Mun Hua Tan

Mun Hua Tan
University of Melbourne | MSD · Department of Microbiology and Immunology

PhD

About

99
Publications
17,284
Reads
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827
Citations
Citations since 2016
60 Research Items
753 Citations
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150

Publications

Publications (99)
Article
The mitochondrial genome of the rare endemic New Guinean dasyurid Phascolosorex doriae ( Thomas 1886 ) has been used to clarify relationships within ‘phascolosoricinae’. The mitochondrial genome has the typical gene arrangement seen in other marsupials. Molecular analyses using complete mitogenomes of other dasyurids resolve the red-bellied dasyure...
Article
Full-text available
Oil spills pose a significant threat to marine biodiversity. Crude oil can partition into sediments where it may be persistent, placing benthic species such as decapods at particular risk of exposure. Transcriptomic and histological tools are often used to investigate the effects of hydrocarbon exposure on marine organisms following oil spill event...
Preprint
Full-text available
At a time when effective tools for monitoring malaria control and eradication efforts are crucial, the increasing availability of molecular data motivates their application to epidemiology. The multiplicity of infection (MOI), defined as the number of genetically distinct parasite strains co-infecting a host, is one key epidemiological parameter fo...
Article
Full-text available
The evolution of Australia’s distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea—the clade comprising kangaroos and their relatives—tha...
Article
The mitochondrial genome of the rare endemic New Guinean dasyurid Phascolosorex doriae (Thomas 1886) has been used to clarify relationships within ‘phascolosoricinae’. The mitochondrial genome has the typical gene arrangement seen in other marsupials. Molecular analyses using complete mitogenomes of other dasyurids resolve the red-bellied dasyure a...
Preprint
Full-text available
The evolution of Australia’s distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea — the clade comprising kangaroos and their relatives —...
Article
Worldwide, rising ocean temperatures are causing declines and range shifts in marine species. The direct effects of climate change on the biology of marine organisms are often well documented, yet knowledge on the indirect effects, particularly through trophic interactions, is largely lacking. We provide evidence of ocean warming decoupling critica...
Article
Full-text available
Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Gi...
Article
Full-text available
Body composition (fat, skeletal muscle and bone mass) is an important determinant of overall health and risk of endocrine disorders such as type 2 diabetes and osteoporosis. Although diet and physical activity are strongly implicated, body composition is also heritable. We conducted a discovery genome-wide association study on 31 phenotypes from th...
Article
Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for crustacean phylogenomics. The recovery of high-copy-number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach based on our research with freshwater crayfishes (Astacidea). We explored the po...
Preprint
Full-text available
Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for animal phylogenomics. The recovery of high copy number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach. In this study, we explore the potential of the genome skimming (GS) to recover addi...
Preprint
Full-text available
Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula virulence and ecology. Given t...
Article
Full-text available
Freshwater catfish of the genus Clarias, known as the airbreathing catfish, are wide spread and important for food security through small scale inland fisheries and aquaculture. Limited genomic data are available for this important group of fishes. The bighead catfish (Clarias macrocephalus) is a commercial aquaculture species in south-east Asia us...
Article
Full-text available
Main conclusion The rice leaf mitochondrial DNA is more methylated compared to the rice grain mitochondrial DNA. The old rice leaf mitochondrial DNA has also a higher methylation level than the young rice leaf mitochondrial DNA. Abstract The presence of DNA methylation in rice organelles has not been well characterized. We have previously shown th...
Article
Full-text available
We present the first draft genome of the snout otter clam (L. rhynchaena) based on relatively large volumes of short and long genomic reads from Illumina and ONT platforms, respectively, providing sufficient sequencing depth to facilitate the generation of one of the best quality genome assemblies for a bivalve mollusk. The use of long Nanopore rea...
Article
Full-text available
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected stud...
Thesis
Decapod crustaceans include popular seafoods such as shrimps, crabs, crayfish and lobsters. High-throughput DNA sequencing was used to study mitochondrial genomes of poorly-known decapod species and conduct large-scale comparative genomic studies. The thesis findings provide valuable insights into the evolution of decapod crustaceans and generated...
Article
Full-text available
Key message Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Abstract Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We h...
Article
Full-text available
Characterising adaptive genetic divergence among conspecific populations is often achieved by studying genetic variation across defined environmental gradients. In marine systems this is challenging due to a paucity of information on habitat heterogeneity at local and regional scales and a dependency on sampling regimes that are typically limited t...
Article
Crude oil is a key contaminant in aquatic environments entering via natural and anthropogenic sources, causing toxicity in marine organisms. Traditionally, biomarkers have been utilised to determine crude oil exposure and effects in aquatic organisms, however advances in genomic technologies has led to increased adoption of transcriptomic approache...
Article
Full-text available
Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphologica...
Article
Full-text available
Background Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism...
Article
Full-text available
The whale shark (Rhincodon typus) is an iconic and endangered species with a broad distribution spanning warm-temperate and tropical oceans. Effective conservation management of the species requires an understanding of the degree of genetic connectivity among populations, which is hampered by the need for sampling that involves invasive techniques....
Article
To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's larges...
Article
Full-text available
One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell, 1838), a freshwater species that can grow to ∼1.8 metres in length and live ≥ 48 years of age. The Murray cod is of conservation concern as a result of strong population contractions, but is also popular for recreational fishing and is of growing aquaculture...
Article
Molecular phylogenetics has benefited tremendously from the advent of next-generation sequencing, enabling quick and cost-effective recovery of whole mitogenomes via an approach referred to as ‘genome skimming’. Recently, genome skimming has been utilised to recover highly repetitive nuclear genes such as 18S and 28S ribosomal RNA genes that are us...
Article
Full-text available
Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups....
Data
Summary of characteristics of mitogenomes presented in this study.
Data
Corrected genbank format files for mitogenomes with possible mis-annotations.
Data
Pairwise nucleotide identity of shrimp mitogenomes.
Data
Phylogeny of shrimps based on different mitochondrial gene set and sequence type. All trees were constructed using IQ-TREE with optimized partitioning scheme. Trees were rooted with members of Dendrobranchiata as the outgroup. Red stars next to tip labels indicate mitogenomes reported in this study. PCG, protein coding gene; ML, maximum likelihood;...
Data
Annotated 5 whole mitogenome reported in this study. Genbank files containing the annotated whole mitogenome sequence of 5 shrimps reported in this study.
Data
Comparison of number of genes, mitogenome lengths, AT content and control region lengths of mitogenomes from Axiidea, Gebiidea and Caridea.
Data
Codon usage for species with Ax1, Ax2 and Gr mitogenome organization. Encoded amino acid and its corresponding p-value (> or <0.001) is shown at the top of each box plot while synonymous codons are indicated on the x-axis.
Data
Relative synonymous codon usage (RSCU) values from codon usage analysis.
Data
Corrected genbank format files for mitogenomes with possible mis-annotations.
Article
Full-text available
The complete mitochondrial genomes of four fish species of the commercially important family Latidae were sequenced using the Illumina MiSeq, thereby significantly increasing the mitogenomic resources for the family. Whole mitogenome-based phylogenetic analysis supports the monophyly of the genus Lates and more generally the family Latidae. The mit...
Article
Full-text available
A total of eight Ensifer sp. strains were isolated from two pristine cave environments. One strain was isolated from a cave water pool located in the Wind Cave National Park, South Dakota, USA and the remaining seven strains were isolated from Lechuguilla Cave of Carlsbad Caverns National Park, New Mexico, USA. Whole genome sequencing and comparati...
Article
Full-text available
The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation seq...
Article
The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442 bp (58% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer R...
Article
Full-text available
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is present...
Article
Full-text available
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is present...
Article
Full-text available
The Australian freshwater crayfish species, Cherax quadricarinatus Von Martens, 1868, is an important commercial and invasive species that is also being increasingly used as a model organism to address important and interesting questions in crustacean biology. Through deep sequencing of the transcriptome of C. quadricarinatus from the hepatopancrea...
Article
Full-text available
The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a c...
Article
Full-text available
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34....
Article
Full-text available
Abstract The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the...