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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

Similarity and number of matches to A. thaliana, T. cacao and G. raimondii.
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pone.0139373.g002: Similarity and number of matches to A. thaliana, T. cacao and G. raimondii.

Mentions: A total of 47,211 unigenes were subjected to BLASTX similarity analysis, and 32,318 (68.5%) showed one or more hits in the NR database. For the rest (31.5%), more than 80% of them are shorter than 400bp in length (Fig 2), indicating that many of them may be too short to get hits, or lack a characterized protein domain, and some others may represent novel genes with uncharacterized functions [35–37]. Based on their top BLAST hits (highest score, S1 Table), a total of 24,370 unigenes were matched to hits in Theobroma cacao, 4,261 in Gossypium arboretum, and 460 in Vitis vinifera. All of the 30 species that provided the greatest numbers of top BLAST hits were plants, indicating extremely low contamination in our experiments. Further, a total of 32,275 unigenes showed significant matches to the protein databases of T. cacao, G. raimondii and A. thaliana (31,857 found in T. cacao, 31,081 in G. arboretum, 26,871 in A. thaliana, and 26,561 shared in these three species, Fig 3 and S1 Table). These results were not surprising, as F. danxiaensis, T. cacao and G. arboretum are all members of Malvaceae. These findings greatly contribute to the annotations of the 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)

Similarity and number of matches to A. thaliana, T. cacao and G. raimondii.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139373.g002: Similarity and number of matches to A. thaliana, T. cacao and G. raimondii.
Mentions: A total of 47,211 unigenes were subjected to BLASTX similarity analysis, and 32,318 (68.5%) showed one or more hits in the NR database. For the rest (31.5%), more than 80% of them are shorter than 400bp in length (Fig 2), indicating that many of them may be too short to get hits, or lack a characterized protein domain, and some others may represent novel genes with uncharacterized functions [35–37]. Based on their top BLAST hits (highest score, S1 Table), a total of 24,370 unigenes were matched to hits in Theobroma cacao, 4,261 in Gossypium arboretum, and 460 in Vitis vinifera. All of the 30 species that provided the greatest numbers of top BLAST hits were plants, indicating extremely low contamination in our experiments. Further, a total of 32,275 unigenes showed significant matches to the protein databases of T. cacao, G. raimondii and A. thaliana (31,857 found in T. cacao, 31,081 in G. arboretum, 26,871 in A. thaliana, and 26,561 shared in these three species, Fig 3 and S1 Table). These results were not surprising, as F. danxiaensis, T. cacao and G. arboretum are all members of Malvaceae. These findings greatly contribute to the annotations of the 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