Biology subjects

Hui, T. Y.

Publications and source records attributed to Hui, T. Y..

3 recordsLinked to original sources

bioRxiv2024

Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of [~]609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

genomics↗

bioRxiv2023

Using CRISPR/Cas9 to identify genes required for mechanosensory neuron development and function

Tunicates are marine, non-vertebrate chordates that comprise the sister group to the vertebrates. Most tunicates have a biphasic lifecycle that alternates between a swimming larva and a sessile adult. Recent advances have shed light on the neural basis for the tunicate larvas ability to sense a proper substrate for settlement and initiate metamorphosis. Work in the highly tractable laboratory model tunicate Ciona robusta suggests that sensory neurons embedded in the anterior papillae of transduce mechanosensory stimuli to trigger larval tail retraction and initiate the process of metamorphosis. Here, we take advantage of the low-cost and simplicity of Ciona by using tissue-specific CRISPR/Cas9-mediated mutagenesis to screen for genes potentially involved in mechanosensation and metamorphosis, in the context of an undergraduate "capstone" research course. This small screen revealed at least one gene, Vamp1/2/3, that appears crucial for the ability of the papillae to trigger metamorphosis. We also provide step-by-step protocols and tutorials associated with this course, in the hope that it might be replicated in similar CRISPR-based laboratory courses wherever Ciona are available.

developmental biology↗

bioRxiv2023

Structural stability of the oyster gut microbiome contributes to the host's physiological tolerance to temperature fluctuations on tropical rocky shores

Extreme high thermal conditions on tropical rocky shores are challenging to the survival of intertidal ectotherms. Yet, many species are highly successful in these environments in part due to their ability to regulate intrinsic mechanisms associated with physiological stress and their metabolic demand. More recently, there has been a growing awareness that other extrinsic mechanisms, such as animal-associated microbial communities, can also influence the tolerance and survival of ectotherms under stressful conditions. However, the extent to which the intrinsic and extrinsic mechanisms are functionally linked as part of the overall adaptive response of intertidal animals to temperature change and stress is poorly understood. Here, we examined the dynamics and potential interactions of intrinsic and extrinsic mechanisms in the tropical high-supratidal oyster, Isognomon nucleus. We found that oysters modulate their internal biochemistry (oxidized PUFA products, including 5-F2t-IsoP, 10-F4t-NeuroP, 13-F4t-NeuroP, and 16-F1t-PhytoP) as part of their adaptive regulation to cope with physiological stress during periods of extreme high temperatures when emersed. However, while we detected variation in alpha diversity (ASV richness and Shannon diversity index), dominant microbial taxa and microbial functions across time, no association was found with the host biochemical profiles. The findings here suggest that the thermal condition within oysters can independently influence their intrinsic biochemical responses and extrinsic microbiome profiles. Together, these mechanisms may contribute to the thermal tolerance and survival of the oysters in the challenging conditions of the tropical high-supratidal zone.

microbiology↗