AUTHOR=Zhou Tao , Chen Chen , Wei Yue , Chang Yongxia , Bai Guoqing , Li Zhonghu , Kanwal Nazish , Zhao Guifang 

TITLE=Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01512

DOI=10.3389/fpls.2016.01512

ISSN=1664-462X

ABSTRACT=<p><italic>Dipteronia</italic> (order Sapindales) is an endangered genus endemic to China and has two living species, <italic>D</italic>.sinensis and <italic>D. dyeriana</italic>. The plants are closely related to the genus <italic>Acer</italic>, which is also classified in the order Sapindales. Evolutionary studies on <italic>Dipteronia</italic> 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 <italic>Dipteronia</italic> 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 &gt;1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks &lt; 0.5 (<italic>p</italic> &lt; 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 <italic>de novo</italic> and reference guided assembly, plastid genomes were obtained; that of <italic>D. sinensis</italic> was 157,080 bp and that of <italic>D. dyeriana</italic> 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 <italic>D. sinensis</italic> and <italic>D. dyeriana</italic> 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 <italic>Dipteronia</italic>.</p>