title: Comparative Transcriptome and Chloroplast Genome Analyses of Two RelatedDipteroniaSpecies.
abstract: Dipteronia(order Sapindales) is an endangered genus endemic to China and has two living species,D.sinensis andD. dyeriana. The plants are closely related to the genusAcer, which is also classified in the order Sapindales. Evolutionary studies onDipteroniahave 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 bothDipteroniaspecies. 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 (p< 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 ofde novoand reference guided assembly, plastid genomes were obtained; that ofD. sinensiswas 157,080 bp and that ofD. dyerianawas 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 ofD. sinensisandD. dyerianaand 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 ofDipteronia.
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Tao
authors: T
authors: Zhou
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Chen
authors: C
authors: Chen
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Yue
authors: Y
authors: Wei
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Yongxia
authors: Y
authors: Chang
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China; Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi ProvinceXi'an, China.
authors: Guoqing
authors: G
authors: Bai
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Zhonghu
authors: Z
authors: Li
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Nazish
authors: N
authors: Kanwal
authors: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China.
authors: Guifang
authors: G
authors: Zhao
keywords: Dipteronia; chloroplast genome; phylogenetic relationship; positive selection; purifying selection; transcriptome