ena-STUDY-Pontificia Universidad Javeriana-24-06-2018-11:55:53:242-6271
de novo transcriptome related with water stress responses in white teak, Gmelina arborea Roxb
White teak is a deciduous tropical tree that grows rapidly, and it is mainly used for the production of different timber products and for the pulp of cardboard or paper. Its rapid growth makes it a potential candidate for the generation of biofuels derived from lignocellulosic biomass. This species has commercial importance in different tropical countries, but very little is known about its biology and genetics to facilitate the use of its phenotypic characteristics. The expansion of forest plantations and reforestation programs in the tropics is largely limited by the effects of global climate change, which have impacted both temperature and rainfall regimes and incidences of abiotic and biotic stress. In Colombia, the main plantations of G. arborea are located in regions with two periods of low water availability, some with a medium-term risk of desertification. Therefore, the identification of mechanisms related to stress responses due to water deficit is relevant in this species.In this study, a transcriptome approach (RNA-seq) was used to identify genes associated with this phenotypic response. RNA from the roots and leaves of stressed Gmelina plants was sequenced by water deficit. As a non-model species, it was necessary to generate a reference transcriptome by performing a de novo assembly of the transcripts: four different methods were evaluated, among which, and according to both classical and functional annotation metrics, the meta-assembly strategy showed the best behavior. Finally, an analysis of differential expression between stressed and non-stressed organs was carried out, which allowed the identification of gene activation in the ABA-dependent and ABA-independent signaling pathways in response to stress as well as transcription factors or effector genes involved in the transport of solutes and different mechanisms of protection of cellular structures. Likewise, the study allowed the identification of EST-SSR polymorphisms associated with these transcripts, which together make this work a new genomic resource for this timber species that will facilitate the study of its response to water stress and support related breeding strategies.
White teak is a deciduous tropical tree that grows rapidly, and it is mainly used for the production of different timber products and for the pulp of cardboard or paper. Its rapid growth makes it a potential candidate for the generation of biofuels derived from lignocellulosic biomass. This species has commercial importance in different tropical countries, but very little is known about its biology and genetics to facilitate the use of its phenotypic characteristics. The expansion of forest plantations and reforestation programs in the tropics is largely limited by the effects of global climate change, which have impacted both temperature and rainfall regimes and incidences of abiotic and biotic stress. In Colombia, the main plantations of G. arborea are located in regions with two periods of low water availability, some with a medium-term risk of desertification. Therefore, the identification of mechanisms related to stress responses due to water deficit is relevant in this species.In this study, a transcriptome approach (RNA-seq) was used to identify genes associated with this phenotypic response. RNA from the roots and leaves of stressed Gmelina plants was sequenced by water deficit. As a non-model species, it was necessary to generate a reference transcriptome by performing a de novo assembly of the transcripts: four different methods were evaluated, among which, and according to both classical and functional annotation metrics, the meta-assembly strategy showed the best behavior. Finally, an analysis of differential expression between stressed and non-stressed organs was carried out, which allowed the identification of gene activation in the ABA-dependent and ABA-independent signaling pathways in response to stress as well as transcription factors or effector genes involved in the transport of solutes and different mechanisms of protection of cellular structures. Likewise, the study allowed the identification of EST-SSR polymorphisms associated with these transcripts, which together make this work a new genomic resource for this timber species that will facilitate the study of its response to water stress and support related breeding strategies.