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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

KOG functional classification of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.
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pone.0139373.g006: KOG functional classification of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.

Mentions: The coding regions obtained for the 28,615 unigenes were translated into proteins, among which 13,664 showed significant matches with the KOG databases and were classified into 26 KOG clusters (Fig 6, S1 Table). The top four categories with the greatest number of unigenes were “Signal transduction mechanisms” (2049), “General function prediction only” (1907), “Posttranslational modification, protein turnover, chaperones” (1581), and “Function unknown” (994). The four categories with the fewest unigenes were “Multiple function” (1), “Cell motility” (7), “Extracellular structures” (74) and “Nuclear structure” (99). Also, we identified 578 unigenes annotated to “Secondary metabolites biosynthesis, transport and catabolism”, which may play important roles in plant defense mechanisms [42].


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)

KOG functional classification 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.g006: KOG functional classification of the assembled unigenes of F. danxiaensis and the protein sequences of T. cacao.
Mentions: The coding regions obtained for the 28,615 unigenes were translated into proteins, among which 13,664 showed significant matches with the KOG databases and were classified into 26 KOG clusters (Fig 6, S1 Table). The top four categories with the greatest number of unigenes were “Signal transduction mechanisms” (2049), “General function prediction only” (1907), “Posttranslational modification, protein turnover, chaperones” (1581), and “Function unknown” (994). The four categories with the fewest unigenes were “Multiple function” (1), “Cell motility” (7), “Extracellular structures” (74) and “Nuclear structure” (99). Also, we identified 578 unigenes annotated to “Secondary metabolites biosynthesis, transport and catabolism”, which may play important roles in plant defense mechanisms [42].

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