Characterization of Firmiana danxiaensis chloroplast genomes and comparative analysis of Firmiana: insight into its adaptive evolution and phylogenetic relationships

Background: Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Therefore, we sequenced its complete chloroplast (cp) genome from four locations and conducted comparative genomics analyses at both interspecific and intrageneric levels. Results The F. danxiaensis cp genomes are about 160,972 bp in size, with 112 unique genes encoded. The genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels, respectively. Selection pressure analysis revealed that Ka/Ks values of F. danxiaensis cp genomes were less than one at the interspecific level. Seven ( clpP, accD , ccsA , ndhH , rpl20 , rpoC2 , and rps4 ) positively selected genes were identified when comparing F. danxiaensis cp genomes to Sterculia monosperma and other Firmiana species, respectively. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex . However, our cp genomes did not cluster phylogenetically according to their habitat types. Conclusions The F. danxiaensis cp genomes reveal both possible environmental associated adaptation and random genetic effects in the species, which encourages further integration of geographical distances, environmental factors, and SNPs on the adaptive evolution study of F. danxiaensis .