Qiao Wen obtained her BSc. in Biological Sciences (Highest Distinction) from Nanyang Technological University in Singapore. Following her passion for plant biology and interest in computational biology, she joined Assoc. Prof. Marek Mutwil's group in Nanyang Technological University as a PhD student and have participated in various projects including the large-scale download and processing of RNA-sequencing data, where she explored the possibility of doing large-scale transcriptomic analysis (LSTrAP) in small and affordable devices (ROCK64) and on cloud computing services (Google Colaboratory), focusing on gene co-expression. To make the analyses possible for non-bioinformaticians, the LSTrAP pipelines were written with biologists in mind and are freely available on GitHub (https://github.com/tqiaowen). Complementing large-scale transcriptomic analyses, the abundance of publicly available data in the era of next generation sequencing contains troves of valuable information to be mined. To make this data accessible to the general scientific community and to combat poor quality of metadata which diminishes the usability of publicly available data, she has set up and updated the online gene expression databases https://malaria.sbs.ntu.edu.sg/ and https://conekt.sbs.ntu.edu.sg/, which also provide tools for analysis. Finally, her PhD project looked at the response of Marchantia, a basal land plant to 7 individual abiotic stresses and 19 pairwise combinations of stresses. Among the many observations, the ability to predict gene expression during combined stress conditions based on the individual stress response opens up new avenues for further investigation. She has successfully published 11 articles and reviews in journals such as Nucleic Acid Research, Nature Communications and Trends in Plant Science.
Monday session 3
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses
Q. W. TAN, P. K. LIM, Z. CHEN, A. PASHA, N. PROVART, M. AREND, Z. NIKOLOSKI, M. MUTWIL
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, SINGAPORE
The response of plants to cross-stress is poorly understood and is reported to be non-additive with respect to its single stress response. Plants are expected to be exposed to multiple stress conditions in higher frequency and of higher intensity amidst the outlook of climate change. In this study, we explored the response of Marchantia polymorpha, an early diverging land plant to 7 abiotic stresses (cold, darkness, heat, light, mannitol, nitrogen deficiency and salt) and 19 pairwise combinations through the lens of differential expression, inferred regulatory relationships, conservation of regulation with respect to Arabidopsis and the relationship between gene expression values (log2 fold-change) during single and cross-stress using linear regression. The observation of dominance, non-additivity and novel responses in cross-stress was congruent with what has been described in the literature. Regulatory relationships inferred were often stress-specific and Arabidopsis TF orthologs were responsive in a wider range of stresses in contrast to stress-specific Marchantia TFs. Remarkably, we discovered that gene expression values of cross-stress datasets could be accurately predicted with the values of single stress through linear regression, and the predictive power of single stress corresponded to its dominance in relation to other stresses.