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Research - Genes and Genomes

What It Is About

The extraordinary progress that has been made in sequencing technologies in the past few years has revolutionized research in genomics studies. During the last decade, the advent of genome sequencing technologies has allowed the deciphering of genome sequences of more than 2,000 individuals of eukaryotes as well as more than 10,000 individuals of prokaryotes. Today’s complex genomic research questions have propelled sequencing technologies to even greater advancements. Some approaches deliver unprecedented throughput and speed, generating a wealth of data that greatly improves the analysis of increasingly complex phenotypes. Alternatively, other approaches now aim to produce long reads that enable the efficient de novo sequencing or characterization of genome of nontraditional species. These and other strategies constitute an opportunity for researchers to understand the genetic basis underlying phenotype and to study biological systems in ways never before possible. Here, at the Centre for Chemical Biology, USM, we characterize the genomes of individual organisms and systems of organisms from the Malaysian environment and study their genes and functions.

Research

Genome of mini-fish

Miniaturization, or the phenomenon of extreme body size reduction compared to other species in the same lineage, is frequently encountered in fishes. Fishes maturing at sizes less than 20 mm have been termed ‘miniature fish’ or ‘mini-fish’. Miniaturized taxa are often paedomorphic, resulting from truncation of development combined with accelerated maturation. Features of mini-fish could also include the tendency to lose bones and scales or having a poorly ossified, largely cartilaginous skeleton. Paedocypris, which has been described as the world’s smallest vertebrate, is a prominent example among ‘mini-fish’. The sequencing of Paedocypris spp. the genome provides an opportunity for understanding miniaturization evolution in teleost and the study of traits associated with the evolution of small size in ‘mini-fish’.


Paedocypris micromegethes




Iso-Seq of terrestrial crab

Lipid metabolism is critical for proper function in animals.  So far, lipid metabolism in a crustacean is poorly understood.  Nothing is known about the ability of crustacean to biosynthesis polyunsaturated fatty acids.  It is speculated that this capacity is related to the niche of the particular crustacean species.  Using the PacBio Iso-seq method, we identify genes related to the biosynthesis of polyunsaturated fatty acids in terrestrial crab and to gain a full picture of lipid metabolism.

  
Gecarcoidea lalandii
  


Microbiome of oral mucus in tilapia fish
Many species of teleost fish exhibit quite an elaborate form of parental care. Species of Oreochromis (tilapia fish) are mouth brooders; female parents hold and incubate the eggs in their buccal cavity for several days. Fry remain in the females’ mouth through yolk-sac absorption. Apart from the protection and transportation of the young, it is unclear if mouthbrooding provides additional advantages to embryos during incubation. Studies of the microbiome have the potential to reveal important oral mucosal evolutionary processes in Oreochromis sp. and discover symbiotic bacteria that can be used in aquaculture to increase the survival of the young.

  
Oreochromis niloticus
  



Metagenomics insight into microbial communities from the best-managed mangrove soil
   

Matang Mangrove Forest Reserve (MMFR) s been acknowledged as the best sustainably-managed mangrove forest in the world.  Metagenomic data was obtained from two sampling sites at MMFR with distinct features: the Productive Zone and Virgin Jungle Forest. The former zone is designated for tree harvesting while the latter is a pristine area. Matang mangrove metagenomes provide insights into managed mangrove microbiome and serve as important resources for the mining of bacterial species and enzymes involved in litter processing. 

   

The rubber tree genome - What it tells?

1.  Genome information reveals possible contributors to rubber tree's capacity to produce a high level of latex.
T
he expansion of rubber biosynthesis-related genes (cis-prenyltransferase, small rubber particle protein and rubber elongation factor) in the genome and the high expression of these in latex are possible reasons for rubber tree's capacity to produce a large amount of latex.
2.  Cap analysis gene expression (CAGE) results show tissue-specific transcription profiles of rubber biosynthesis related genes.
Tissue-specific transcriptions of genes are possible alternative means of transcriptional regulation.
3.  Comparative genomic analysis indicates conserved synteny between genomes of the rubber tree, cassava, castor bean and jatropha.
Rubber tree gene blocks showed one-to-one, one-to-two and one-to-three synteny relationships with their orthologues in jatropha, cassava and castor bean, respectively.

  

 

 

The polysaccharide-degrading marine bacterium, Persicobacter sp. CCB-QB2

Numerous bacteria isolated from the marine environment are known for their agarolytic property. These agarolytic microorganisms produce agarases to hydrolyze and metabolize agar as carbon and energy sources. Persicobacter sp. CCB-QB2, isolated from seaweed collected from the coastal area of Penang, was found to exhibit diauxic growth in the presence of two nutrients: tryptone and agar. Whole-genome and transcriptome sequencing were performed to study the diauxic growth in strain CCB-QB2.


Agar hydrolyzing activity from culture supernatant: (a) culture supernatant with agar; (b) culture supernatant without agar.

 

Novel Mangrovimonas-like strains isolated from estuarine mangrove sediment

Three Mangrovimonas-like strains, TPB4T (=LMG 28913T, = JCM 30882T), ST2L12T(=LMG 28914T, =JCM 30880T) and ST2L15T(=LMG 28915T,=JCM 30881T) were isolated from estuarine mangrove sediment of Matang Mangrove Forest.  Genome information of these isolates reveals xylan and arabaian utilization genes that are not reported in other Mangrovimonas.

 

The marine predatory bacterium, Aureispira sp. CCB-QB1

The genus Aureispira is known for its predatory lifestyle that preys on other marine bacteria via 'ixotrophy'.  Aureispira sp. strain CCB-QB! was isolated from the coastal area of Penang, Malaysia and selected for genome sequencing as there was no genome information available so far from the genus Aureispira.  Analysis of the genome reveals pathways for polyunsaturated fatty acid and diterpenoid biosynthesis.

Globin
Phase contrast image of Aureispirasp. CCB-QB1.

 

 



  

Publications

    1. Complete genome sequence of the novel agarolytic Catenovulum-like strain CCB-QB4      
      Nyok-Sean Lau, Wei Run Tan, Go Furusawa and Al-Ashraf Abdullah Amirul.2019 Marine Genomics, 43:50-53.
    2. Diversity and coding potential of the microbiota in the photic and aphotic zones of tropical man-made lake with intensive aquaculture activities: a case study on Temengor Lake, Malaysia                  
      Nyok-Sean Lau, Kamarul Zaman Zarkasi, Amir Shah Ruddin Md Sah and Alexander Chong Shu-Chien.2018Microbial Ecology, https://doi.org/10.1007/s00248-018-1283-0.
    3. Metagenomic insights into the phylogenetic and functional profiles of soil microbiome from a managed mangrove in Malaysia                                                                                         
      Gunaselvam Priya, Nyok-Sean Lau, Go Furusawa, Balachandran Dinesh, Swee Yeok Foong and Al-Ashraf Abdullah Amirul.               2018 AgriGene, 9:5-15.
    4. Genome organization of Escherichia Phage YD-2008.s: A new entry to Siphoviridae family
      Dharmela Sellvam, Nyok-Sean Lau and Yahya Mat Arip.  2018Tropical Life Sciences Research, 29:37-50.
    5. Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber research
      Yuko Makita, Mika Kawashima, Nyok-Sean Lau, Ahmad Sofiman Othman and Minami Matsui.2018BMC Genomics, doi: 10.1186/s12864-017-433-y.
    6. Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis
      Yuko Makita, Kiaw Kiaw Ng, G. Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman and Minami Matsui.   017 DNA Research, 24(2):159–167.
    7. Draft genome sequence of halophilic Hahella sp. strain CCB-MM4, isolated from Matang Mangrove Forest in Perak, Malaysia
      Ka-Kei Sam, Nyok-Sean Lau, Go Furusawa and Al-Ashraf Abdullah Amirul.     2017 
      Genome Announcements, 5(42):e01147-17. 
    8. Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7
      Jayaram Nanthini, Su Yean Ong and Kumar Sudesh.   017 
      Gene, 628:146-155.
    9. Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.
      Tsu Horng Moh, Nyok-Sean Lau, Go Furusawa and Al-Ashraf Abdullah Amirul.  2017 
      Standards in Genomic Sciences, 12(1):36. 
    10. Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway.                                                                                                           
      Go Furusawa, Nyok-Sean Lau, Suganthi Appalasamy, Al-Ashraf Abdullah Amirul.   2017 Microbiology Open, .
    11. Complete genome sequence of Proteus mirabilis phage pPM_01 isolated from raw sewage
      Wirjon I.A., Nyok-Sean Lau, Arip Y.M.  2017 
      Intervirology, 59: 243-253. 
    12. Genome features of moderately halophilic polyhdroxyalkanoate-producing Yangia sp. CCB-MM3
      Nyok-Sean Lau, Ka-Kei Sam and Al-Ashraf Abdullah Amirul.  2017 
      Standards in Genomic Sciences, 12:12.
    13. Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environmentsNur Asilla Hani Shafie, Nyok-Sean Lau, Hema Ramachandran and Al-Ashraf Abdullah Amirul.  2017 Genome Announcements.
    14. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
      Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu-Chien and Minami Matsui.  2016 
      Scientific Reports.
    15. Comparative genome analyses of novel Mangroviomas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes
      Balachandran Dinesh, Nyok-Sean Lau, Furusawa Go, Seok-Won Kim, Todd D Taylor, Swee Yeok Foong and Alexander Chong Shu-Chien.  2016
       Marine Genomics.
    16. Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1
      Furusawa Go, Nyok-Sean Lau, Alexander Chong Shu-Chien, Annette Jaya Ram and Al-Ashraf Abdullah Amirul.  2015 
      Marine Genomics,19:39.
    17. Draft genome sequence of the rubber tree Hevea brasiliensis
      Ahmad Yamin Abdul Rahman, Abhilash O. Usharraj, Biswapriya B. Misra, Gincy P. Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock 

Members

Prof. Dr. Alexander Chong Shu Chien (Principal Investigator)
Prof. Dr. Ahmad Sofiman Othman (Principal Investigator)
Dr. Lau Nyok Sean (Research Officer)
Teng Seng Yeat (PhD Student)
Sam Ka Kei (PhD Student)
 

Highlights

BIOLOG MICROBIAL IDENTIFICATION

BIOLOG MICROBIAL IDENTIFICATION

CHECK THIS OUT! `Scopus hits indicate almost 200 peer-reviewed’ papers in 2018 utilizing Biolog for microbial identification’           

“SAYING GOODBYE” to Student Interns

“SAYING GOODBYE” to Student Interns

A small celebration involving all CCB staff and students (CCBians) was held at CCB Meeting Room on 23 August 2019 to bid farewell to student interns from Universiti Sains Malaysia...

INDUSTRIAL TRAINING SUPERVISION VISIT FROM UTM

INDUSTRIAL TRAINING SUPERVISION VISIT FROM UTM

On 22 August 2019 Dr. Nurriza Ab. Latif, the supervisor for Student Internship programme from UTM, visited CCB for performance evaluation of their student interns.  During their brief presentation, each...