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De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform.

Chen SF, Li MW, Jing HJ, Zhou RC, Yang GL, Wu W, Fan Q, Liao WB - PLoS ONE (2015)

Bottom Line: Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao.Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species.Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

ABSTRACT
Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.

No MeSH data available.


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GO classification of the assembled unigenes of F. danxiaensis and the coding sequences of T. cacao.
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pone.0139373.g005: GO classification of the assembled unigenes of F. danxiaensis and the coding sequences of T. cacao.

Mentions: According to WEGO, all of the GO terms were subdivided into 50 categories. Regarding the cellular component ontology, proteins related to the “cell,” “cell part,” and “organelle” categories were the best represented. Under the molecular function ontology, proteins assigned to the “binding” and “catalytic” terms were highly encoded. Among the various biological processes, the “metabolic process,” “response to stimulus” and “biological regulation” categories were found to show the greatest number of unigenes (more than 20% in the three main categories, Fig 5). A comparison between F. danxiaensis and T. cacao showed marginally more GO-annotated unigenes in T. cacao (22,619 GO-annotated proteins in total), yet the number of annotated unigenes in each GO category was close to each other and highly significantly correlated (r = 0.996, P < 0.001, Fig 5).


De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform.

Chen SF, Li MW, Jing HJ, Zhou RC, Yang GL, Wu W, Fan Q, Liao WB - PLoS ONE (2015)

GO classification of the assembled unigenes of F. danxiaensis and the coding sequences of T. cacao.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591120&req=5

pone.0139373.g005: GO classification of the assembled unigenes of F. danxiaensis and the coding sequences of T. cacao.
Mentions: According to WEGO, all of the GO terms were subdivided into 50 categories. Regarding the cellular component ontology, proteins related to the “cell,” “cell part,” and “organelle” categories were the best represented. Under the molecular function ontology, proteins assigned to the “binding” and “catalytic” terms were highly encoded. Among the various biological processes, the “metabolic process,” “response to stimulus” and “biological regulation” categories were found to show the greatest number of unigenes (more than 20% in the three main categories, Fig 5). A comparison between F. danxiaensis and T. cacao showed marginally more GO-annotated unigenes in T. cacao (22,619 GO-annotated proteins in total), yet the number of annotated unigenes in each GO category was close to each other and highly significantly correlated (r = 0.996, P < 0.001, Fig 5).

Bottom Line: Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao.Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species.Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

ABSTRACT
Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.

No MeSH data available.


Related in: MedlinePlus