In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

BMC Genomics

Jian-Feng Mao¹  Qiong Gao¹  Jie Xu¹  Hui Liu¹  Shan-Shan Zhou¹  Xian-Ge Hu¹  Kai-Hua Jia¹  Wei Zhao¹  Si-Qian Jiao¹  Yu Qing Jin¹  Yousry A. El-Kassaby²  Ilga Porth³  Zhen Xing⁴ 

[1] Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University;Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia;Départment des Sciences du Bois et de la Forêt, Avenue de la Médecine, Université Laval;Resources & Environmental College, Tibet Agriculture & Animal Husbandry University;

关键词: Cupressus gigantea;    De novo transcriptome assembly;    Ecology;    Gene family evolution;    Gene functional annotation;   

DOI  :  10.1186/s12864-019-5584-6

来源: DOAJ

【 摘 要 】

Abstract Background Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization. Results We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult C. gigantea. In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between C. gigantea and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to C. gigantea, and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members. Conclusions This study presents the first comprehensive transcriptome characterization of C. gigantea. Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer.

【 授权许可】

Unknown