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.

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

“…The Ks approach identified a Ks peak in most species, corroborating prior analyses (Paterson et al ; Chen et al ; Kim et al ; Teh et al ; Gao et al ). While the modes of these distributions differ between species, the full distributions overlap markedly among species, and also overlap with speciation estimates.…”

“…RNA‐Seq data were downloaded from the NCBI Sequence Read Archive for Durio zibethinus (Helicteroideae; SRR6040092; Teh et al ), Firmiana danxiaensis H.H.Hsue & H.S.Kiu (Sterculioideae; PRJNA274165; Chen et al ) and Heritiera littoralis Aiton (Sterculioideae; SRR5138318; Dassanayake et al ), Hibiscus cannabinus L. (Malvoideae; SRR2089299; Li et al ), and Corchorus capsularis L. (Grewoideae; SRR2089352; Zhang et al ,b). Table S1 summarizes transcriptome assembly statistics.…”

“…Subsequent analyses (using various lines of evidence) have attempted to infer whether this event consisted of two successive whole genome duplication/triplication events, or a single deca‐ or dodecaploidization event (Wang et al ). In addition, studies have investigated if any other Malvaceae taxa show evidence of the same event(s), namely Durio zibethinus (Teh et al ) and Firmiana danxiaensis (Chen et al ). The draft genome of D. zibethinus (Teh et al ) suggested a shared WGM history with G. raimondii ; however, while the 28 chromosomes of D. zibethinus show remarkable (hexaploid, 3×) synteny with respect to the 10 chromosomes of T. cacao , this inference is insufficient to explain the decaploid (5×) or dodecaploid (6×) multiplication history of G. raimondii relative to Theobroma .…”

The complete chloroplast genome of Firmiana danxiaensis, an endangered species endemic to Danxia landform in Southern China

“…It is considered as a dominant species and distributed only in Danxia Mountain, Guangdong Province, China. This tree species has been the focus of field investigation, community characters, and population genetic studies over the last 30 years by researchers (Fan et al 2013;Chen et al 2014;Chen et al 2015). However, the chloroplast (cp) genome information and systematics of Firmiana genus remains unclear.…”

Detection of Firmiana danxiaensis Canopies by a Customized Imaging System Mounted on an UAV Platform

“…However, in some cases where vegetation species presented low dissimilarity in spectra and texture in remote sensing images, it was difficult to distinguish among them. For instance, Firmiana danxiaensis (FD), a Chinese unique and endangered Indus species, is one example that is difficult to be detected due to its growth condition and characteristics [18].…”