Biology subjects

Chong, J. P. J.

Publications and source records attributed to Chong, J. P. J..

4 recordsLinked to original sources

bioRxiv2023

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes

Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions, and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires a measure of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities means community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. The MIMAG standards (Bowers et al., 2017) aim to provide a method to assess metagenome quality for comparison but have not been widely adopted. To bridge this gap, the MAGqual pipeline outlined here offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability and its open-source nature promotes accessibility, community development, and ease of updates. Here, we introduce the pipeline MAGqual (metagenome-assembled genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality when compared to the MIMAG standards. MAGqual is built in Snakemake, R, and Python and is available under the MIT License on GitHub at https://github.com/ac1513/MAGqual.

bioinformatics↗

bioRxiv2023

Emergent lag phase in flux-regulation models of diauxie

Lag phase is observed in bacterial growth during a sudden change in conditions: growth is inhibited whilst cells adapt to the environment. Bi-phasic, or diauxic growth is commonly exhibited by many species. In the presence of two sugars, cells initially grow by consuming the preferred sugar then undergo a lag phase before resuming growth on the second. Biomass increase is characterised by a diauxic growth curve: exponential growth followed by a period of no growth before a second exponential growth. Recent literature lacks a complete dynamic description, artificially modelling lag phase and employing non-physical representations of precursor pools. Here, we focus on glucoselactose diauxie of Escherichia coli formulating a rational mechanistic model based on flux-regulation/proteome partitioning with a finite precursor pool that reveals core mechanisms in a compact form. Unlike earlier systems, the characteristic dynamics emerge as part of the solution, including the lag phase, and results accurately reproduce experiments. We show that for a single strain of E. coli, diauxic growth yields mathematically optimised growth rates. However, intriguingly, for two competing strains diauxic growth is not always the best strategy. Our description can be generalised to model multiple different microorganisms and investigate competition between species/strains.

microbiology↗

bioRxiv2022

Comparisons between Complete Genomes of the Eukaryotic Extremophile Galdieria sulphuraria Reveals Complex Nuclear Chromosomal Structures

Extremophiles, while typically bacteria and archaea, are also found in the eukaryotic domain of life. The eukaryote Galdieria sulphuraria is a thermoacidophilic red alga belonging to the class Cyanidiophyceae, an especially unique class as it comprises the basal clade of eukaryotic extremophiles. Galdieria species can grow both photosynthetically and heterotrophically on a variety of carbon sources, thriving down to pH 0 and temperatures up to 56 {degrees}C, while tolerating high levels of reactive oxygen species and high levels of heavy metals. Here we report whole-genome sequencing of three G. sulphuraria strains, uncovering a compact (13.1 Mb - 16.0 Mb) nuclear genome with 72-73 chromosomes, dependent on the strain.Comparative analyses of the macro synteny revealed significant structural rearrangement between G. sulphuraria isolates and the genome shows signs of sexual recombination. This, along with the large number of nuclear chromosomes compared to the genome size, reveals a mechanism of intrinsic adaptability in this eukaryotic extremophile, uncovering how G. sulphuraria can thrive in a rapidly changing extreme environment.

genomics↗

bioRxiv2022

Resolving Complexities in Taxonomic Lineages of the Organellar and Nuclear Genomes of Galdieria through Comparative Phylogenomic Analysis

Exploration of life in extreme environments allows the discovery of intriguing organisms with extraordinary biotechnological potential. An example of extreme environments is represented by hot springs, where harsh conditions (pH < 1; Temperature > 50{degrees}C; high concentrations of metals) are prohibitive for most living organisms, except for archaea, bacteria and a few eukaryotes like the unicellular red alga Galdieria. Phylogenetic analysis based on a few plastid and nuclear genes highlighted the intricate genetic structure of Galdieria and the hypothesis of diverging clades within the G. sulphuraria species. To resolve enigmatic relationships between lineages, we used plastid, mitochondrial and nuclear genome-scale data obtained from numerous strains from around the world. The resulting phylogenomic analysis identified: i) the divergence of each of the mitochondrial, plastid, and nuclear genomes into the same six clear lineages; ii) the independent evolution of the lineages; iii) the incongruent interlineages relationships between the three genomes. Differential evolutionary pressure between the strains and the genomes were also highlighted by synonymous and non-synonymous substitutions.

genomics↗