J Syst Evol ›› 2019, Vol. 57 ›› Issue (5): 440-450.DOI: 10.1111/jse.12469

• Research Articles • Previous Articles     Next Articles

Comparative transcriptomes and development of expressed sequence tag‐simple sequence repeat markers for two closely related oak species

Jing-Jing Sun1, Tao Zhou2, Rui-Ting Zhang1, Yun Jia1, Yue-Mei Zhao3, Jia Yang1, and Gui-Fang Zhao1*   

  1. 1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
    2School of Pharmary, Xi’an Jiaotong University, Xi’an 710061, China
    3College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, Shaanxi, China
  • Received:2017-12-01 Accepted:2018-10-07 Online:2019-01-15 Published:2019-09-01


Quercus species comprise the major genera in the family Fagaceae and they are widely distributed in the Northern Hemisphere. Many Quercus species, including several endemics, are distributed in China. Genetic resources have been established for the important genera but few transcriptomes are available for Quercus species in China. In this study, we used Illumina paired‐end sequencing to obtain the transcriptomes of two oak species, Q. liaotungensis Koidz. and Q. mongolica Fisch. ex Turcz. Approximately 24 million reads were generated and then a total of 103 618 unigenes were obtained after assembly for both species. Comparative transcriptome analyses of both species identified a total of 12 981 orthologous contigs. The Ka/Ks estimation and enrichment analysis indicated that 1179 (9.08%) orthologs showed rapid evolution, and most of these orthologs were related to functions comprising “DNA repair”, “response to cold”, and “response to drought”. This findings could provide some insights into how these two closely related Quercus species adapted to extreme environments characterized by aridity and cold. The divergence time (approximately 4.27–5.93 Mya) between the two Quercus species was estimated according to the Ks distribution. Moreover, 16 608 simple sequence repeat loci were detected and 12 363 primer pairs were designed. Subsequently, 158 of the 12 363 primer pairs were randomly selected to test the polymorphisms and 92 of the primer pairs were successfully amplified in the two oak species. The resultant orthologs and simple sequence repeat markers are valuable for genetic differentiation analyses and evolutionary studies of Quercus.

Key words: de novo assembly, genetic differentiation, positive selection, Quercus, RNA sequencing