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Carpinetti PDA, Fioresi VS, Ignez da Cruz T, de Almeida FAN, Canal D, Ferreira A, Ferreira MFDS. Efficient method for isolation of high-quality RNA from Psidium guajava L. tissues. PLoS One 2021; 16:e0255245. [PMID: 34310664 PMCID: PMC8312961 DOI: 10.1371/journal.pone.0255245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Acquiring high-quality RNA in sufficient amounts is crucial in plant molecular biology and genetic studies. Several methods for RNA extraction from plants are available in the literature, mainly due to the great biochemical diversity present in each species and tissue, which can complicate or prevent the extraction. Psidium guajava (Myrtaceae family) is a perennial fruit tree of medicinal and economic value; nevertheless, only a few molecular studies are available for the species. One reason is the difficulty in obtaining RNA due to the content of the samples, which are rich in polyphenols, polysaccharides, and secondary metabolites. Furthermore, there are few studies available for the isolation of RNA from guava or Psidium samples, which hampers advances in the study of the genus. Here, quality and yields of RNA isolates were compared using six extraction protocols: two protocols based on the application of cetyltrimethylammonium bromide (CTAB) lysis buffer, one protocol which uses the TRIzol reagent, one which applies guanidine thiocyanate lysis buffer followed by organic phase extraction, and two commercial kits (PureLink RNA Mini Kit and RNeasy Plant Mini Kit). The CTAB-based method provided the highest RNA yields and quality for five different tissues (flower bud, immature leaf, young leaf, mature leaf, and root), genotypes, and stress conditions. For the most efficient protocol, the average yield of RNA from guava leaves was 203.06 μg/g of tissue, and the A260/A280 and A260/A230 ratios were 2.1 and 2.2, respectively. RT-qPCR analysis demonstrated that the purity of the samples was sufficient for molecular biology experiments. CTAB-based methods for RNA isolation were found to be the most efficient, providing the highest RNA yields and quality for tissues from P. guajava. Additionally, they were compatible for downstream RNA-based applications, besides being simple and cost-effective.
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Affiliation(s)
- Paola de Avelar Carpinetti
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Vinicius Sartori Fioresi
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Thais Ignez da Cruz
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Francine Alves Nogueira de Almeida
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Drielli Canal
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Adésio Ferreira
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
| | - Marcia Flores da Silva Ferreira
- Laboratory of Genetics and Plant Improvement, Department of Agronomy, Centre for Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, ES, Brazil
- * E-mail:
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2
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Zhou GL, Zhu P. De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites. BMC PLANT BIOLOGY 2020; 20:414. [PMID: 32887550 PMCID: PMC7487690 DOI: 10.1186/s12870-020-02586-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 08/03/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. RESULTS To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower. CONCLUSIONS To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.
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Affiliation(s)
- Guo-Lin Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biosynthesis of Natural Products, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biosynthesis of Natural Products, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China.
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3
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Rodrigues NF, Balbinott N, Paim I, Guzman F, Margis R. Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae). Genet Mol Biol 2020; 43:e20190302. [PMID: 32384134 PMCID: PMC7212760 DOI: 10.1590/1678-4685-gmb-2019-0302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/29/2020] [Indexed: 01/15/2023] Open
Abstract
Myrteae is the largest and most diverse tribe within Myrtaceae and represents the majority of its diversity in the Neotropics. Members of Myrteae hold ecological importance in tropical biomes for the provision of food sources for many animal species. Thus, due to its several roles, a growing interest has been addressed to this group. In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structural changes among species. Increased sequence diversity was observed in some intergenic regions, suggesting their suitability for investigating intraand interspecific genetic diversity in populational studies. These data also contribute to the improvement of taxa sampling in further phylogenetic investigations to understand Myrtaceae evolution.
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Affiliation(s)
- Nureyev F Rodrigues
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Igor Paim
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Porto Alegre, RS, Brazil
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4
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Vetö NM, Guzman F, Kulcheski FR, Segatto ALA, Lacerda MEG, Margis R, Turchetto-Zolet AC. Transcriptomics analysis of Psidium cattleyanum Sabine (Myrtaceae) unveil potential genes involved in fruit pigmentation. Genet Mol Biol 2020; 43:e20190255. [PMID: 32353098 PMCID: PMC7199922 DOI: 10.1590/1678-4685-gmb-2019-0255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/16/2020] [Indexed: 01/09/2023] Open
Abstract
Psidium cattleyanum Sabine is an Atlantic Forest native species
that presents some populations with red fruits and others with yellow fruits.
This variation in fruit pigmentation in this species is an intriguing character
that could be related to species evolution but still needs to be further
explored. Our goal was to provide genomic information for these morphotypes to
understand the molecular mechanisms of differences in fruit colour in this
species. In this study, we performed a comparative transcriptome analysis of red
and yellow morphotypes of P. cattleyanum, considering two
stages of fruit ripening. The transcriptomic analysis performed encompassing
leaves, unripe and ripe fruits, in triplicate for each morphotype. The
transcriptome consensus from each morphotype showed 301,058 and 298,310 contigs
from plants with yellow and red fruits, respectively. The differential
expression revealed important genes that were involved in anthocyanins
biosynthesis, such as the anthocyanidin synthase (ANS) and
UDP-glucose:flavonoid-o-glucosyltransferase (UFGT) that were differentially
regulated during fruit ripening. This study reveals stimulating data for the
understanding of the pathways and mechanisms involved in the maturation and
colouring of P. cattleyanum fruits and suggests that the ANS
and UFGT genes are key factors involved in the synthase and pigmentation
accumulation in red fruits.
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Affiliation(s)
- Nicole M Vetö
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brazil.,Instituto Nacional de Innovación Agraria, Dirección de Recursos Genéticos y Biotecnología, Lima, Peru
| | - Franceli R Kulcheski
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, Programa de Pós-graduação em Biologia Celular e o Desenvolvimento, Florianópolis, SC, Brazil
| | - Ana Lúcia A Segatto
- Universidade Federal de Santa Maria, Departamento de Bioquímica e Biologia Molecular, Santa Maria, RS, Brazil
| | - Maria Eduarda G Lacerda
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Porto Alegre, RS, Brazil
| | - Andreia C Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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5
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Srivastava G, Garg A, Misra RC, Chanotiya CS, Ghosh S. Transcriptome analysis and functional characterization of oxidosqualene cyclases of the arjuna triterpene saponin pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110382. [PMID: 32005387 DOI: 10.1016/j.plantsci.2019.110382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/25/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Arjuna (Terminalia arjuna) tree has been popular in Indian traditional medicine to treat cardiovascular ailments. The tree accumulates bioactive triterpene glycosides (saponins) and aglycones (sapogenins), in a tissue-preferential manner. Oleanane triterpenes/saponins (derived from β-amyrin) with potential cardioprotective function predominantly accumulate in the bark. However, arjuna triterpene saponin pathway enzymes remain to be identified and biochemically characterized. Here, we employed a combined transcriptomics, metabolomics and biochemical approach to functionally define a suite of oxidosqualene cyclases (OSCs) that catalyzed key reactions towards triterpene scaffold diversification. De novo assembly of 131 millions Illumina NextSeq500 sequencing reads obtained from leaf and stem bark samples led to a total of 156,650 reference transcripts. Four distinct OSCs (TaOSC1-4) with 54-71 % sequence identities were identified and functionally characterized. TaOSC1, TaOSC3 and TaOSC4 were biochemically characterized as β-amyrin synthase, cycloartenol synthase and lupeol synthase, respectively. However, TaOSC2 was found to be a multifunctional OSC producing both α-amyrin and β-amyrin, but showed a preference for α-amyrin product. Both TaOSC1 and TaOSC2 produced β-amyrin, the direct precursor for oleanane triterpene/saponin biosynthesis; but, TaOSC1 transcript expressed preferentially in bark, suggesting a major role of TaOSC1 in the biosynthesis of oleanane triterpenes/saponins in bark.
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Affiliation(s)
- Gaurav Srivastava
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Chemical Sciences Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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6
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Anton DB, Guzman FL, Vetö NM, Krause FA, Kulcheski FR, Coelho APD, Duarte GL, Margis R, Dillenburg LR, Turchetto-Zolet AC. Characterization and expression analysis of P5CS (Δ1-pyrroline-5-carboxylate synthase) gene in two distinct populations of the Atlantic Forest native species Eugenia uniflora L. Mol Biol Rep 2019; 47:1033-1043. [PMID: 31749121 DOI: 10.1007/s11033-019-05195-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
Eugenia uniflora is an Atlantic Forest native species, occurring in contrasting edaphoclimatic environments. The identification of genes involved in response to abiotic factors is very relevant to help in understanding the processes of local adaptation. 1-Pyrroline-5-carboxylate synthetase (P5CS) is one interesting gene to study in this species since it encodes a key enzyme of proline biosynthesis, which is an osmoprotectant during abiotic stress. Applying in silico analysis, we identified one P5CS gene sequence of E. uniflora (EuniP5CS). Phylogenetic analysis, as well as, gene and protein structure investigation, revealed that EuniP5CS is a member of P5CS gene family. Plants of E. uniflora from two distinct environments (restinga and riparian forest) presented differences in the proline accumulation and P5CS expression levels under growth-controlled conditions. Both proline accumulation and gene expression level of EuniP5CS were higher in the genotypes from riparian forest than those from restinga. When these plants were submitted to drought stress, EuniP5CS gene was up-regulated in the plants from restinga, but not in those from riparian forest. These results demonstrated that EuniP5CS is involved in proline biosynthesis in this species and suggest that P5CS gene may be an interesting candidate gene in future studies to understand the processes of local adaptation in E. uniflora.
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Affiliation(s)
- Débora Bublitz Anton
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM) Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Prédio 43312, Porto Alegre, 91501-970, Brazil.,Graduação em Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Frank Lino Guzman
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Nicole Moreira Vetö
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM) Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Prédio 43312, Porto Alegre, 91501-970, Brazil
| | - Felipe Augusto Krause
- Graduação em Agronomia, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Franceli Rodrigues Kulcheski
- Programa de Pós-Graduação em Biologia Celular e do Desenvolvimento (PPGBCD) Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina (UFSC), Porto Alegre, Brazil
| | - Ana Paula Durand Coelho
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Guilherme Leitão Duarte
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rogério Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM) Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Prédio 43312, Porto Alegre, 91501-970, Brazil.,Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lúcia Rebello Dillenburg
- Laboratório de Ecofisiologia Vegetal, Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Andreia Carina Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM) Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Prédio 43312, Porto Alegre, 91501-970, Brazil.
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7
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Bai Q, He B, Cai Y, Lian H, Zhang Q. Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana. Mol Genet Genomics 2019; 295:327-341. [PMID: 31735985 DOI: 10.1007/s00438-019-01624-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
Pine resin, which typically consists of terpenoids, is a natural product used in various industrial applications. Oleoresin can be obtained from the xylem tissue by wounding the stem bark. Pinus massoniana (masson pine) is an important resin-tapping tree species that originated in southern China. Masson pines with different genetic backgrounds typically have different resin-yielding capacities (RYCs). However, the mechanisms underlying high resin yield in masson pines are unclear. The aim of this study was to identify the possible genetic regulation pathways and functional genes that influence the resin yield. In this study, we conducted transcriptomic and metabolomic studies of masson pine secondary xylem with high, medium, and low RYCs. A total of 230,068 unigenes and 3894 metabolites were identified from the tissue of the secondary xylem. Several differentially expressed regulation factors, including WRKY, bHLH, and ERF, and functional genes such as PKc and LRR-RLKs, were identified among these masson pines. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly focused on diterpenoid biosynthesis, plant hormone signal transduction, and ABC transporters. Furthermore, integration of the transcriptomic and metabolomic data indicated that the PKc- and LRR-RLK-related regulatory and metabolic pathways may play critical roles in the biosynthesis of terpenoids. These above results improve our understanding of the biosynthesis mechanism of oleoresin in P. massoniana and facilitate further research work into the functional analysis of these candidate genes.
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Affiliation(s)
- Qingsong Bai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Huiming Lian
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
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8
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Petry VS, Stefenon VM, Machado LO, Klabunde GHF, Pedrosa FO, Nodari RO. Repetitive genomic elements in Campomanesia xanthocarpa: prospection, characterization and cross amplification of molecular markers. 3 Biotech 2019; 9:423. [PMID: 31696028 DOI: 10.1007/s13205-019-1953-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/13/2019] [Indexed: 11/28/2022] Open
Abstract
Repetitive genomic elements were prospected in Campomanesia xanthocarpa, aiming to characterize these elements in a non-model plant species and to develop species-specific microsatellite markers. Approximately 4.12% of the partial genome of C. xanthocarpa is composed of repetitive elements, being retrotransposons the most widely represented. A total of nine polymorphic microsatellite markers were obtained: four nuclear-neutral, two nuclear EST, two plastidial and one mitochondrial. Levels of population genetic diversity of four natural populations of C. xanthocarpa were characterized using these markers. In addition, the cross-species amplification of the microsatellite markers was tested in seven species of tribe Myrteae (Myrtaceae). The characterized microsatellite markers revealed low to moderate levels of genetic diversity (expected heterozygosity range: 0.33-0.57; observed heterozygosity: 0.26-0.74 and number of alleles: 2.25-4.25). Cross-species amplification was successful for all loci, except Cxant76. These nine markers will contribute for studies on genetic diversity, gene flow, plant selection and breeding of this species, towards the conservation of natural populations, as well as its commercial use.
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Affiliation(s)
- Vanessa S Petry
- 1Graduate Program in Plant Genetic Resources, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - Valdir Marcos Stefenon
- 1Graduate Program in Plant Genetic Resources, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
- 2Nucleus of Molecular Ecology and Plant Micropropagation, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul Brazil
| | - Lilian O Machado
- 1Graduate Program in Plant Genetic Resources, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - Gustavo H F Klabunde
- 3Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina (EPAGRI), Itajaí, Santa Catarina Brazil
| | - Fábio O Pedrosa
- 4Department of Biochemistry and Molecular Biology, Nucleus of Nitrogen Fixation, Universidade Federal do Paraná, Curitiba, Paraná Brazil
| | - Rubens O Nodari
- 1Graduate Program in Plant Genetic Resources, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
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9
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Wang C, Peng D, Zhu J, Zhao D, Shi Y, Zhang S, Ma K, Wu J, Huang L. Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis. PLANT METHODS 2019; 15:65. [PMID: 31289459 PMCID: PMC6593569 DOI: 10.1186/s13007-019-0441-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/17/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Polygonatum cyrtonema Hua (P. cyrtonema) is one of the most important herbs in traditional Chinese medicine. Polysaccharides in P. cyrtonema plants comprise a class of important secondary metabolites and exhibit a broad range of pharmacological functions. RESULTS In order to identify genes involved in polysaccharide biosynthesis, we performed RNA sequencing analysis of leaf, root, and rhizome tissues of P. cyrtonema. A total of 164,573 unigenes were obtained by assembling transcripts from all three tissues and 86,063 of these were annotated in public databases. Differentially expressed genes (DEGs) were determined based on expression profile analysis, and DEG levels in rhizome tissues were then compared with their counterparts in leaf and root tissues. This analysis revealed numerous genes that were either up-regulated or uniquely expressed in the rhizome. Multiple genes encoding important enzymes, such as UDP glycosyltransferases (UGTs), or transcription factors involved in polysaccharide biosynthesis were identified and further analyzed, while a few genes encoding key enzymes were experimentally validated using quantitative real-time PCR. CONCLUSION Our results substantially expand the public transcriptome dataset of P. cyrtonema and provide valuable clues for the identification of candidate genes involved in metabolic pathways.
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Affiliation(s)
- Chenkai Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Daiyin Peng
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012 China
| | - Jinhang Zhu
- Anhui Medical University, Hefei, 230032 China
| | - Derui Zhao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Kelong Ma
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Clinical College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012 China
| | - Luqi Huang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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10
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High-throughput sequencing analysis of Eugenia uniflora: insights into repetitive DNA, gene content and potential biotechnological applications. 3 Biotech 2019; 9:200. [PMID: 31065500 DOI: 10.1007/s13205-019-1729-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/24/2019] [Indexed: 10/26/2022] Open
Abstract
In this study, the Ion Torrent PGM platform was employed to conduct a whole-genome sequencing analysis of Eugenia uniflora L., aiming to generate new genomic information for this non-model species. The whole-genome set of assembled sequences (WGSAS) generated 2601 contigs, with a cumulative length of 3.15 Mbp. About 2.60% of the WGSAS was characterized by repetitive sequences, while 71.66% of the WGSAS was represented by predicted genes. A total of 147 metabolic pathways related to enzymes characterized in the E. uniflora WGSAS were detected. Proteins related to antifungal activity and to bacterium and fungi defense response as well as transcriptions factors related to abiotic stress responses were also identified. This sequencing provides important genomic resources for future breeding and selection regarding plants with higher production of such metabolites, as well as source of genes for genetic engineering of cultivated species, supporting a wide application of marker-assisted and genomic selection, towards the establishment of commercial orchards with improved cultivars of E. uniflora.
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11
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Santos LD, Campos A, Cechinel Filho V, Nesello LAN. PHYTOCHEMICAL PROFILE AND GASTROPROTECTIVE ACTIVITY OF EUGENIA MATTOSII FRUITS. ARQUIVOS DE GASTROENTEROLOGIA 2018; 55:138-141. [PMID: 30043862 DOI: 10.1590/s0004-2803.201800000-24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/09/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND Extracts obtained from plants and fruits provide a relatively safe and practical alternative for the conventional medicine of gastrointestinal diseases. The specie Eugenia mattosii, popularly known in Brazil as "cerejinha", belongs to Myrtaceae family. Species of this family present pharmacological properties, and can be used in the treatment of gastrointestinal disorders. OBJECTIVE The aim of this study was to determine the phytochemical profile and evaluate the gastroprotective activity of Eugenia mattosii fruits. METHODS Phytochemical analysis was carried out by thin layer chromatography and gastroprotective assays were performed using two experimental models: acute ulcer model induced by ethanol/HCl and acute ulcer model induced by non-steroidal anti-inflammatory drug (indomethacin). Total lesion area (mm2) and relative lesion area (%) were determined. RESULTS The results of the phytochemical analysis indicated that the bark and pulp and seeds of E. mattosii present phenolic compounds, terpenes and/or steroids. In gastric ulcer model induced by ethanol was evidenced significant reduction of damaged areas for doses of 50 and 250 mg/ kg of seeds methanol extract, while in the indomethacin-induced ulcer model, all parts of the fruit presented defense capability of the gastric mucosa by reducing lesions at doses of 50, 125 and 250 mg/kg. CONCLUSION The results demonstrate that the specie E. mattosii has bioactive compounds that provide gastroprotective activity, presenting possible therapeutic potential.
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Affiliation(s)
- Luana Dos Santos
- Universidade do Vale do Itajaí - UNIVALI, Centro de Ciências da Saúde (CCS), Curso de Nutrição, Itajaí, SC, Brasil
| | - Adriana Campos
- Universidade do Vale do Itajaí - UNIVALI, Grupo de Pesquisa em Produtos Naturais Bioativos e Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Itajaí, SC, Brasil
| | - Valdir Cechinel Filho
- Universidade do Vale do Itajaí - UNIVALI, Grupo de Pesquisa em Produtos Naturais Bioativos e Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Itajaí, SC, Brasil
| | - Luciane Angela Nottar Nesello
- Universidade do Vale do Itajaí - UNIVALI, Grupo de Pesquisa em Produtos Naturais Bioativos e Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Itajaí, SC, Brasil
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12
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He SM, Wang X, Yang SC, Dong Y, Zhao QM, Yang JL, Cong K, Zhang JJ, Zhang GH, Wang Y, Fan W. De novo Transcriptome Characterization of Rhodomyrtus tomentosa Leaves and Identification of Genes Involved in α/β-Pinene and β-Caryophyllene Biosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1231. [PMID: 30197651 PMCID: PMC6117411 DOI: 10.3389/fpls.2018.01231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/03/2018] [Indexed: 06/01/2023]
Abstract
Plant-derived terpenes are effective in treating chronic dysentery, rheumatism, hepatitis, and hyperlipemia. Thus, understanding the molecular basis of terpene biosynthesis in some terpene-abundant Chinese medicinal plants is of great importance. Abundant in mono- and sesqui-terpenes, Rhodomyrtus tomentosa (Ait.) Hassk, an evergreen shrub belonging to the family Myrtaceae, is widely used as a traditional Chinese medicine. In this study, (+)-α-pinene and β-caryophyllene were detected to be the two major components in the leaves of R. tomentosa, in which (+)-α-pinene is higher in the young leaves than in the mature leaves, whereas the distribution of β-caryophyllene is opposite. Genome-wide transcriptome analysis of leaves identified 138 unigenes potentially involved in terpenoid biosynthesis. By integrating known biosynthetic pathways for terpenoids, 7 candidate genes encoding terpene synthase (RtTPS1-7) that potentially catalyze the last step in pinene and caryophyllene biosynthesis were further characterized. Sequence alignment analysis showed that RtTPS1, RtTPS3 and RtTPS4 do not contain typical N-terminal transit peptides (62-64aa), thus probably producing multiple isomers and enantiomers by terpenoid isomerization. Further enzyme activity in vitro confirmed that RtTPS1-4 mainly produce (+)-α-pinene and (+)-β-pinene, as well as small amounts of (-)-α-pinene and (-)-β-pinene with GPP, while RtTPS1 and RtTPS3 are also active with FPP, producing β-caryophyllene, along with a smaller amount of α-humulene. Our results deepen the understanding of molecular mechanisms of terpenes biosynthesis in Myrtaceae.
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Affiliation(s)
- Si-Mei He
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Sheng-Chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Yang Dong
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, China
| | - Qi-Ming Zhao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Jian-Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kun Cong
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Jia-Jin Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guang-Hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
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13
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De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis. Sci Rep 2018; 8:5824. [PMID: 29643397 PMCID: PMC5895812 DOI: 10.1038/s41598-018-24201-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/28/2018] [Indexed: 01/24/2023] Open
Abstract
Artemisia argyi Lev. et Vant. (A. argyi) is widely utilized for moxibustion in Chinese medicine, and the mechanism underlying terpenoid biosynthesis in its leaves is suggested to play an important role in its medicinal use. However, the A. argyi transcriptome has not been sequenced. Herein, we performed RNA sequencing for A. argyi leaf, root and stem tissues to identify as many as possible of the transcribed genes. In total, 99,807 unigenes were assembled by analysing the expression profiles generated from the three tissue types, and 67,446 of those unigenes were annotated in public databases. We further performed differential gene expression analysis to compare leaf tissue with the other two tissue types and identified numerous genes that were specifically expressed or up-regulated in leaf tissue. Specifically, we identified multiple genes encoding significant enzymes or transcription factors related to terpenoid synthesis. This study serves as a valuable resource for transcriptome information, as many transcribed genes related to terpenoid biosynthesis were identified in the A. argyi transcriptome, providing a functional genomic basis for additional studies on molecular mechanisms underlying the medicinal use of A. argyi.
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Cao X, Zhang F, Yuan B, Meng L, Yang X, Jiang J. De novo transcriptome sequencing and analysis of Euphorbia pekinensis Rupr. and identification of genes involved in diterpenoid biosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Huang H, Xia EH, Zhang HB, Yao QY, Gao LZ. De novo transcriptome sequencing of Camellia sasanqua and the analysis of major candidate genes related to floral traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:103-111. [PMID: 28992542 DOI: 10.1016/j.plaphy.2017.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Camellia sasanqua is one of the most famous horticultural plants in Camellia (Theaceae) due to its aesthetic appeal as landscape plant. Knowledge regarding the genetic basis of flowering time, floral aroma and color in C. sasanqua is limited, but is essential to breed new varieties with desired floral traits. Here, we described the de novo transcriptome of young leaves, flower buds and flowers of C. sasanqua. A total of 60,127 unigenes were functionally annotated based on the sequence similarity. After analysis, we found that two floral integrator genes, SOC1 and AP1, in flowering time pathway showed evidence of gene family expansion. Compared with 1-deoxy-D-xylulose-5-phosphate pathway, some genes in the mevalonate pathway were most highly expressed, suggesting that this might represent the major pathway for terpenoid biosynthesis related to floral aroma in C. sasanqua. In flavonoid biosynthesis pathway, PAL, CHI, DFR and ANS showing significantly higher expression levels in flowers and flower buds might have important role in regulation of floral color. The top five most transcription factors (TFs) families in C. sasanqua transcriptome were MYB, MIKC, C3H, FAR1 and HD-ZIP, many of which have a direct relationship with floral traits. In addition, we also identified 33,540 simple sequence repeats (SSRs) in the C. sasanqua transcriptome. Collectively, the C. sasanqua transcriptome dataset generated from this study along with the SSR markers provide a new resource for the identification of novel regulatory transcripts and will accelerate the genetic improvement of C. sasanqua breeding programs.
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Affiliation(s)
- Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qiu-Yang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
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16
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LC–MS characterization, anti-kinetoplastide and cytotoxic activities of natural products from Eugenia jambolana Lam. and Eugenia uniflora. Asian Pac J Trop Biomed 2017. [DOI: 10.1016/j.apjtb.2017.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Torre S, Tattini M, Brunetti C, Guidi L, Gori A, Marzano C, Landi M, Sebastiani F. De Novo Assembly and Comparative Transcriptome Analyses of Red and Green Morphs of Sweet Basil Grown in Full Sunlight. PLoS One 2016; 11:e0160370. [PMID: 27483170 PMCID: PMC4970699 DOI: 10.1371/journal.pone.0160370] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Sweet basil (Ocimum basilicum), one of the most popular cultivated herbs worldwide, displays a number of varieties differing in several characteristics, such as the color of the leaves. The development of a reference transcriptome for sweet basil, and the analysis of differentially expressed genes in acyanic and cyanic cultivars exposed to natural sunlight irradiance, has interest from horticultural and biological point of views. There is still great uncertainty about the significance of anthocyanins in photoprotection, and how green and red morphs may perform when exposed to photo-inhibitory light, a condition plants face on daily and seasonal basis. We sequenced the leaf transcriptome of the green-leaved Tigullio (TIG) and the purple-leaved Red Rubin (RR) exposed to full sunlight over a four-week experimental period. We assembled and annotated 111,007 transcripts. A total of 5,468 and 5,969 potential SSRs were identified in TIG and RR, respectively, out of which 66 were polymorphic in silico. Comparative analysis of the two transcriptomes showed 2,372 differentially expressed genes (DEGs) clustered in 222 enriched Gene ontology terms. Green and red basil mostly differed for transcripts abundance of genes involved in secondary metabolism. While the biosynthesis of waxes was up-regulated in red basil, the biosynthesis of flavonols and carotenoids was up-regulated in green basil. Data from our study provides a comprehensive transcriptome survey, gene sequence resources and microsatellites that can be used for further investigations in sweet basil. The analysis of DEGs and their functional classification also offers new insights on the functional role of anthocyanins in photoprotection.
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Affiliation(s)
- Sara Torre
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
| | - Cecilia Brunetti
- Trees and Timber Institute, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Lucia Guidi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Antonella Gori
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Cristina Marzano
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
- * E-mail:
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18
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Nie S, Li C, Xu L, Wang Y, Huang D, Muleke EM, Sun X, Xie Y, Liu L. De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering. BMC Genomics 2016; 17:389. [PMID: 27216755 PMCID: PMC4877741 DOI: 10.1186/s12864-016-2633-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 04/21/2016] [Indexed: 01/02/2023] Open
Abstract
Background The appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq). Results A total of 54.64 million clean reads and 111,167 contigs representing 53,642 unigenes were obtained from the radish leaf transcriptome. Among these, 50,385 unigenes were successfully annotated by BLAST searching against the public protein databases. Functional classification and annotation indicated that 42,903 and 15,382 unique sequences were assigned to 55 GO terms and 25 COG categories, respectively. KEGG pathway analysis revealed that 25,973 unigenes were classified into 128 functional pathways, among which 24 candidate genes related to plant circadian rhythm were identified. Moreover, 142 potential bolting and flowering-related genes involved in various flowering pathways were identified. In addition, seven critical bolting and flowering-related genes were isolated and profiled by T-A cloning and RT-qPCR analysis. Finally, a schematic network model of bolting and flowering regulation and pathways was put forward in radish. Conclusions This study is the first report on systematic identification of bolting and flowering-related genes based on transcriptome sequencing and assembly in radish. These results could provide a foundation for further investigating bolting and flowering regulatory networks in radish, and facilitate dissecting molecular genetic mechanisms underlying bolting and flowering in Brassicaceae vegetable crops. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2633-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shanshan Nie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Chao Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Danqiong Huang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Everlyne M Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Xiaochuan Sun
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, Nanjing, 210095, People's Republic of China.
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Palma-Silva C, Ferro M, Bacci M, Turchetto-Zolet AC. De novo assembly and characterization of leaf and floral transcriptomes of the hybridizing bromeliad species (Pitcairnia spp.) adapted to Neotropical Inselbergs. Mol Ecol Resour 2016; 16:1012-22. [PMID: 26849180 DOI: 10.1111/1755-0998.12504] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
Abstract
We present the leaf and floral transcriptomes of two hybridizing bromeliad species that differ in their major pollinator systems. Here we identified candidate genes responsible for pollinator attraction and reproductive isolation in these two species. We searched for candidate genes involved in floral traits, such as colour. Approximately 34 Gbp of cDNA sequence data were produced from both tissues and species, resulting in a total of 424 506 914 raw reads. The de novo-assembled transcriptomes consisted of a total of 263 955 contigs, further clustered into 110 977 unigenes. Over 58% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The transcriptomes revealed 144 unique transcripts that encode key enzymes in the flavonoid and anthocyanin biosynthesis pathways. The domain/family annotation and phylogenetic analysis allowed us to infer, by homology, potential functions of the genes encoding MYB, HD-ZIP and bZIP-HY5 transcription factors, as well as WD40 protein, which may be involved in anthocyanin and flavonoid regulation in these species. These candidate genes are associated with natural regulation in flower colour in other plant species and will facilitate future studies aimed at elucidating the molecular basis of adaptive differentiation and the evolution of mechanisms of pollinator-mediated reproductive isolation in these two bromeliads. In addition, we identified a total of 49 439 microsatellite loci. These resources will assist future research into adaptation and speciation events in bromeliad species, thus providing a starting point for investigation of the molecular mechanisms of the traits responsible for their reproductive isolation.
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Affiliation(s)
- C Palma-Silva
- Departamento de Ecologia, Programa de Pós-graduação em Ecologia e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - M Ferro
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - M Bacci
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - A C Turchetto-Zolet
- Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
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20
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Wang X, Zhou C, Yang X, Miao D, Zhang Y. De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis. PLoS One 2015; 10:e0135724. [PMID: 26305373 PMCID: PMC4549110 DOI: 10.1371/journal.pone.0135724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/24/2015] [Indexed: 12/24/2022] Open
Abstract
The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xianpeng Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Di Miao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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