A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

Abstract

Background Agarwood, generated from the Aquilaria sinensis, has high economic and medicinal value. Although its genome has been sequenced, the ploidy of A. sinensis paleopolyploid remains unclear. Moreover, the expression changes of genes associated with agarwood formation were not analyzed either. Results In the present work, we reanalyzed the genome of A. sinensis and found that it experienced a recent tetraploidization event ~ 63–71 million years ago (Mya). The results also demonstrated that the A. sinensis genome had suffered extensive gene deletion or relocation after the tetraploidization event, and exhibited accelerated evolutionary rates. At the same time, an alignment of homologous genes related to different events of polyploidization and speciation were generated as well, which provides an important comparative genomics resource for Thymelaeaceae and related families. Interestingly, the expression changes of genes related to sesquiterpene synthesis in wounded stems of A. sinensis were also observed. Further analysis demonstrated that polyploidization promotes the functional differentiation of the key genes in the sesquiterpene synthesis pathway. Conclusions By reanalyzing its genome, we found that the tetraploidization event shaped the A. sinensis genome and contributed to the ability of sesquiterpenes synthesis. We hope that these results will facilitate our understanding of the evolution of A. sinensis and the function of genes involved in agarwood formation.

Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis

“…This included, 62, 78, 120, 251, 58, 46, 41, 107, 103, 172, 68, and 44 bZIP genes in agarwood tree, A. thaliana, cotton, durian, cocoa, C. capsularis, C. olitorius, D. turbinatus, H. hainanensis, kenaf, grape, and A. trichopoda, respectively. Polyploidization might always contribute to the gene functions differentiation and number change (Song et al, 2018;Meng et al, 2021;Hou et al, 2022). Duplications and gene losses in this process are the important driving forces for shaping bZIP families The differences in bZIP genes in numerous species might result from Expression profiles of AsbZIP genes in A. sinensis stems treated with agarwood-inducer.…”

“…The ancestry of all angiosperms suffered from an ancestral whole genome triplication (WGT), followed by an additional recent WGD event that affected agarwood tree, cotton, durian, D. turbinatus, H. hainanensis, and H. cannabinus (Vanneste et al, 2014). In contrast, no additional recent polyploidization event was found in cocoa, C. capsularis, C. olitorius, grape, and A. trichopoda (Figure 3B) (Argout et al, 2011;Guan et al, 2014;Zheng et al, 2015;Canaguier et al, 2017;Lian et al, 2018;Wang et al, 2019;Meng et al, 2021;Zhang et al, 2021;Wang et al, 2022b). Interestingly, the number of bZIP genes in A. sinensis was similar to that of cocoa and grape which only experienced the angiosperms-common hexaploidy, but was noticeably less than Malvales experienced additional WGD.…”