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, 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 Centre for Chemical Biology, USM, we characterize the genomes of individual organisms and systems of organisms from Malaysian environment and study their genes and functions.


    • The industrially-important crop, rubber (Hevea brasiliensis)

      Rubber tree (Hevea brasiliensis), is the main source for world’s natural rubber production. The rubber tree is native to rainforests in the Amazon region of South America, but is now widely planted in Southeast Asia, especially in Malaysia, Indonesia and Thailand. Natural rubber latex has superior performance properties and has been widely used in the manufacturing of tires for automobiles, aircrafts and parts for medical devices. Despite rubber tree’s economic importance, comprehensive whole-genome information on the tree is scarce. Genome information is a basis for scientific breeding and high-quality genome assembly is important for discovering genes and pathways controlling the tree’s desirable agronomic traits.

      Rubber Plantation 

      Rubber Trees

      The rubber tree genome- What it tells?
      1. Genome information reveals possible contributors to rubber tree’s capacity to produce high level of latex.
      The 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 genes in latex are possible reasons for rubber tree’s capacity to produce large amount of latex.
      2. Cap analysis gene expression (CAGE) results shows tissue-specific transcription profiles of rubber biosynthesis related genes.
      Tissue-specific transcription of genes are possible alternative means of transcriptional regulation.
      3. Comparative genomics analysis indicates conserved synteny between genomes of 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.
      Metagenomics insight into microbial communities from the best managed mangrove soil
      Matang Mangrove Forest Reserve (MMFR) has 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 the microbial diversity and metabolic potential of Malaysia mangrove soil.
    • 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-QB1 was isolated from 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.

      GlobinPhase contrast image of Aureispira sp. CCB-QB1.

      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. A locally isolated Persicobacter sp., strain CCB-QB2 was found to exhibit similar agar-degrading property. The genome sequence information is important for the identification of underlying pathways for the production of agarases in this bacterium.

      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, TPBH4T(= 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 arabinan utilization genes that are not reported in other Mangrovimonas

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  1. 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, Minami Matsui.
    2017 DNA Research, 24(2): 159–167. *These authors contributed equally  to this work
  2. Draft genome sequence of halophilic Hahella sp. strain CCB-MM4, isolated from Matang Mangrove Forest in Perak, Malaysia
    Sam, K.-K., Lau, N.-S., Furusawa, G., Amirula, A.-A.A.
    2017 Genome Announcements, 5(42),e01147-17

  3. Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7
    Nanthini, J., Ong, S.Y., Sudesh, K.
    2017 Gene, 628, pp. 146-155
  4. Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.
    Moh, T.H., Lau, N.-S., Furusawa, G., Amirul, A.-A.A.
    2017 Standards in Genomic Sciences, 12(1),36

  5. Synthesis of high 4-hydroxybutyrate copolymer by Cupriavidus sp. transformants using one-stage cultivation and mixed precursor substrates strategy.
    Syafiq I.M., Bhubalan K., Huong K.-H., Vigneswari S., Amirul A.A., Shantini K., Aziz N.A.

    2017 Enzyme and Microbial Technology, 98, pp. 1-8
  6. Complete Genome Sequence of Proteus mirabilis Phage pPM_01 Isolated from Raw Sewage
    Wirjon I.A.,Lau N.-S, Arip Y.M.
    2017 Intervirology, 59:243-253

  7. 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.
  8. Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environments
    Nur Asilla Hani Shafie, Nyok-Sean Lau, Hema Ramachandran and Al-Ashraf Abdullah Amirul.
    2017 Genome Announcements.
  9. 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.
    Scientific Reports.
  10. 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.
  11. 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. 19:39.
    2015 Marine Genomics, 19:39.
  12. 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 Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne-Laporte, Nokuthula P. Mchunu, Qingyi Yu, Brennick J. Langston, Tracey Allen K. Freitas, Aaron G. Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A. Saito and Maqsudul Alam.
    2013 BMC Genomics, 14:75.