Góngora-Castillo E, López-Rosas I, Simpson J, Alatorre-Cobos F. Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots. 3 Biotech 2021; 11:75. [PMID: 33505830 DOI: 10.1007/s13205-020-02620-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/26/2020] [Indexed: 12/30/2022] Open
Abstract
Together with their undeniable role in the ecology of arid and semiarid ecosystems, Agave species are emerging as a model to dissect the relationships between crassulacean acid metabolism and high efficiency of light and water use, and as an energy crop for bioethanol production. Transcriptome resources from economically valuable Agaves species, such as Agave tequilana and A. salmiana, as well as hybrids for fibers, are now available, and multiple gene expression landscape analyses have been reported. Key components in molecular mechanisms underlying drought tolerance could be uncovered by analyzing gene expression patterns of roots. This study describes an efficient protocol for high-quality total RNA isolation from phenolic compounds-rich Agave roots. Our methodology involves suitable root handling and collecting in the field and using saving-time commercial kits available. RNA isolated from roots free of lignified out-layers and clean cortex showed high values of quality and integrity according to electrophoresis and microfluidics-based platform. Synthesis of long full-length cDNAs and PCR amplification tested the suitability for downstream applications of extracted RNA. The protocol was applied successfully to A. tequilana roots but can be used for other Agave species that also develop lignified epidermis/exodermis in roots.
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Affiliation(s)
- Luis F Maceda-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - José L Villalpando-Aguilar
- Tecnológico Nacional de México, Instituto Tecnológico de Chiná, Calle 11entre 22 y 28, 24050 Chiná, Mexico
| | - Eleazar García-Hernández
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Emmanuel Ávila de Dios
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Silvia B Andrade-Canto
- Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Dalia C Morán-Velázquez
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Lorena Rodríguez-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Demetrio Hernández-Díaz
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Manuel A Chablé-Vega
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Laura Trejo
- CONACYT Research Fellow, Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, UNAM, 90640 Santa Cruz Tlaxcala, Tlaxcala Mexico
| | - Elsa Góngora-Castillo
- CONACYT Research Fellow, Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Itzel López-Rosas
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Fulgencio Alatorre-Cobos
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
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15
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Huang X, Bai X, Guo T, Xie Z, Laimer M, Du D, Gbokie T, Zhang Z, He C, Lu Y, Wu W, Yi K. Genome-Wide Analysis of the PIN Auxin Efflux Carrier Gene Family in Coffee. PLANTS 2020; 9:plants9091061. [PMID: 32825074 PMCID: PMC7570243 DOI: 10.3390/plants9091061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022]
Abstract
Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.
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Affiliation(s)
- Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Xuehui Bai
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China; (X.B.); (T.G.)
| | - Tieying Guo
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China; (X.B.); (T.G.)
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China;
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Vienna 1190, Austria
- Correspondence: (M.L.); (W.W.)
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Thomas Gbokie
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhirun Zhang
- Coffee Engineering Research Center of China, Mangshi 678400, China;
| | - Chunping He
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Ying Lu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Weihuai Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
- Correspondence: (M.L.); (W.W.)
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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16
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Identification and Expression of SAUR Genes in the CAM Plant Agave. Genes (Basel) 2019; 10:genes10070555. [PMID: 31340544 PMCID: PMC6679190 DOI: 10.3390/genes10070555] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 01/04/2023] Open
Abstract
Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave's leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.
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Abstract
Sisal is widely cultivated in tropical areas for fiber production. The main sisal cultivar, Agave H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) has a relatively scarce molecular basis and no genomic information. Next-generation sequencing technology has offered a great opportunity for functional gene mining in Agave species. Several published Agave transcriptomes have already been reused for gene cloning and selection pressure analysis. There are also other potential uses of the published transcriptomes, such as meta-analysis, molecular marker detection, alternative splicing analysis, multi-omics analysis, genome assembly, weighted gene co-expression network analysis, expression quantitative trait loci analysis, miRNA target site prediction, etc. In order to make the best of our published transcriptome of A. H11648 leaf, we here represent a data descriptor, with the aim to expand Agave bio information and benefit Agave genetic researches.
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