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Ramni Jamnadass - One of the best experts on this subject based on the ideXlab platform.
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analysis of the impact of domestication of warburgia ugandensis sprague on its genetic diversity based on amplified fragment length polymorphism
African Journal of Biotechnology, 2016Co-Authors: Nkatha Gacheri, Bramwel Wanjala, Ramni Jamnadass, Alice MuchugiAbstract:Warburgia ugandensis Sprague (Canellaceae) occurs in East and Central Africa and is an important multipurpose tree species. Over-exploitation of natural forests for medicinal purposes and clearance for farming threaten the species survival. Cultivation of the tree species would ensure sustainable medicinal source and its conservation. However, on-farm genetic diversity of the species is currently unknown. The genetic diversity of the on-farm W. ugandensis populations and their proximate natural populations were analyzed using the amplified fragment length polymorphism (AFLP). Four primer combinations produced a total of 223 polymorphic bands. Both the natural and on-farm populations had high genetic diversity ranging from H = 0.2892 to H = 0.1278. Principal co-ordinates analysis and dendrogram separated the ten populations into two major groups corresponding to Kenyan and Tanzanian populations, respectively. Ugandan populations were shared between the two major groups; this is probably because Uganda is believed to be the centre of diversity for W. ugandensis. Close genetic relationships between the on-farm and their proximate natural population were revealed. Analysis of molecular variance (AMOVA) revealed that a total of 54% AFLP variation resided within populations with 46% reside among populations. The high genetic diversity of W. ugandensis on-farm populations could be useful in germplasm collection and conservation strategies. Key words : Warburgia ugandensis, amplified fragment length polymorphism (AFLP), domestication, genetic diversity, on-farm, natural.
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antimicrobial drimane sesquiterpenes and their effect on endophyte communities in the medical tree warburgia ugandensis
Frontiers in Microbiology, 2014Co-Authors: Sigrid Drage, Alice Muchugi, Angela Sessitsch, Birgit Mitter, Ramni Jamnadass, Franz HadacekAbstract:Metabolite profiles (GC–MS), drimane sesquiterpenes, sugars and sugar alcohols, were compared with bacterial and fungal endophyte communities (T-RFLP, DNA clones, qPCR) in leaves and roots of the pepper bark tree, Warburgia ugandensis (Canellaceae). Ten individuals each were assessed from two locations east and west of the Great Rift Valley, Kenya, Africa, which differed in humidity and vegetation, closed forest versus open savannah. Despite organ- and partially site-specific variation of drimane sesquiterpenes, no clear effects on bacterial and fungal endophyte communities could be detected. The former were dominated by gram-negative Gammaproteobacteria, Pseudomonadaceae and Enterobacteriaceae, as well as gram-positive Firmicutes; the fungal endophyte communities were more diverse but no specific groups dominated. Despite initial expectations, the endophyte community of the pepper bark tree did not differ from other trees that much.
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isolation of high quality dna and rna from cambium of the east african greenheart warburgia ugandensis
African Journal of Biotechnology, 2009Co-Authors: Edward Muge, S Lemurt, Kornel Burg, C. A. C. Kadu, Alice Muchugi, Ramni JamnadassAbstract:The genus Warburgia belongs to the Canellaceae, a small family of tropical aromatic tree species important for their antibacterial and antifungal medicinal qualities amongst many other functions. Many published protocols for nucleic acid isolation failed to yield sufficiently good quality amounts for analysis. We have therefore developed a simple and fast CTAB (cetyl-trimethyl ammonium bromide)-based extraction protocol for routine isolation of high-quality nucleic acids. Good quality genomic DNA (gDNA) and RNA was obtained and was suitable for PCR amplification, restriction endonuclease digestion, Southern blotting and RT-PCR, respectively.
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genetic structuring of important medicinal species of genus warburgia as revealed by aflp analysis
Tree Genetics & Genomes, 2008Co-Authors: C. A. C. Kadu, Geoffrey M. Muluvi, Alice Muchugi, A J Simons, Roeland Kindt, Ramni JamnadassAbstract:The genus Warburgia (Canellaceae) contains four tree species that are of valuable medicinal importance and are all found in Africa. Genetic diversity present in wild populations of these species is under great threat due to unsustainable harvesting for medicines and indiscrimi- nate felling for timber and agricultural expansion. There is therefore an urgent need for conservation of these species. Some authors disagree about the taxonomy of the genus and list different species as synonyms. Amplified fragment length polymorphism (AFLP) technique was used to determine the genetic relationships between three species to resolve the taxonomic confusion. The amount of genetic variation within and among populations was assessed to guide strategies for their conservation and sustainable utilization. Four AFLP primer pairs (EcoRI/MseI) generated a total of 185 amplification products. Analysis of molecular variance revealed most variation among individuals within populations (63%, P<0.0001), but variation among pop- ulations (37%, P<0.0001) was highly significant as well. Constrained analysis of principal coordinates based on the Jaccard distance confirmed the separation among popula- tions (38.2%, P<0.0001). A phenetic tree and ordination graphs showed a clear distinction of W. ugandensis from W. salutaris and W. stuhlmannii. W. ugandensis populations from Uganda and western Kenya formed a subgroup that clustered away from the rest of the W. ugandensis populations. W. salutaris and W. stuhlmannii populations showed little genetic differentiation. An implication of the data to genetic management and taxonomic clarification is discussed.
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estimation of out crossing rate in a natural breeding population of warburgia ugandensis using aflp marker
African Journal of Biotechnology, 2008Co-Authors: Geoffrey M. Muluvi, F N Wachira, A J Simons, Ramni JamnadassAbstract:Warburgia ugandensis Sprague (Canellaceae) occurs in East and Central Africa, and the species is of great medicinal importance to the local communities where it occurs. As the wild populations diminish, planted stands will in future be used as the source of medicinal products as well as germplasm. This study investigated the levels of out-crossing rates to provide knowledge for proper planning in future cultivation programmes. The mating parameters estimated using the mixed mating model (software MLTR) showed the species to be predominantly out-crossing (89%) with significant levels of selfing. The multi-locus population out-crossing rate was higher than the single-locus population out-crossing rate (tm- ts= 0.023; SE = 0.010), implying that there was less likelihood of mating between relatives (biparental inbreeding). Low values were also obtained for the correlation of paternity, rp(s) = 0.028 (SE = 0.040) and correlation of selfing among family, rs = 0.016 (SE = 0.015). For most loci, allele frequencies of pollen and ovule contributions to the progeny genotypes were significantly different (P
Alice Muchugi - One of the best experts on this subject based on the ideXlab platform.
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analysis of the impact of domestication of warburgia ugandensis sprague on its genetic diversity based on amplified fragment length polymorphism
African Journal of Biotechnology, 2016Co-Authors: Nkatha Gacheri, Bramwel Wanjala, Ramni Jamnadass, Alice MuchugiAbstract:Warburgia ugandensis Sprague (Canellaceae) occurs in East and Central Africa and is an important multipurpose tree species. Over-exploitation of natural forests for medicinal purposes and clearance for farming threaten the species survival. Cultivation of the tree species would ensure sustainable medicinal source and its conservation. However, on-farm genetic diversity of the species is currently unknown. The genetic diversity of the on-farm W. ugandensis populations and their proximate natural populations were analyzed using the amplified fragment length polymorphism (AFLP). Four primer combinations produced a total of 223 polymorphic bands. Both the natural and on-farm populations had high genetic diversity ranging from H = 0.2892 to H = 0.1278. Principal co-ordinates analysis and dendrogram separated the ten populations into two major groups corresponding to Kenyan and Tanzanian populations, respectively. Ugandan populations were shared between the two major groups; this is probably because Uganda is believed to be the centre of diversity for W. ugandensis. Close genetic relationships between the on-farm and their proximate natural population were revealed. Analysis of molecular variance (AMOVA) revealed that a total of 54% AFLP variation resided within populations with 46% reside among populations. The high genetic diversity of W. ugandensis on-farm populations could be useful in germplasm collection and conservation strategies. Key words : Warburgia ugandensis, amplified fragment length polymorphism (AFLP), domestication, genetic diversity, on-farm, natural.
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antimicrobial drimane sesquiterpenes and their effect on endophyte communities in the medical tree warburgia ugandensis
Frontiers in Microbiology, 2014Co-Authors: Sigrid Drage, Alice Muchugi, Angela Sessitsch, Birgit Mitter, Ramni Jamnadass, Franz HadacekAbstract:Metabolite profiles (GC–MS), drimane sesquiterpenes, sugars and sugar alcohols, were compared with bacterial and fungal endophyte communities (T-RFLP, DNA clones, qPCR) in leaves and roots of the pepper bark tree, Warburgia ugandensis (Canellaceae). Ten individuals each were assessed from two locations east and west of the Great Rift Valley, Kenya, Africa, which differed in humidity and vegetation, closed forest versus open savannah. Despite organ- and partially site-specific variation of drimane sesquiterpenes, no clear effects on bacterial and fungal endophyte communities could be detected. The former were dominated by gram-negative Gammaproteobacteria, Pseudomonadaceae and Enterobacteriaceae, as well as gram-positive Firmicutes; the fungal endophyte communities were more diverse but no specific groups dominated. Despite initial expectations, the endophyte community of the pepper bark tree did not differ from other trees that much.
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vegetative propagation of warburgia ugandensis sprague an important medicinal tree species in eastern africa
Journal of Medicinal Plants Research, 2011Co-Authors: Alice Muchugi, F Akwatulira, Samson Gwali, John Bosco Lamoris Okullo, P Ssegawa, S B Tumwebaze, J R MbwamboAbstract:Warburgia ugandensis is an important medicinal tree species whose bark is widely harvested for its valuable anti-bacterial and anti-fungal properties. Consequently, this tree species is considered threatened. Therefore, this species is ranked as one of the priority species for management and conservation. This study investigated an appropriate technique for propagation of W. ugandensis using stem cuttings. Three types of stem cutting (hardwood, semi-hardwood and softwood) were obtained from Mabira Forest Reserve, Uganda and propagated in a factorial experiment using non-misting tunnels. Data on callusing root and shoot formation, number and length of roots and shoots were collected over a period of 93 days. Data manipulation was done by employing general linear model analysis of variance and Chi - square tests. There was significant variation (p < 0.05) in callus formation, root and shoot development, number and length of roots and shoots for different stem cutting types. The highest percentage of callusing, rooting and shoot regeneration (46, 49 and 57%) was recorded in softwood cuttings which also produced the highest number and longest roots and shoots. Successful propagation of W. ugandensis can therefore be appropriately achieved through softwood stem cuttings rather than either hardwood or semi-hardwood cuttings. Key words: Warburgia ugandensis, vegetative propagation, Mabira forest reserve, Canellaceae.
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isolation of high quality dna and rna from cambium of the east african greenheart warburgia ugandensis
African Journal of Biotechnology, 2009Co-Authors: Edward Muge, S Lemurt, Kornel Burg, C. A. C. Kadu, Alice Muchugi, Ramni JamnadassAbstract:The genus Warburgia belongs to the Canellaceae, a small family of tropical aromatic tree species important for their antibacterial and antifungal medicinal qualities amongst many other functions. Many published protocols for nucleic acid isolation failed to yield sufficiently good quality amounts for analysis. We have therefore developed a simple and fast CTAB (cetyl-trimethyl ammonium bromide)-based extraction protocol for routine isolation of high-quality nucleic acids. Good quality genomic DNA (gDNA) and RNA was obtained and was suitable for PCR amplification, restriction endonuclease digestion, Southern blotting and RT-PCR, respectively.
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genetic structuring of important medicinal species of genus warburgia as revealed by aflp analysis
Tree Genetics & Genomes, 2008Co-Authors: C. A. C. Kadu, Geoffrey M. Muluvi, Alice Muchugi, A J Simons, Roeland Kindt, Ramni JamnadassAbstract:The genus Warburgia (Canellaceae) contains four tree species that are of valuable medicinal importance and are all found in Africa. Genetic diversity present in wild populations of these species is under great threat due to unsustainable harvesting for medicines and indiscrimi- nate felling for timber and agricultural expansion. There is therefore an urgent need for conservation of these species. Some authors disagree about the taxonomy of the genus and list different species as synonyms. Amplified fragment length polymorphism (AFLP) technique was used to determine the genetic relationships between three species to resolve the taxonomic confusion. The amount of genetic variation within and among populations was assessed to guide strategies for their conservation and sustainable utilization. Four AFLP primer pairs (EcoRI/MseI) generated a total of 185 amplification products. Analysis of molecular variance revealed most variation among individuals within populations (63%, P<0.0001), but variation among pop- ulations (37%, P<0.0001) was highly significant as well. Constrained analysis of principal coordinates based on the Jaccard distance confirmed the separation among popula- tions (38.2%, P<0.0001). A phenetic tree and ordination graphs showed a clear distinction of W. ugandensis from W. salutaris and W. stuhlmannii. W. ugandensis populations from Uganda and western Kenya formed a subgroup that clustered away from the rest of the W. ugandensis populations. W. salutaris and W. stuhlmannii populations showed little genetic differentiation. An implication of the data to genetic management and taxonomic clarification is discussed.
Luciano Budant Schaaf - One of the best experts on this subject based on the ideXlab platform.
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MODIFICAÇÕES FLORÍSTICO-ESTRUTURAIS DE UM REMANESCENTE DE FLORESTA OMBRÓFILA MISTA MONTANA NO PERÍODO ENTRE 1979 E 2000
Universidade Federal de Santa Maria, 2006Co-Authors: Solon Jonas Longhi, Carlos Roberto Sanquetta, Franklin Galvão, Afonso Figueiredo Filho, Luciano Budant SchaafAbstract:Com o objetivo de estudar as alterações florísticas e estruturais ocorridas em uma Floresta Ombrófila Mista, localizada na Estação Experimental da UFPR (São João do Triunfo-PR), nove parcelas de 1 ha cada, avaliadas inicialmente em 1979, foram remedidas em 2000. Em 1979, todos os indivíduos arbóreos com DAP igual ou superior a 20 cm foram identificados e etiquetados e tiveram as suas alturas total e comercial e o diâmetro medidos. Em 2000, usando os mesmos critérios de inclusão, os indivíduos que não haviam sido computados em 1979 foram considerados como ingressos e os não-encontrados como mortos. Em 1979, foram encontradas 2.133 indivíduos, 51 espécies e 29 famílias. No levantamento realizado em 2000, foram encontradas 2.202 indivíduos, 55 espécies e 31 famílias. As famílias Araucariaceae, Aquifoliaceae, Lauraceae, Sapindaceae, Myrtaceae e Canellaceae foram as mais expressivas em termos de quantidade de indivíduos em ambos os levantamentos. Embora nas duas ocasiões, houvesse mais que cinquenta espécies, apenas sete espécies (Araucaria angustifolia, Ilex dumosa, Matayba elaeagnoides, Ocotea porosa, Capsicodendron dinisii, Nectandra grandiflora e Campomanesia xanthocarpa) representavam 80,4% dos indivíduos em 1979 e, no ano 2000, as mesmas sete espécies acrescidas de Ocotea corymbosa responderam por 80,9% do número total de indivíduos. Hovenia dulcis (uva-do-japão), espécie exótica, pelo número de indivíduos adultos e de regeneração, passou a configurar como uma invasora importante do ecossistema. Todos os indicadores estruturais analisados mostraram que a comunidade amadureceu no período estudado e que Araucaria angustifolia acentuou sua dominância. Houve um aumento sensível no grau de ocupação, indicado pela dominância absoluta que passou de 23,52 m2/ha, em 1979, para 28,53 m2/ha em 2000, ou seja, houve um aumento de 21,3%. Isso indica que essa comunidade está em processo de desenvolvimento, ainda não se encontrando completamente estocada. Ficou evidenciado também que a dominância da araucária se acentuou no período, sendo bem provável que tal dominância venha a aumentar ainda mais no futuro. Em relação à diversidade, observou-se que os índices que consideram tanto a quantidade de espécies (riqueza) como a uniformidade da distribuição da densidade, ou seja, os índices de Simpson, U e D de McIntosh, são os que melhor representam as alterações ocorridas no período
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Modificações florístico-estruturais de um remanescente de floresta ombrófila mista montana no período entre 1979 e 2000
Universidade Federal de Santa Maria, 2006Co-Authors: Luciano Budant Schaaf, Franklin Galvão, Carlos Roberto Sanquetta, Afonso Figueiredo Filho, Solon Jonas LonghiAbstract:The floristic and structure alterations were studied in an Ombrophyllous Mixed Forest located in São João do Triunfo (Paraná State - Brazil). Nine plots of 1ha, first evaluated in 1979, were recovered and, measured in 2000. In 1979, all the trees with dbh ≥ 20 cm were identified and tagged, and they had their commercial height and diameter measured. In 2000, based on the same criteria described before, the trees which had not been counted in 1979 were considered as ingrowth, and the missing ones were considered mortality. In 1979, 2133 individuals, 51 species and 29 families were found and in the 2000 survey, 2202 individuals, 55 species and 31 families ware journal. In both surveys, the families Araucariaceae, Aquifoliaceae, Lauraceae, Sapindaceae, Myrtaceae and Canellaceae were the most represented in terms of quantity of individuals. Although in both times more than 50 species were counted, in 1979 only 7 species (Araucaria angustifolia, Ilex dumosa, Matayba elaeagnoides, Ocotea porous, Capsicodendron dinisii, Nectandra grandiflora and Campomanesia xanthocarpa) represented 80.4% of the individuals and, in 2000, the same 7 species plus Ocotea corymbosa covered 80.9% of the total number of individuals. Hovenia dulcis, exotic specie, based on the number of adult and regeneration individuals, became to be seen as a threat to the autocnons species. All the structural indicators which were analyzed showed that the community has become more mature during the studied period and that the Araucaria angustifolia increased its dominance. There was a sensible increase of the occupancy grade, indicated by the absolutely dominance that changes from 23.52 m2/ha in 1979, to 28.53 m2/ha, in 2000, an increase of 21.3%. These results indicate that this community is still in development, and has not yet found its equilibrium. It also demonstrates that the Araucaria dominance increased in this period, suggesting that this profile can even increase future in the future. Regarding to the diversity, it was observed that the indices that consider, the amount of species (richness) and the homogeneity of the density distribution (the indexes of Simpson, U and D of McIntosh) are the ones that best represent the alterations of the period
Solon Jonas Longhi - One of the best experts on this subject based on the ideXlab platform.
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MODIFICAÇÕES FLORÍSTICO-ESTRUTURAIS DE UM REMANESCENTE DE FLORESTA OMBRÓFILA MISTA MONTANA NO PERÍODO ENTRE 1979 E 2000
Universidade Federal de Santa Maria, 2006Co-Authors: Solon Jonas Longhi, Carlos Roberto Sanquetta, Franklin Galvão, Afonso Figueiredo Filho, Luciano Budant SchaafAbstract:Com o objetivo de estudar as alterações florísticas e estruturais ocorridas em uma Floresta Ombrófila Mista, localizada na Estação Experimental da UFPR (São João do Triunfo-PR), nove parcelas de 1 ha cada, avaliadas inicialmente em 1979, foram remedidas em 2000. Em 1979, todos os indivíduos arbóreos com DAP igual ou superior a 20 cm foram identificados e etiquetados e tiveram as suas alturas total e comercial e o diâmetro medidos. Em 2000, usando os mesmos critérios de inclusão, os indivíduos que não haviam sido computados em 1979 foram considerados como ingressos e os não-encontrados como mortos. Em 1979, foram encontradas 2.133 indivíduos, 51 espécies e 29 famílias. No levantamento realizado em 2000, foram encontradas 2.202 indivíduos, 55 espécies e 31 famílias. As famílias Araucariaceae, Aquifoliaceae, Lauraceae, Sapindaceae, Myrtaceae e Canellaceae foram as mais expressivas em termos de quantidade de indivíduos em ambos os levantamentos. Embora nas duas ocasiões, houvesse mais que cinquenta espécies, apenas sete espécies (Araucaria angustifolia, Ilex dumosa, Matayba elaeagnoides, Ocotea porosa, Capsicodendron dinisii, Nectandra grandiflora e Campomanesia xanthocarpa) representavam 80,4% dos indivíduos em 1979 e, no ano 2000, as mesmas sete espécies acrescidas de Ocotea corymbosa responderam por 80,9% do número total de indivíduos. Hovenia dulcis (uva-do-japão), espécie exótica, pelo número de indivíduos adultos e de regeneração, passou a configurar como uma invasora importante do ecossistema. Todos os indicadores estruturais analisados mostraram que a comunidade amadureceu no período estudado e que Araucaria angustifolia acentuou sua dominância. Houve um aumento sensível no grau de ocupação, indicado pela dominância absoluta que passou de 23,52 m2/ha, em 1979, para 28,53 m2/ha em 2000, ou seja, houve um aumento de 21,3%. Isso indica que essa comunidade está em processo de desenvolvimento, ainda não se encontrando completamente estocada. Ficou evidenciado também que a dominância da araucária se acentuou no período, sendo bem provável que tal dominância venha a aumentar ainda mais no futuro. Em relação à diversidade, observou-se que os índices que consideram tanto a quantidade de espécies (riqueza) como a uniformidade da distribuição da densidade, ou seja, os índices de Simpson, U e D de McIntosh, são os que melhor representam as alterações ocorridas no período
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Modificações florístico-estruturais de um remanescente de floresta ombrófila mista montana no período entre 1979 e 2000
Universidade Federal de Santa Maria, 2006Co-Authors: Luciano Budant Schaaf, Franklin Galvão, Carlos Roberto Sanquetta, Afonso Figueiredo Filho, Solon Jonas LonghiAbstract:The floristic and structure alterations were studied in an Ombrophyllous Mixed Forest located in São João do Triunfo (Paraná State - Brazil). Nine plots of 1ha, first evaluated in 1979, were recovered and, measured in 2000. In 1979, all the trees with dbh ≥ 20 cm were identified and tagged, and they had their commercial height and diameter measured. In 2000, based on the same criteria described before, the trees which had not been counted in 1979 were considered as ingrowth, and the missing ones were considered mortality. In 1979, 2133 individuals, 51 species and 29 families were found and in the 2000 survey, 2202 individuals, 55 species and 31 families ware journal. In both surveys, the families Araucariaceae, Aquifoliaceae, Lauraceae, Sapindaceae, Myrtaceae and Canellaceae were the most represented in terms of quantity of individuals. Although in both times more than 50 species were counted, in 1979 only 7 species (Araucaria angustifolia, Ilex dumosa, Matayba elaeagnoides, Ocotea porous, Capsicodendron dinisii, Nectandra grandiflora and Campomanesia xanthocarpa) represented 80.4% of the individuals and, in 2000, the same 7 species plus Ocotea corymbosa covered 80.9% of the total number of individuals. Hovenia dulcis, exotic specie, based on the number of adult and regeneration individuals, became to be seen as a threat to the autocnons species. All the structural indicators which were analyzed showed that the community has become more mature during the studied period and that the Araucaria angustifolia increased its dominance. There was a sensible increase of the occupancy grade, indicated by the absolutely dominance that changes from 23.52 m2/ha in 1979, to 28.53 m2/ha, in 2000, an increase of 21.3%. These results indicate that this community is still in development, and has not yet found its equilibrium. It also demonstrates that the Araucaria dominance increased in this period, suggesting that this profile can even increase future in the future. Regarding to the diversity, it was observed that the indices that consider, the amount of species (richness) and the homogeneity of the density distribution (the indexes of Simpson, U and D of McIntosh) are the ones that best represent the alterations of the period
Yansheng Zhang - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome analysis of warburgia ugandensis to identify genes involved in terpenoids and unsaturated fatty acids biosynthesis
PLOS ONE, 2015Co-Authors: Xin Wang, Chen Zhou, Xianpeng Yang, Di Miao, Yansheng ZhangAbstract: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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De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis
2015Co-Authors: Xin Wang, Chen Zhou, Xianpeng Yang, Di Miao, Yansheng ZhangAbstract: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.
