title: De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform.
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.
authors.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.
authors.forename: Su-Fang
authors.initials: SF
authors.lastname: Chen
authors.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.
authors.forename: Ming-Wan
authors.initials: MW
authors.lastname: Li
authors.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.
authors.forename: Hui-Juan
authors.initials: HJ
authors.lastname: Jing
authors.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.
authors.forename: Ren-Chao
authors.initials: RC
authors.lastname: Zhou
authors.affiliation: National Engineering Resarch Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Gui-Li
authors.initials: GL
authors.lastname: Yang
authors.affiliation: South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.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.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fan
authors.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.
authors.forename: Wen-Bo
authors.initials: WB
authors.lastname: Liao
mesh_terms: D000222:Adaptation, Physiological; D002681:China; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D063990:Gene Ontology; D017343:Genes, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D014197:Trees / Q000235:genetics* / Q000254:growth & development