Virtual Nanopore Day, Singapore

Speaker abstracts

Niranjan Nagarajan - Genome Institute of Singapore, A*STAR

Singaporean Platinum Metagenomes – Leveraging nanopore reads for comprehensive characterization of microbial diversity in Asia

Emily Curren - National University of Singapore

Rapid profiling of cyanobacteria communities in coastal waters

Cyanobacteria are important organisms in the marine ecosystem. In this study, tropical marine cyanobacterial communities from various sites in Southeast Asia and their associated ecological parameters were examined. 16S rRNA sequences were obtained for barcode amplicon sequencing using the Nanopore MinION sequencing platform. A total of 40 genera and 46 species of cyanobacteria were identified. Species richness between sites varied according to ecological parameters such as rainfall, salinity and temperature. This is the first study that has employed this technology for phytoplankton samples with species resolution, enabling real-time monitoring and identification of harmful algal bloom species.

Jonathan Göke - Genome Institute of Singapore, National Cancer Centre Singapore

Quantification of transcript expression and RNA modifications using Nanopore RNA-Seq data

Nanopore RNA-Seq data enables the analysis of individual isoforms by providing reads that cover the full length of RNAs in the cell. In order to use the information from such long reads we have developed computational methods that enable the analysis of transcript expression and RNA modifications with high accuracy. Here I will introduce these methods (bambu and xPore) and show a comprehensive analysis of alternative splicing, promoters, novel genes, and RNA modifications using the Singapore Nanopore Expression data.

Rudolf Meier - National University of Singapore

DNA Barcoding with MinION: from food authentication to biodiversity discovery

Species identification of animal specimens and tissues via “DNA barcodes” is important for food security, pest control, environmental impact assessment, systematics, conservation, and biodiversity discovery; i.e., species identification is an essential step in many life science projects, but many projects use barcoding methods that are outdated, overly complicated, and/or too expensive. We here describe how to efficiently sequence DNA barcode amplicons with MinION. The new MinION flowcell (R10.3) can be used to barcode >5000 samples and while the Flongle is a convenient solution for up to 300 samples.

Yue Wan - Genome Institute of Singapore, A*STAR

Determination of isoform-specific RNA structure with nanopore long reads

Current methods for determening RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here, we present RNA structure analysis using nanopore sequencing (PORE-cupine),which combines structure probing using chemical modifications with direct long-read RNA sequencing and machine learning to detect secondary structures in cellular RNAs. PORE-cupine also captures global structural features, such as RNA binding protein (RBP) binding sites and reactivity differences at single nucleotide variants (SNVs). We show that shared sequences in different transcript isoforms of the same gene can fold into different structures, highlighting the importance of long-read sequencing for obtaining phase information. We also demonstrate that structural differences between transcript isoforms of the same gene lead to differences in translation efficiency. By revealing isoform-specific RNA structure, PORE-cupine will deepen our understanding of the role of structures in controlling gene regulation.