ArticlePloS one2015
De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 12 citations in OpenAlex.
- A nearly telomere-to-telomere diploid genome assembly of Firmiana kwangsiensis, a threatened species in China.Scientific data · 2024Article
- Characterizing the microbiome recruited by the endangered plantFrontiers in microbiology · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2019Article
- Transcriptome Analysis of Cadmium-Treated Roots in Maize (Zea mays L.).Frontiers in plant science · 2016Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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