Biology subjects

Chung, H.-H.

Publications and source records attributed to Chung, H.-H..

5 recordsLinked to original sources

bioRxiv2025

Crowning the King of Fruits: Genomic Evidence of Population Structure and Relatedness in Malaysian Durians

Durian (Durio zibethinus), often dubbed the King of Fruits, is a high-value tropical crop native to Southeast Asia and widely cultivated in Malaysia. Revered for its unique flavor yet polarizing for its pungent aroma, durian holds significant cultural and economic importance across the region. Despite this, genomic research on Malaysian durian cultivars remains limited. We performed whole-genome sequencing of several renowned and local durian cultivars, including Musang King (D197), Sultan (D24), Black Thorn (D200), Muar Gold (D101), and Red Prawn (D13) collected from distinct geographic regions across Malaysia. Illumina sequencing yielded approximately 20 to 30x coverage per sample, sufficient for single-nucleotide polymorphism (SNP) detection and population genomic analyses. Principal component analysis (PCA) based on genome-wide SNPs revealed visible population stratification and varying degrees of genetic relatedness among Malaysian durians. Subsequent KING kinship analysis indicated that most cultivars are relatively clonal, with the notable exception of the reference Musang King genome, which appeared genetically heterogeneous compared to other Musang King samples, a finding further supported by population structure inference from admixture analysis and ITS1-5.8S-ITS2 haplotyping. Notably, the Black Thorn cultivar showed no relatedness to Malaysian varieties but exhibited distant genetic similarity to the northern Thai Kan Yao variety. These results provide new genomic insights into the population structure, cultivar differentiation, and potential hybridization among Malaysian durians, forming a valuable foundation for future molecular marker development and breeding programs aimed at different variety authentication and genetic improvement.

genomics↗

bioRxiv2022

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.5 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 84.3%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 53 Actinopterygii species and two outgroups was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.

genomics↗

bioRxiv2021

First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)

The sago palm (Metroxylon sagu Rottboll) is a all-rounder palm, it is both a tropical halophytic starch-producing palm as well as an ornamental plant. Recently, a genome survey was conducted on this palm using Illumina sequencing platform but the BUSCO genome completeness is very low (21.5%) and most of them ([~]78%) are either fragmented or missing. Thus, in this study, the sago palm genome completeness was further improved with the utilization of the Nanopore sequencing platform that produced longer reads. A hybrid genome assembly was conducted and the outcome was a much complete sago palm genome with BUSCO completeness achieved at as high as 97.9% with only [~]2% of them either fragmented or missing. The estimated genome size of the sago palm is 509,812,790 bp in this study. A sum of 33,242 protein-coding genes were revealed from the sago palm genome and around 96.39% of them had been functionally annotated. An investigation on the carbohydrate metabolism KEGG pathways also unearthed that starch synthesis was one of the major sago palm activities. These data are indispensable for future molecular evolutionary and genome-wide association studies. Specifications Table O_TBL View this table: org.highwire.dtl.DTLVardef@1a2dc6aorg.highwire.dtl.DTLVardef@134e433org.highwire.dtl.DTLVardef@171efa9org.highwire.dtl.DTLVardef@12d6f26org.highwire.dtl.DTLVardef@1dc32a6_HPS_FORMAT_FIGEXP M_TBL C_TBL Value of the DataO_LIFirst complete genome dataset for the eco-economic important sago palm (Metroxylon sagu Rottboll). C_LIO_LIHigh completeness of sago palm genomic dataset will facilitate future researches, such as genome-wide association studies. C_LIO_LIThe data is useful in pioneering sago palm genetic landscape investigations which in turn unmask the mystery behind its high starch yield, salinity tolerance and disease resistance. C_LI

genomics↗

bioRxiv2019

High Spatial Resolution Ambient Ionization Mass Spectrometry Imaging Using Microscopy Image Fusion

Mass spectrometry imaging (MSI) using ambient ionization technique enables a direct chemical investigation of biological samples with minimal sample pretreatment. However, detailed morphological information of the sample is often lost due to its limited spatial resolution. In this study, predictive high-resolution molecular imaging was produced by the fusion of ambient ionization MSI with optical microscopy of routine hematoxylin and eosin (H&E) staining produces. Specifically, desorption electrospray ionization (DESI) and nanospray desorption electrospray ionization (nanoDESI) mass spectrometry are employed to visualize lipid and protein species on mice tissue sections. The resulting molecular distributions obtained by ambient ionization MSI-microscopy fusion are verified with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MSI and immunohistochemistry (IHC) staining. Label-free molecular imaging with 5-m spatial resolution can be acquired using DESI and nanoDESI, whereas the typical spatial resolution of ambient ionization MSI is ~100 m. In this regard, sharpened molecular histology of tissue sections is achieved, providing complementary references to the pathology. Such a multimodality integration enables the discovery of potential tumor biomarkers. After image fusion, more than a dozen of potential biomarkers that could be used to determine the tumor margins on a metastatic mouse lung tissue section and Luminal B breast tumor tissue section are identified.

bioinformatics↗

bioRxiv2019

Structural Lipidomics and Molecular Imaging of C=C Positional Isomers Enabled by mCPBA Epoxidation with Tandem Mass Spectrometry

Cellular lipidome is highly regulated through lipogenesis, rendering diverse double-bond positional isomers (C=C isomer) of a given unsaturated lipid species. In recent years, there are increasing reports indicating the physiological roles of C=C isomer compositions associated with diseases, while the biochemistry has not been fully understood due to the challenge in characterizing lipid isomers inherent to conventional mass spectrometry-based lipidomics. To address this challenge, we reported a universal, user-friendly, derivatization-based strategy, MELDI (mCPBA Epoxidation for Lipid Double-bond Identification), which enables both large-scale identification and spatial mapping of biological C=C isomers using commercial mass spectrometers without any instrument modification. With the developed liquid-chromatography mass spectrometry (LC-MS) lipidomics workflow, we elucidated more than 100 isomers among mono- and poly-unsaturated fatty acids and glycerophospholipids in both human serum, where novel isomers of low abundance were unambiguously quantified for the first time. The capability of MELDI-LC-MS in lipidome analysis was further demonstrated using the differentiated 3T3-L1 adipocytes, providing an insight into the cellular lipid reprogramming upon stearoyl-coenzyme A desaturase 1 (SCD1) inhibition. Finally, we highlighted the versatility of MELDI coupled with mass spectrometry imaging to spatially resolve cancer-associated alteration of lipid isomers in a metastatic mouse tissue section. Our results suggested that MELDI will contribute to current lipidomics pipelines with a deeper level of structural information, allowing us to investigate underlying lipid biochemistry.

biochemistry↗