Biology subjects

Tan, B. C.

Publications and source records attributed to Tan, B. C..

4 recordsLinked to original sources

bioRxiv2022

In silico comparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames in Cucumis sativus L.

Small open reading frames (sORFs) have been reported to play important roles in growth, regulation of morphogenesis, and abiotic stress responses in various plant species. However, their sequences and functions remain poorly understood in many plant species including Cucumis sativus. Cucumis sativus (commonly known as cucumber) is Asias fourth most important vegetable and the second most important crop in Western Europe. The breeding of climate-resilient cucumbers is of great importance to ensure their sustainability under extreme climate conditions. In this study, we aim to isolate the intergenic sORFs from C. sativus var. hardwickii genome and determine their sequence diversity and expression profiles in C. sativus var. hardwickii and different cultivars of C. sativus var. sativus using bioinformatics tools. We identified a total of 50,191 coding sORFs with coding potential (coding sORFs) from C. sativus var. hardwickii genome. In addition, 1,311 transcribed sORFs were detected in RNA-seq datasets of C. sativus var. hardwickii and shared homology to sequences deposited in the cucumber EST database, and among these, 91 transcribed sORFs with translation potential were detected. A total of 629 high-confident C. sativus-specific sORFs were identified in both varieties. Varietal-specific transcribed sORFs were also identified in C. sativus var. hardwickii (87) and C. sativus var. sativus (2,906). Furthermore, cultivar- and tissue-specific transcribed sORFs were identified in different cultivars and tissue samples. The findings of this study provide insight into sequence diversity and expression patterns of sORFs in C. sativus, which could help in developing climate-resilient cucumbers.

bioinformatics↗

bioRxiv2022

CRISPRi-mediated down-regulation of the cinnamate-4-hydroxylase (C4H) gene enhances the flavonoid biosynthesis in Nicotiana tabacum

Flavonoids are an important class of natural compounds present in plants. However, despite various known biological activities and therapeutic potential, the low abundance of flavonoids in nature limits their development for industrial applications. In this study, we aimed to enhance flavonoid production by silencing cinnamate-4-hydroxylase (C4H), an enzyme involved in the branch point of the flavonoid biosynthetic pathway, using the clustered regularly interspaced short palindromic repeats interference (CRISPRi) approach. We designed three sgRNAs targeting the promoter region of NtC4H and cloned them into a CRISPRi construct. After introducing into Nicotiana tabacum cell suspension culture, the transformed cells were sampled for qPCR and liquid chromatography-mass spectrometry analyses. Sixteen of 21 cell lines showed PCR-positive, confirming the presence of CRISPRi transgene. The NtC4H transcript in the transgenic cells was 0.44-fold lower than in the wild-type. In contrast, the flavonoid-related genes at the other branching pathway, such as Nt4CL and NtCHS, in the C4H-silenced cells showed a higher expression than wild-type. The upregulation of these genes increased their respective products, including pinostrobin, naringenin, and chlorogenic acid. This study provides valuable insight into the future development of CRISPRi-based metabolic engineering to suppress target genes in plants.

plant biology↗

bioRxiv2022

Waterlogging stress induces antioxidant defense responses and aerenchyma formation and alters metabolisms of banana plants

Flooding caused or exacerbated by climate change has threatened plant growth and food production worldwide. The lack of knowledge on how crops respond and adapt to flooding stress imposes a major barrier to enhancing their productivity. Hence, understanding the flooding-responsive mechanisms of crops is indispensable for developing new flooding-tolerant varieties. Here, we examined the banana (Musa acuminata cv. Berangan) responses to soil waterlogging for 1, 3, 5, 7, 14, and 24 days. After waterlogging stress, banana root samples were analyzed for their molecular and biochemical changes. We found that waterlogging treatment induced the formation of adventitious roots and aerenchyma with conspicuous gas spaces. In addition, the antioxidant activities, hydrogen peroxide and malondialdehyde contents of the waterlogged bananas increased in response to waterlogging stress. To assess the initial response of bananas toward waterlogging stress, we analyzed the transcriptome changes of banana roots. A total of 3,508 unigenes were differentially expressed under 1-day waterlogging conditions. These unigenes comprise abiotic stress-related transcription factors, such as ethylene response factors, basic helix-loop-helix, myeloblastosis, plant signal transduction, and carbohydrate metabolisms. The findings of the study provide insight into the complex molecular events of bananas in response to waterlogging stress, which could later help develop waterlogging resilient crops for the future climate.

plant biology↗

bioRxiv2021

Drought stress induces morpho-physiological and proteome changes of Pandanus amaryllifolius

Drought is one of the significant threats to the agricultural sector. However, there is limited knowledge on the plant response to drought stress and post-drought recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, is well known for its ability to survive in low-level soil moisture conditions. Understanding the molecular regulation of drought stress signaling in this plant could help guide the rational design of crop plants to counter this environmental challenge. This study aimed to determine the morpho-physiological, biochemical and protein changes of P. amaryllifolius in response to drought stress and during recovery. Drought significantly reduced leaf relative water content of P. amaryllifolius. In contrast, relative electrolyte leakage, proline and malondialdehyde contents, and the activities of antioxidant enzymes in the drought-treated and recovered samples were relatively higher than the well-watered sample. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. Of the 1,415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.

plant biology↗