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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.


Related in: MedlinePlus

Ks frequency plots for paralogous gene pairs from F. danxiaensis.Ks distribution components estimated using EMMIX are superimposed on the histogram. These components are hypothesized to represent background gene duplications (green) and gene duplication associated with polyploidy events (red).
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pone.0139373.g008: Ks frequency plots for paralogous gene pairs from F. danxiaensis.Ks distribution components estimated using EMMIX are superimposed on the histogram. These components are hypothesized to represent background gene duplications (green) and gene duplication associated with polyploidy events (red).

Mentions: A total of 529 paralogous genes were identified (Ks < 2). The average Ks and Ka values between these paralogous genes were 0.322 ± 0.262 and 0.070 ± 0.038, respectively. The Ks plot for paralogous genes showed one obvious peak, where Ks = 0.25 (Fig 8). Mixture model analyses revealed that two distinct components were determined for the lowest BIC (Fig 9, Table 1): the first component (centered at approximately 0.25) was considered to be indicative of a single duplication event occurring approximately 20 Mya, and the second component (centered at approximately 0.29) exhibited a large standard deviation (0.828) and was considered to reflect numerous independent duplications across time (background gene duplication) (Table 1). Three distinct components were revealed when the AIC was lowest and the BIC was slightly greater than its lowest value (Fig 9, Table 1): the first component (centered at approximately 0.21) was deemed to represent a background gene duplication, as it also showed a large standard deviation, and the second component (centered at approximately 0.25) agreed with the first component when the BIC was lowest, while the third component (centered approximately 1.33) indicated another duplication event occurring approximately 109 Mya (Table 1).


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)

Ks frequency plots for paralogous gene pairs from F. danxiaensis.Ks distribution components estimated using EMMIX are superimposed on the histogram. These components are hypothesized to represent background gene duplications (green) and gene duplication associated with polyploidy events (red).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139373.g008: Ks frequency plots for paralogous gene pairs from F. danxiaensis.Ks distribution components estimated using EMMIX are superimposed on the histogram. These components are hypothesized to represent background gene duplications (green) and gene duplication associated with polyploidy events (red).
Mentions: A total of 529 paralogous genes were identified (Ks < 2). The average Ks and Ka values between these paralogous genes were 0.322 ± 0.262 and 0.070 ± 0.038, respectively. The Ks plot for paralogous genes showed one obvious peak, where Ks = 0.25 (Fig 8). Mixture model analyses revealed that two distinct components were determined for the lowest BIC (Fig 9, Table 1): the first component (centered at approximately 0.25) was considered to be indicative of a single duplication event occurring approximately 20 Mya, and the second component (centered at approximately 0.29) exhibited a large standard deviation (0.828) and was considered to reflect numerous independent duplications across time (background gene duplication) (Table 1). Three distinct components were revealed when the AIC was lowest and the BIC was slightly greater than its lowest value (Fig 9, Table 1): the first component (centered at approximately 0.21) was deemed to represent a background gene duplication, as it also showed a large standard deviation, and the second component (centered at approximately 0.25) agreed with the first component when the BIC was lowest, while the third component (centered approximately 1.33) indicated another duplication event occurring approximately 109 Mya (Table 1).

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