Chu Hou - Profile on Academia.edu (original) (raw)

Papers by Chu Hou

Journal of Crustacean Biology, 2004

The galatheid genus Raymunida Macpherson and Machordom, 2000, is reported for the first time from... more The galatheid genus Raymunida Macpherson and Machordom, 2000, is reported for the first time from Taiwan, and the species collected is also new to science. The new species is most closely related to R. confundens Macpherson and Machordom, 2001, but differs in having a more robust cheliped and walking legs covered with distinct squammae. The coloration of the new species is probably unique in the genus by both the carapace and abdomen being uniform in color. Analysis of the mitochondrial cytochrome oxidase I gene sequences also supports the specific status of this Taiwanese form.

Mitochondrial DNA Part B, Dec 27, 2018

Macrobrachium rosenbergii de Man, 1879 (Caridea: Palaemonidae), commonly referred to as giant fre... more Macrobrachium rosenbergii de Man, 1879 (Caridea: Palaemonidae), commonly referred to as giant freshwater prawn, is commercially important worldwide, and a primary inland cultured species. The first complete mitochondrial genome of M. rosenbergii from China (CN) was sequenced and compared with that in Indonesia (ID) in this study. The results show that the total length of CN-mtDNA sequence is 15,767 bp (GenBank accession number: KY865098), which is shorter than that of ID-mtDNA (15,772 bp). It encodes 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The heavy strand and light strand encode 23 and 14 genes, respectively, and the content of A þ T is 61.81%. The gene order and content of CN-mtDNA and ID-mtDNA are identical to the primitive Pancrustacean ground pattern. Phylogenetic analysis shows that CN-mtDNA is clustered into one clade with ID-mtDNA (BP ¼100). Pairwise genetic distance analyses indicate that the genetic distance of CN-mtDNA and ID-mtDNA is 0.086, which is smaller than values between species in the Macrobrachium genus. In summary, both phylogenetic analysis and gene re-arrrangement analysis between the M. rosenbergii in China and Indonesia have revealed that their differences are within intraspecific variation.

BMC Evolutionary Biology, Jun 22, 2010

The vast sequence divergence among different virus groups has presented a great challenge to alig... more The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Bioinformatics, Apr 13, 2006

Motivation: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, b... more Motivation: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species. Result: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes.

Scientific Reports, Oct 28, 2015

Quaternary climatic cycles have influenced marine organisms' spatial distribution and population ... more Quaternary climatic cycles have influenced marine organisms' spatial distribution and population dynamics. This study aimed to elucidate the evolutionary influences of contemporary and glacial physical barriers on the population structure, demography and colonization history of the mudskipper (Periophthalmus modestus) based on a mitochondrial gene segment (ND5) from 131 individual fish sampled in the northwestern Pacific Ocean. The current Kuroshio Current and the glacial exposure of the Taiwan Strait appeared to have restricted migration among the South China Sea, coastal East China and Japan. However, genetic homogeneity (Nm>1) also suggested contemporary larval transportation by sea circulation between the East China Sea and the South China Sea or historical dispersal along the glacial exposed shoreline among China, Japan and the Ryukyu Islands. Evolutionary signals of the strengthened East Asian Summer Monsoon in the mid-Pleistocene and regional difference in intertidal primary productions were indicated by a late-Pleistocene population expansion of P. modestus with a higher effective population size in the South China Sea than in the East China Sea. Furthermore, a potential colonization origin from the South China Sea was consistently inferred by different clues, including the populations' coalescence times, the ancestral haplotype distribution, the number of private haplotypes and species/genetic diversity. Historical climatic changes are believed to have greatly influenced the coastal environment 1 and the evolutionary history of its biota 2,3 . With periodic sea-level fluctuations, marine organisms have experienced repeated habitat expansions and contractions. These historic events were imprinted in the evolutionary processes, affecting the distribution and dynamics of populations 4,5 . It has been hypothesized that a rising sea level and range expansion could result in genetic homogeneity and rapid population growth 6-9 , whereas a lowering sea level and habitat fragmentation could lead to a heterogeneous population structure 4 and a genetic bottleneck for many marine organisms 10 . The marginal seas of the northwestern Pacific Ocean (such as Indonesian seas, China seas, and the Sea of Japan/East Sea) have attracted considerable attention in phylogeographical studies due to their complicated topography and high genetic diversity . China seas (including the South China Sea, the East China Sea, the Yellow Sea and Bohai) provide a good dynamic physical model with which to test the

Scientific Reports, Dec 10, 2020

Osmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to sal... more Osmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to salinity fluctuations. The euryhaline crab Scylla paramamosain, being both an osmoconformer and osmoregulator, is an excellent model organism to investigate salinity adaptation mechanisms in brachyurans. In the present study, we used transcriptomic and proteomic approaches to investigate the response of S. paramamosain to salinity stress. Crabs were transferred from a salinity of 25 ppt to salinities of 5 ppt or 33 ppt for 6 h and 10 days. Data from both approaches revealed that exposure to 5 ppt resulted in upregulation of ion transport and energy metabolism associated genes. Notably, acclimation to low salinity was associated with early changes in gene expression for signal transduction and stress response. In contrast, exposure to 33 ppt resulted in upregulation of genes related to amino acid metabolism, and amino acid transport genes were upregulated only at the early stage of acclimation to this salinity. Our study reveals contrasting mechanisms underlying osmoregulation and osmoconformation within the salinity range of 5-33 ppt in the mud crab, and provides novel candidate genes for osmotic signal transduction, thereby providing insights on understanding the salinity adaptation mechanisms of brachyuran crabs. Osmoconformation and osmoregulation are two mechanisms that aquatic animals adopt to cope with osmotic perturbations in the environment. Most marine invertebrates and some vertebrates (e.g., sharks, skates and hagfish) osmoconform by using organic osmolytes to keep osmotic pressure of body fluids equal to that of the external environment. Organic osmolytes do not perturb cellular macromolecules but instead protect macromolecules from denaturation 1 , which is the main reason why they are utilized in osmoconformation. There are many kinds of organic osmolytes employed by different organisms 1 . In general, elasmobranchs' primary organic osmolytes are urea and trimethylamine oxide 2,3 , while most marine invertebrates mainly use free amino acids and methylamines as organic osmolytes 4 . In contrast to osmoconformation, other organisms osmoregulate, maintaining the osmotic pressure of their body fluids at levels different from that of the environment. It is widely known that most vertebrates and freshwater/estuarine invertebrates are osmoregulators, which display a differing array of osmoregulatory organs and mechanisms. For example, bony fishes osmoregulate using kidneys, gills and gut 5 , while gills and antennal glands are the primary osmoregulatory tissues in crustaceans 6 . Nevertheless, some ion transporters and ion channels, such as V-type H + ATPase, Na + /K + ATPase, Na + channel, Na + -K + -2Cl -cotransporter, and Cl -/HCO 3 -exchanger contribute to osmoregulation in both fishes and crustaceans 5-7 . As a group of crustaceans, brachyuran crabs widely distribute in waters of different salinities, including freshwater, marine, estuarine and intertidal habitats. Accordingly, different salinity adaptation strategies are found in crabs from different habitats, including both osmoconformation and osmoregulation. In details, freshwater crabs (e.g., Dilocarcinus pagei) can osmoregulate via active ion transport . It is proposed that active salt absorption in the gills of freshwater crabs is accomplished via a suite of ion transporters and supporting enzymes: Na + absorption occurs via a combination of apical Na + channel and V-type H + ATPase, and the basolateral Na + /K + ATPase, while Cl -absorption is accomplished via apical co-transport, Cl -/HCO 3 -exchanger and basolateral

Molecular Ecology, 2010

Sargassum hemiphyllum is commonly found in Japan and Korea, with a variety, var. chinense, that i... more Sargassum hemiphyllum is commonly found in Japan and Korea, with a variety, var. chinense, that is found distributed in the southern Chinese coast. We previously reported distinct genetic differentiation between the two taxa based on the PCR-RFLP data of plastid RubiscoL-S spacer. The present study aims at elucidating the phylogeographic pattern of S. hemiphyllum based on more markers in the nuclear and extranuclear genomes, with a view to reveal the occurrence of hybridization. The two allopatrically distributed taxa were found to be genetically distinct in nuclear ITS2, plastidial Rubisco (Rbc) and mitochondrial TrnW_I (Trn) spacers. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the late Miocene (6.58-11.25 Mya). Divergence within both S. hemiphyllum and the chinense variety was observed based on Trn spacer, while the divergence in S. hemiphyllum was further confirmed in Rbc spacer. This divergence appears to correspond to the separation of the Japanese populations between the Sea of Japan and the Pacific that occurred around 0.92-2.88 Mya (the early Pleistocene). The presence of an ITS2 clone resembling var. chinense sequences in a Japanese population of S. hemiphyllum (JpNS) raises the possibility of the introgression of var. chinense individuals into S. hemiphyllum population. Compared to that between S. hemiphyllum and the chinense variety, hybridization among the Japanese and Korean populations of S. hemiphyllum is highly probable as all these individuals share a pool of nuclear ITS2 sequences, possibly attributable to incomplete concerted evolution of ITS2.

The First Internal Transcribed Spacer (ITS-1) of Ribosomal DNA as a Molecular Marker for Phylogenetic and Population Analyses in Crustacea

Marine Biotechnology, 2001

The objective of the present study is to explore the feasibility of using the first internal tran... more The objective of the present study is to explore the feasibility of using the first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for studying the interspecific and intraspecific genetic variations among crustaceans. We designed primers that could amplify ITS-1 from a majority of taxonomic groups of crustaceans. The gene was found to exhibit a high degree of length polymorphism among different groups, ranging from 182 bp in the barnacle Balanus amphitrite to approximately 820 bp in the spiny lobster Panulirus japonicus. With respect to differences between congeneric species, it was found that the ITS-1 sequences of 3 mitten crabs, Eriocheir sinensis, Eriocheir leptognathus, and Eriocheir formosa, exhibit 5.4% to 16.3% nucleotide divergence, suggesting that ITS-1 is informative for phylogenetic analysis at the species level. Yet there are extensive (0.9%-2.3%) variations within individual E. formosa, so that phylogenetic analyses could be obscured. ITS-1 was found to vary between 2 geographical populations of the shrimp Penaeus japonicus. The variations involved substitutions as well as insertions/deletions between shrimp from Australia and South China Sea. These results show that ITS-1 is highly divergent among different crustaceans and could be an appropriate marker for molecular systematic studies at the species and population levels, although the presence of intragenomic variation needs to be taken into consideration.

Molecular Coordinated Regulation of Gene Expression During Ovarian Development in the Penaeid Shrimp

Marine Biotechnology, 2007

To understand the molecular events of ovarian development in penaeid shrimp, RNA arbitrarily prim... more To understand the molecular events of ovarian development in penaeid shrimp, RNA arbitrarily primed polymerase chain reaction (RAP-PCR) was used to identify differentially expressed genes during ovarian maturation in Metapenaeus ensis. From a screening of 700 clones in a cDNA library of the shrimp ovary by the products of RAP-PCR of different maturation stages, 91 fragments with differentially expressed pattern as revealed by dot-blot hybridization were isolated and sequenced. Forty-two of these fragments show significant sequence similarity to known gene products and the differentially expressed pattern of 10 putative genes were further characterized via Northern hybridization. Putative glyceraldehyde-3-phosphate dehydrogenase and arginine kinase are related to provision of energy for active cellular function in oocyte development. Translationally controlled tumor protein, actin, and keratin are related to the organization of cytoskeleton to accomplish growth and development of oocytes. High mobility group protein DSP1, heat shock protein 70, and nucleoside diphosphate kinase may act as repressors before the onset of ovarian maturation. Peptidyl-prolyl cis-trans isomerase and glutathione peroxidase are related to the stabilization of proteins and oocytes. This study provides new insights on the molecular events in the ovarian development in the shrimp.

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Journal of Experimental Marine Biology and Ecology, 2006

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from Chi... more Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which ...

Animal Genetics, 2006

SummaryIn this study, microsatellite markers were developed for the genetic linkage mapping and b... more SummaryIn this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite‐containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT‐rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35–48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon‐primed intron‐crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non‐EST‐associated microsatellites and tw...

Molecular Phylogenetics and Evolution, May 1, 2019

One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or... more One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or cold water Pandaloidea, largely because this species-rich group of nearly 200 species in 25 genera exhibits a very high diversity of body forms and ecology. Although the relationships amongst the taxa within Pandaloidea have been repeatedly discussed based on morphology, no comprehensive molecular phylogeny exists. In this study, we present the first molecular phylogeny of the group, based on a combined dataset of two mitochondrial (12S and 16S rRNA) and six nuclear (ATP synthase β-subunit, enolase, glyceraldehyde-3-phosphate dehydrogenase, histone 3, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase α-subunit) markers, based on 62 species (about 1/3 of known biodiversity) in 22 genera (88% of genera) of two pandaloid families (Pandalidae, Thalassocarididae) and outgroups from seven other caridean families. With generally high support, the relationships within the clade are fully resolved. Pandalidae is shown to be paraphyletic with Thalassocarididae deeply nested within as a monophyletic group, and the latter is herein considered to be a synonym of Pandalidae. Five major clades are recovered, with the shallow water genera Anachlorocurtis, Chlorocurtis, Chlorotocella and Miropandalus forming a sister clade to the remaining genera. At the genus level, the phylogeny indicates Plesionika, Heterocarpus and Pandalus to be not monophyletic. The validity of Pandalopsis, Stylopandalus and Calipandalus is challenged and these genera are considered herein to be junior synonyms of Pandalus (Pandalopsis) and Plesionika (Stylopandalus and Calipandalus). Although not fully resolved, some evidence potentially considers Nothocaris to be a valid genus. Ancestral State Reconstruction successfully recovered 15 synapomorphies for the major clades, with 11 of them reported to be of systematic significance for the first time.

$Research paper thumbnail of The genomic tree of living organisms based on a fractal model$

Physics Letters, Oct 1, 2003

Accumulation of complete genome sequences of living organisms creates new possibilities to discus... more Accumulation of complete genome sequences of living organisms creates new possibilities to discuss the phylogenetic relationships at the genomic level. In the present study, a fractal model is proposed to simulate a kind of visual representation of complete genome. The estimated parameters in the fractal model is used to define the genetic distance between two organisms. Because we take into account all genome content including both coding and non-coding regions, the phylogenetic tree from such an analysis leads to alternate classification of genomes that is called a genomic tree. This method of phylogenetic analysis does not require sequence alignment of homologous genes and relies instead on our fractal analysis, so it can avoid artefacts associated with sequence alignment. The similarity in related organisms based on the fractal model of the complete genome is global. Our result from such an analysis of more than 50 genomes indicates that lateral gene transfer must have been very common in the early history of life and thus constitutes a major source of variations in a substantial proportion of prokaryotic genome.

International Journal of Molecular Sciences, Mar 18, 2010

A shortcoming of most correlation distance methods based on the composition vectors without align... more A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the "distances" are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old "distance" and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis.

Journal of Proteomics, Feb 1, 2017

Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryoni... more Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata, a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others. Comparison of gene expression levels between tissues showed that 22 PVF genes were exclusively expressed in albumen gland, the female organ that secretes PVF. Base substitution analysis of PVF and housekeeping genes between P. maculata and its closely related species Pomacea canaliculata showed that the reproductive proteins had a higher mean evolutionary rate. Predicted 3D structures of selected PVF proteins showed that some nonsynonymous substitutions are located at or near the binding regions that may affect protein function. The proteome and sequence divergence analysis revealed a substantial amount of maternal investment in embryonic nutrition and defense, and higher adaptive selective pressure on PVF protein-coding genes when compared with housekeeping genes, providing insight into the adaptations associated with the unusual reproductive strategy in these mollusks. Significance: There has been great interest in studying reproduction-related proteins as such studies may not only answer fundamental questions about speciation and evolution, but also solve practical problems of animal infertility and pest outbreak. Our study has demonstrated the effectiveness of an integrated proteomic and transcriptomic approach in understanding the heavy maternal investment of proteins in the eggs of a nonmodel snail, and how the reproductive proteins may have evolved during the transition from laying underwater eggs to aerial eggs.

BMC Genomics, Apr 30, 2021

Background: The complex life cycle of the coconut crab, Birgus latro, begins when an obligate ter... more Background: The complex life cycle of the coconut crab, Birgus latro, begins when an obligate terrestrial adult female visits the intertidal to hatch zoea larvae into the surf. After drifting for several weeks in the ocean, the postlarval glaucothoes settle in the shallow subtidal zone, undergo metamorphosis, and the early juveniles then subsequently make their way to land where they undergo further physiological changes that prevent them from ever entering the sea again. Here, we sequenced, assembled and analyzed the coconut crab genome to shed light on its adaptation to terrestrial life. For comparison, we also assembled the genomes of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus, and the short-tailed marine-living red king crab, Paralithodes camtschaticus. Our selection of the latter two organisms furthermore allowed us to explore parallel evolution of the crab-like form in anomurans. Results: All three assembled genomes are large, repeat-rich and AT-rich. Functional analysis reveals that the coconut crab has undergone proliferation of genes involved in the visual, respiratory, olfactory and cytoskeletal systems. Given that the coconut crab has atypical mitochondrial DNA compared to other anomurans, we argue that an abundance of kif22 and other significantly proliferated genes annotated with mitochondrial and microtubule functions, point to unique mechanisms involved in providing cellular energy via nuclear proteincoding genes supplementing mitochondrial and microtubule function. We furthermore detected in the coconut crab a significantly proliferated HOX gene, caudal, that has been associated with posterior development in Drosophila, but we could not definitively associate this gene with carcinization in the Anomura since it is also significantly proliferated in the ornate spiny lobster. However, a cuticle-associated coatomer gene, gammacop, that is significantly proliferated in the coconut crab, may play a role in hardening of the adult coconut crab abdomen in order to mitigate desiccation in terrestrial environments.

International Archives of Allergy and Immunology, 2015

Background: Shellfish hypersensitivity is among the most common food allergies. A murine model of... more Background: Shellfish hypersensitivity is among the most common food allergies. A murine model of IgE-mediated shrimp allergy has been established in our laboratory. The aim of this study is to determine the intestinal histological changes and cytokine expression profile of this model sensitized with the major shellfish allergen tropomyosin. Methods: Female Balb/c mice orally sensitized and challenged with recombinant tropomyosin were sacrificed. Continuous sections of duodenum, jejunum and ileum were prepared using the Swiss roll technique for histological and immunological analysis. Duodenal epithelial cell apoptosis and migration were examined. mRNA expression of IL-4, IL-6, IL-10, IL-13, IL-18 and IFN-γ in intestinal tissue was measured via RT-PCR. Results: In tropomyosin-sensitized and challenged mice, an increased number of eosinophils, mast cells and

Frontiers in Cell and Developmental Biology

Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well kno... more Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that ar...

Journal of Marine Science and Engineering, 2022

The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a... more The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species native to the estuarine-coast of the Pearl River Delta in southern China. The species—with scientific, ecological, cultural, and nutritional importance—has been farmed for hundreds of years. However, there is only limited information on its genetics, stress adaptation mechanisms, and gut microbiota, restricting the sustainable production and use of oyster resources. Here, we present population structure analysis on M. hongkongensis oysters collected from Deep Bay and Lantau Island in Hong Kong, as well as transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis oysters collected from Deep Bay. Single nucleotide polymorphisms (SNPs), including those on the homeobox genes and heat shock protein genes, were revealed by the whole genome resequencing. Transcriptomes of oysters incubated at 25 °C and 32 °C for 24 h were sequenced wh...