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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

KEGG pathway assignment of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.
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pone.0139373.g007: KEGG pathway assignment of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.

Mentions: A total of 13,692 unigenes were mapped to 288 KEGG pathways corresponding to six KEGG modules (Fig 7, S1 Table). Most of them involved in “Environmental adaptation” (1315 unigenes), “Folding, sorting and degradation” (1220), “Carbohydrate metabolism” (1165), and “Cell growth and death” (1162). Among the 1315 unigenes participating in “Environmental adaptation”, 1233 play roles in “plant-pathogen interaction” and 156 in “Circadian rhythm—plant”. Also, we identify many unigenes mapped to important pathways for the biosynthesis of secondary metabolites, such as 293 unigenes in “Phenylpropanoid biosynthesis”, 168 in “Phenylalanine metabolism” and 180 in “Flavonoid biosynthesis” [45,46]. These unigenes may greatly contribute to the survivor and success of Firmiana species in extreme environments. By comparison with T. cacao (26,632 KEGG-annotated proteins), the number of annotated unigenes in most KEGG pathways was also less in F. danxiaensis, yet both species possessed similar percentages of annotated genes in the vast majority of KEGG pathways (Fig 7). Altogether, these nearly identical patterns observed in the GO, KOG, and KEGG annotations between F. danxiaensis and T. cacao suggested the completeness of the assembled transcriptome of F. danxiaensis.


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)

KEGG pathway assignment of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139373.g007: KEGG pathway assignment of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.
Mentions: A total of 13,692 unigenes were mapped to 288 KEGG pathways corresponding to six KEGG modules (Fig 7, S1 Table). Most of them involved in “Environmental adaptation” (1315 unigenes), “Folding, sorting and degradation” (1220), “Carbohydrate metabolism” (1165), and “Cell growth and death” (1162). Among the 1315 unigenes participating in “Environmental adaptation”, 1233 play roles in “plant-pathogen interaction” and 156 in “Circadian rhythm—plant”. Also, we identify many unigenes mapped to important pathways for the biosynthesis of secondary metabolites, such as 293 unigenes in “Phenylpropanoid biosynthesis”, 168 in “Phenylalanine metabolism” and 180 in “Flavonoid biosynthesis” [45,46]. These unigenes may greatly contribute to the survivor and success of Firmiana species in extreme environments. By comparison with T. cacao (26,632 KEGG-annotated proteins), the number of annotated unigenes in most KEGG pathways was also less in F. danxiaensis, yet both species possessed similar percentages of annotated genes in the vast majority of KEGG pathways (Fig 7). Altogether, these nearly identical patterns observed in the GO, KOG, and KEGG annotations between F. danxiaensis and T. cacao suggested the completeness of the assembled transcriptome of F. danxiaensis.

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