Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

Abstract

<i>Dipteronia</i> (order Sapindales) is an endangered genus endemic to China and has two living species, <i>D</i>.sinensis and <i>D. dyeriana</i>. The plants are closely related to the genus <i>Acer</i>, which is also classified in the order Sapindales. Evolutionary studies on <i>Dipteronia</i> have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both <i>Dipteronia</i> species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (<i>p</i> < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of <i>de novo</i> and reference guided assembly, plastid genomes were obtained; that of <i>D. sinensis</i> was 157,080 bp and that of <i>D. dyeriana</i> was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of <i>D. sinensis</i> and <i>D. dyeriana</i> and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of <i>Dipteronia</i>.