| dc.description.abstract | P. cheesemanii is a close relative of A. thaliana and is an allotetraploid perennial herb that is widespread in the South Island of New Zealand. It grows at altitudes of up to 1,000 m where it is subject to relatively high levels of UV-B radiation. However, to date the origin of this species and the mechanisms underlying its tolerance to its harsh living environmental conditions such as moderate–high UV-B radiation, cold and drought is unclear.
To gain the first insights into how Pachycladon copes with UV-B stress, I sequenced the P. cheesemanii genome and compared the UV-B tolerance of plants from Wye Creek (~300-m altitude) and Kingston (~500-m altitude) with that of A. thaliana from Col-0 (~100-m altitude) and Kondara (1,000–1,100-m altitude). A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologues. A synteny analysis involving genomes from other species of the Brassicaceae family suggested that the two subgenomes of P. cheesemanii may have the same origin as species from Brassicaceae Lineage I and EII. While UV-B radiation caused greater growth reduction in A. thaliana Col-0 and Kondara than in P. cheesemanii Wye Creek, growth was not reduced in P. cheesemanii Kingston. Homologues of the A. thaliana UV-B radiation response genes have multiple copies in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii Wye Creek and Kingston may differ from that in A. thaliana. Although the P. cheesemanii genome shows close similarity with that of A. thaliana, the uniqueness of the strongly UV-B-induced UVR8-independent pathway in P. cheesemanii may help this species to tolerate relatively high UV-B radiation.
Next, to understand the different stress responses of A. thaliana and P. cheesemanii, I designed a project to build multiple-stress transcriptomes for A. thaliana and P. cheesemanii. Since plant responses to salt and drought are related and have overlapping mechanisms, and salt stress can easily be applied in the laboratory, high salinity rather than drought stress was used to stress A. thaliana and P. cheesemanii plants in this study. Transcriptomes of A. thaliana and P. cheesemanii plants in response to cold, salt and UV-B radiation stresses were created. A high-quality de novo transcriptome assembly of allopolyploid P. cheesemanii was obtained by using multiple assemblers with further downstream processing. Differential expression analysis revealed a strong bias, in terms of the number of DEGs, towards upregulation in both A. thaliana and P. cheesemanii in responding to salt stress, as well as in P. cheesemanii’s cold and UV-B treatment responses. Meanwhile, in each species, a number of DEGs was shared between stresses, although the majority were unique in responding to each stress in upregulation and downregulation, respectively.
Further, GO enrichment analysis revealed that these responsive genes were involved in some biological processes shared by A. thaliana and P. cheesemanii. Immune system processes, response to stimuli, signalling, developmental processes, growth, negative regulation of biological processes, multi-organism processes, biological regulation, secondary metabolic processes, cell communication, and cellular aromatic compound metabolic processes were common in the responses of both A. thaliana and P. cheesemanii to all three stresses. In both A. thaliana and P. cheesemanii, a number of these biological processes were also stress specific. First of all, in A. thaliana, cold stress may easily affect photomorphogenesis in cold responses, while the majority of the P. cheesemanii unique cold responses occurred in root differentiation, floral whorl development and regulation of programmed cell death. Second, A. thaliana responses to salt stress affected starch metabolism and lipid modification, whereas disaccharide and polysaccharide metabolism, as well as microtubule structure, were affected by salt stress uniquely in P. cheesemanii. Finally, A. thaliana responses to UV-B radiation involved a combination of physical and biological defences, including cell wall modification defence, stomatal movement, vitamin B6 metabolic processes and oxygen metabolic processes. In contrast, seed germination biological regulation was affected in P. cheesemanii under UV-B radiation stress. Further, P. cheesemanii had a larger number of unique GO enrichments in cold responses than did A. thaliana.
There was a wide range of crosstalk among the biological processes in responding to the three stresses in A. thaliana, while only one main cluster was identified in crosstalk for the three stress responses in P. cheesemanii. In this main cluster, the biosynthetic process for anthocyanins was in the centre position, and it was found that multiple stress-responsive biological processes probably involved anthocyanins in P. cheesemanii.
Thus, although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies such as a highly UV-B-activated UVR8-independent pathway, allowing the plant to tolerate relatively high UV-B radiation. The stress process is highly conserved in plant species under various stresses, but species also develop a few unique characteristics that may help them adapt to their own ecological niche and survive particular environmental stresses. | en_US |
