The development of a highly efficient tissue culture system for indica rice is crucial to speed u... more The development of a highly efficient tissue culture system for indica rice is crucial to speed up the implementation of gene editing in breeding programmes as well as to explore the roles of indica genes. However, because indica rice types are recalcitrant to in vitro response, there are only a few reports on the successful transformation process on indica rice due to recalcitrant response to in vitro response. The present study attempted to identify the effects of plant growth regulator (PGR), carbon sources and different concentrations of gelling agent on embryogenic callus induction and rice regeneration of Oryza sativa var MR219. The PGR used were 1 or 2 mg/L 6-benzylaminopurine (BAP) and 1-Naphthaleneacetic acid (NAA) and the carbon sources were 30 g/L sucrose and maltose. Three different gelling agent concentrations (3 mg/L, 6 mg/L or 9 mg/L) were evaluated. The highest frequency of friable callus induction (87%) was observed in callus induction media (CI) containing Murashig...
Musa is a large genus that includes many important staple crops particular in Asia and Africa. Ps... more Musa is a large genus that includes many important staple crops particular in Asia and Africa. Pseudoviridae, LARD-like and three different groups of Metaviridae elements were identified based on their RT sequence heterogeneity. Additionally, full length elements were identified in published BAC sequences. Most of the LTR-retrotransposons were degenerated and disrupted at different positions, by other types of repetitive DNAs (retrotransposons and tandem repeats). Metaviridae elements are generally present in higher copy numbers than Pseudoviridae elements, and the A genome contains more retrotransposons than the B genome, possibly explaining the larger genome size of the A genome. However, genome specific LTR-retrotransposons were not detected. Retrotransposons were clustered in the centromeric regions, Pseudoviridae elements showing a more dispersed pattern while LARD-like and some of the Metaviridae elements were also found at the Nucleolar Organizing Region (NOR). Two genome-specific repeats, organised in long arrays are located at the NOR loci of seven Musa taxa and additionally at some to all centromeres of selected taxa. Different degrees of methylation of LTR retrotransposons and tandem repeat DNA, the latter generally being under-methylated were observed. The transcribed copies of the 45SrDNA sequences at the NOR are interspersed by MuTR repeats and weakly methylated, while the distal part of the NOR region and the chromosomal satellite beyond contains MuTR, Metavirdae and LARD-like sequences that are heavily methylated. The close chromosomal proximity and insertion within each other postulates a possible link in the evolution of LTR-retrotransposons, tandem repeats and 5S rRNA genes, but also a role of retrotransposon sequences in gene regulation RNA transcripts of both metaviridae and MuTR repeats indicates their activity, but also that they might be involved in siRNA silencing mechanisms
Open Access Journal of Microbiology & Biotechnology, 2019
Fusarium wilt of banana constantly causing considerable losses on banana industry of both local a... more Fusarium wilt of banana constantly causing considerable losses on banana industry of both local and global markets. Global exportation of banana was greatly affected by this disease since 1950s. After the emergence of a hypervirulent Tropical Race 4 strain of Fusarium oxysporum f. sp. cubense, many genetic improvements aiming to create resistant cultivars were attempted, mainly through transgenic approach. This review provides the recent finding of potential resistant genes and various efforts in creating resistant cultivar from year 2008 to year 2018.
Asia Pacific Journal of Molecular Biology and Biotechnology
Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demandin... more Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune respo...
Journal of Systematics and Evolution, Jan 18, 2007
Musa beccarii N. W. Simmonds var. beccarii and Musa beccarii N. W. Simmonds var. hottana Hakkinen... more Musa beccarii N. W. Simmonds var. beccarii and Musa beccarii N. W. Simmonds var. hottana Hakkinen were described earlier in Acta Phytotaxonomica et Geobotanica based on their morphological characteristics. In order to distinguish the genomes between the two M. beccarii varieties and M. coccinea Andrews, we have now studied them with the Inter-Retrotransposon Amplified Polymorphism (IRAP) marker analyses. The high levels of IRAP polymorphism detected in this study showed that M. beccarii var. beccarii and M. beccarii var. hottana are two distinct varieties. Additional IRAP bands found in M. beccarii var. beccarii indicated that M. beccarii var. hottana might be evolutionarily more ancient than M. beccarii var. beccarii because LTR retrotransposons are not transpositionally removed.
Homologues of Secreted in Xylem (SIX) genes, a group of known fungal effectors, were here identif... more Homologues of Secreted in Xylem (SIX) genes, a group of known fungal effectors, were here identified in the genome of Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4). Expression of FocSIX genes was analyzed in FocTR4 vegetative mycelia and FocTR4-infected banana roots using quantitative reverse transcription PCR (qRT-PCR). Differential gene expression of all FocSIX genes identified in the genome was assessed over time in banana roots inoculated with FocTR4. Two groups of FocSIX genes expression pattern were found; Group I (FocSIX8a, FocSIX1b, FocSIX1c and FocSIX2) represents FocSIX genes that were only expressed in planta, and Group II consists of the remaining FocSIX genes (FocSIX1a, FocSIX6, FocSIX9 and FocSIX13) that were expressed in vitro and in planta. With the FocTR4 genomic information, Group I members can potentially serve as biomarkers for the early detection of Fusarium wilt infection in banana.
Global production of tomato has been hampered by the increased incidences of tomato viral disease... more Global production of tomato has been hampered by the increased incidences of tomato viral disease. The high genetic heterogeneity of tomato plant viruses, because of their high mutation rates, has lead to ineffective control strategies and the fast spread of the viruses. Viruses utilize the resources in host plants for their replication. Therefore, identification and removal of the non-redundant proteins in the tomato plant based on the biological properties of the virus combined with an RNAi strategy may be a future control strategy. In this review, fourteen tomato viral diseases and their causal agents are reviewed and the control strategies for tomato viral diseases are discussed.
<b>Copyright information:</b>Taken from "Endogenous pararetroviral sequences in ... more <b>Copyright information:</b>Taken from "Endogenous pararetroviral sequences in tomato () and related species"http://www.biomedcentral.com/1471-2229/7/24BMC Plant Biology 2007;7():24-24.Published online 21 May 2007PMCID:PMC1899175.leaves of an interspecific hybrid (5) was hybridized to riboprobes derived from three different TAV clones (top) and from a clone carrying the conserved part of the IGR (bottom). Ethidium bromide staining of the major RNA on the gel is shown as a loading control below each blot.
Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the f... more Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM Â DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.
We studied the structure, organization and relationship of repetitive DNA sequences in the genome... more We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.
bioRxiv (Cold Spring Harbor Laboratory), Oct 17, 2022
In silico comparative RNA-seq analysis reveals varietal-specific intergenic small open reading fr... more In silico comparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames in Cucumis sativus L.
The prototypic cyclotide (Kalata B1), isolated from African plant Oldenlandia affinis (Rubiceae),... more The prototypic cyclotide (Kalata B1), isolated from African plant Oldenlandia affinis (Rubiceae), exhibits molluscicidal property against golden apple snails. Given their naturally high mollucicidal activities against golden apple snail, and reports on the introduction of the Oak 1 gene into various plant species, there is a possibility to generate transgenic rice that is able to produce cyclotides protein. In this study, the full-length Oak 1 gene was synthesized and amplified using two specific oligonucleotide primers. The Oak 1 gene was cloned into the pCAMBIA1301 vector using a conventional molecular cloning method. The expression of the Oak 1 gene will be driven by strong constitutive Zea mays Ubiquitin (UBI) promoter. This construct can be transformed into rice callus through Agrobacterium-mediated system to produce transgenic rice.
The current study recognised the issues encountered in regenerating Malaysia MR219 rice plantlet ... more The current study recognised the issues encountered in regenerating Malaysia MR219 rice plantlet via microspore culture and attempted to develop an efficient protocol in overcoming the restraints. In the present study, a high proportion of uninucleate microspores (49.17%) was isolated from Stage 2-Segment II panicle (59–61 days), which also exhibited the highest callus initiation rate of 8.50%. Maintenance of the panicles under a cool temperature of 4 °C for 7 days before isolating the microspores, resulted in the highest microspore viability of 58.33% and callus initiation rate of 9.33%. The microspore isolation protocol was also optimised in the present study. The filtration sieve engagement with a pore size of 80 µm and further suspension centrifugation at 800 rpm for 5 min produced the highest microspore viability percentage and callus initiation rate. The incorporation of 3.0 mg/L kinetin in conjunction with 0.5 mg/L 2,4-D greatly enhanced the callus initiation rate, with 11.33%. The callus proliferation capacity, with the formation of 481.67 mg callus, was significantly promoted by the addition of 1.0 mg/L kinetin and 0.5 mg/L 2,4-D into the growth medium. Moreover, a higher green plantlet regeneration frequency of 2.83% was induced by the supplementation of 8% sucrose, which produced an average of 3.50 green plantlets.
Although plants and animals are evolutionarily distant, the structure and function of their chrom... more Although plants and animals are evolutionarily distant, the structure and function of their chromosomes are largely conserved. This allowed the establishment of a human-Arabidopsis hybrid cell line in which a neo-chromosome was formed by insertion of segments of Arabidopsis chromosomes into human chromosome 15. We used this unique system to investigate how the introgressed part of a plant genome was maintained in human genetic background. The analysis of the neo-chromosome in 60-and 300-day-old cell cultures by next-generation sequencing and molecular cytogenetics suggested its origin by fusion of DNA fragments of different sizes from Arabidopsis chromosomes 2, 3, 4, and 5, which were randomly intermingled rather than joined end-to-end. The neo-chromosome harbored Arabidopsis centromeric repeats and terminal human telomeres. Arabidopsis centromere wasn't found to be functional. Most of the introgressed Arabidopsis DNA was eliminated during the culture, and the Arabidopsis genome in 300-day-old culture showed significant variation in copy number as compared with the copy number variation in the 60-day-old culture. Amplified Arabidopsis centromere DNA and satellite repeats were localized at particular loci and some fragments were inserted into various positions of human chromosome. Neo-chromosome reorganization and behavior in somatic cell hybrids between the plant and animal kingdoms are discussed. The unique structure of eukaryotic chromosomes played important roles in genome evolution, speciation, and transmission of genetic information to progenies. The study of chromosome functions, including replication, segregation, gene expression, and inheritance, is necessary to reveal the differences between plant and animal chromosome organization and function. Understanding chromosome conservation among different organisms can contribute not only to genetics, but also to studies of the biosynthesis and genome evolution of the organisms. Cell fusion is a useful technique commonly used in biomedical research for gene mapping 1, 2. It has also been used to produce hybridoma cells through fusion of murine myeloma cells with human lymphocytes to produce monoclonal antibodies 3. However, cell fusion often induces chromosomal instability. Production of somatic hybrid cell lines is often accompanied by chromosome loss whose mechanism is not clear. Human-rodent somatic cell hybrids are useful tools for mapping human chromosomes and understanding gene functions. Human-mouse hybrid cell lines 4 showed preferential loss of human chromosomes and at least 75% of the human component was lost. The clones had a relatively stable karyotype, and to some extent, the human chromosome content was found to be dependent on the culture conditions. After the hybrid population was formed, Weiss and Green 4 noted that continued subculture resulted in slow elimination of the human chromosome component. However, no evidence of chromosomal rearrangement was found in a majority of hybrid cell lines. In a mouse chimeric line, several human chromosome fragments were retained and expressed in chimeric mice 5. A human chromosome fragment of about 1-2 Mb carrying human Ig genes was maintained as an independent chromosome in the chimeric mice, and chromosomal rearrangement occurred in some of the clones.
bioRxiv (Cold Spring Harbor Laboratory), Jun 22, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
The development of a highly efficient tissue culture system for indica rice is crucial to speed u... more The development of a highly efficient tissue culture system for indica rice is crucial to speed up the implementation of gene editing in breeding programmes as well as to explore the roles of indica genes. However, because indica rice types are recalcitrant to in vitro response, there are only a few reports on the successful transformation process on indica rice due to recalcitrant response to in vitro response. The present study attempted to identify the effects of plant growth regulator (PGR), carbon sources and different concentrations of gelling agent on embryogenic callus induction and rice regeneration of Oryza sativa var MR219. The PGR used were 1 or 2 mg/L 6-benzylaminopurine (BAP) and 1-Naphthaleneacetic acid (NAA) and the carbon sources were 30 g/L sucrose and maltose. Three different gelling agent concentrations (3 mg/L, 6 mg/L or 9 mg/L) were evaluated. The highest frequency of friable callus induction (87%) was observed in callus induction media (CI) containing Murashig...
Musa is a large genus that includes many important staple crops particular in Asia and Africa. Ps... more Musa is a large genus that includes many important staple crops particular in Asia and Africa. Pseudoviridae, LARD-like and three different groups of Metaviridae elements were identified based on their RT sequence heterogeneity. Additionally, full length elements were identified in published BAC sequences. Most of the LTR-retrotransposons were degenerated and disrupted at different positions, by other types of repetitive DNAs (retrotransposons and tandem repeats). Metaviridae elements are generally present in higher copy numbers than Pseudoviridae elements, and the A genome contains more retrotransposons than the B genome, possibly explaining the larger genome size of the A genome. However, genome specific LTR-retrotransposons were not detected. Retrotransposons were clustered in the centromeric regions, Pseudoviridae elements showing a more dispersed pattern while LARD-like and some of the Metaviridae elements were also found at the Nucleolar Organizing Region (NOR). Two genome-specific repeats, organised in long arrays are located at the NOR loci of seven Musa taxa and additionally at some to all centromeres of selected taxa. Different degrees of methylation of LTR retrotransposons and tandem repeat DNA, the latter generally being under-methylated were observed. The transcribed copies of the 45SrDNA sequences at the NOR are interspersed by MuTR repeats and weakly methylated, while the distal part of the NOR region and the chromosomal satellite beyond contains MuTR, Metavirdae and LARD-like sequences that are heavily methylated. The close chromosomal proximity and insertion within each other postulates a possible link in the evolution of LTR-retrotransposons, tandem repeats and 5S rRNA genes, but also a role of retrotransposon sequences in gene regulation RNA transcripts of both metaviridae and MuTR repeats indicates their activity, but also that they might be involved in siRNA silencing mechanisms
Open Access Journal of Microbiology & Biotechnology, 2019
Fusarium wilt of banana constantly causing considerable losses on banana industry of both local a... more Fusarium wilt of banana constantly causing considerable losses on banana industry of both local and global markets. Global exportation of banana was greatly affected by this disease since 1950s. After the emergence of a hypervirulent Tropical Race 4 strain of Fusarium oxysporum f. sp. cubense, many genetic improvements aiming to create resistant cultivars were attempted, mainly through transgenic approach. This review provides the recent finding of potential resistant genes and various efforts in creating resistant cultivar from year 2008 to year 2018.
Asia Pacific Journal of Molecular Biology and Biotechnology
Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demandin... more Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune respo...
Journal of Systematics and Evolution, Jan 18, 2007
Musa beccarii N. W. Simmonds var. beccarii and Musa beccarii N. W. Simmonds var. hottana Hakkinen... more Musa beccarii N. W. Simmonds var. beccarii and Musa beccarii N. W. Simmonds var. hottana Hakkinen were described earlier in Acta Phytotaxonomica et Geobotanica based on their morphological characteristics. In order to distinguish the genomes between the two M. beccarii varieties and M. coccinea Andrews, we have now studied them with the Inter-Retrotransposon Amplified Polymorphism (IRAP) marker analyses. The high levels of IRAP polymorphism detected in this study showed that M. beccarii var. beccarii and M. beccarii var. hottana are two distinct varieties. Additional IRAP bands found in M. beccarii var. beccarii indicated that M. beccarii var. hottana might be evolutionarily more ancient than M. beccarii var. beccarii because LTR retrotransposons are not transpositionally removed.
Homologues of Secreted in Xylem (SIX) genes, a group of known fungal effectors, were here identif... more Homologues of Secreted in Xylem (SIX) genes, a group of known fungal effectors, were here identified in the genome of Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4). Expression of FocSIX genes was analyzed in FocTR4 vegetative mycelia and FocTR4-infected banana roots using quantitative reverse transcription PCR (qRT-PCR). Differential gene expression of all FocSIX genes identified in the genome was assessed over time in banana roots inoculated with FocTR4. Two groups of FocSIX genes expression pattern were found; Group I (FocSIX8a, FocSIX1b, FocSIX1c and FocSIX2) represents FocSIX genes that were only expressed in planta, and Group II consists of the remaining FocSIX genes (FocSIX1a, FocSIX6, FocSIX9 and FocSIX13) that were expressed in vitro and in planta. With the FocTR4 genomic information, Group I members can potentially serve as biomarkers for the early detection of Fusarium wilt infection in banana.
Global production of tomato has been hampered by the increased incidences of tomato viral disease... more Global production of tomato has been hampered by the increased incidences of tomato viral disease. The high genetic heterogeneity of tomato plant viruses, because of their high mutation rates, has lead to ineffective control strategies and the fast spread of the viruses. Viruses utilize the resources in host plants for their replication. Therefore, identification and removal of the non-redundant proteins in the tomato plant based on the biological properties of the virus combined with an RNAi strategy may be a future control strategy. In this review, fourteen tomato viral diseases and their causal agents are reviewed and the control strategies for tomato viral diseases are discussed.
<b>Copyright information:</b>Taken from "Endogenous pararetroviral sequences in ... more <b>Copyright information:</b>Taken from "Endogenous pararetroviral sequences in tomato () and related species"http://www.biomedcentral.com/1471-2229/7/24BMC Plant Biology 2007;7():24-24.Published online 21 May 2007PMCID:PMC1899175.leaves of an interspecific hybrid (5) was hybridized to riboprobes derived from three different TAV clones (top) and from a clone carrying the conserved part of the IGR (bottom). Ethidium bromide staining of the major RNA on the gel is shown as a loading control below each blot.
Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the f... more Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM Â DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.
We studied the structure, organization and relationship of repetitive DNA sequences in the genome... more We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.
bioRxiv (Cold Spring Harbor Laboratory), Oct 17, 2022
In silico comparative RNA-seq analysis reveals varietal-specific intergenic small open reading fr... more In silico comparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames in Cucumis sativus L.
The prototypic cyclotide (Kalata B1), isolated from African plant Oldenlandia affinis (Rubiceae),... more The prototypic cyclotide (Kalata B1), isolated from African plant Oldenlandia affinis (Rubiceae), exhibits molluscicidal property against golden apple snails. Given their naturally high mollucicidal activities against golden apple snail, and reports on the introduction of the Oak 1 gene into various plant species, there is a possibility to generate transgenic rice that is able to produce cyclotides protein. In this study, the full-length Oak 1 gene was synthesized and amplified using two specific oligonucleotide primers. The Oak 1 gene was cloned into the pCAMBIA1301 vector using a conventional molecular cloning method. The expression of the Oak 1 gene will be driven by strong constitutive Zea mays Ubiquitin (UBI) promoter. This construct can be transformed into rice callus through Agrobacterium-mediated system to produce transgenic rice.
The current study recognised the issues encountered in regenerating Malaysia MR219 rice plantlet ... more The current study recognised the issues encountered in regenerating Malaysia MR219 rice plantlet via microspore culture and attempted to develop an efficient protocol in overcoming the restraints. In the present study, a high proportion of uninucleate microspores (49.17%) was isolated from Stage 2-Segment II panicle (59–61 days), which also exhibited the highest callus initiation rate of 8.50%. Maintenance of the panicles under a cool temperature of 4 °C for 7 days before isolating the microspores, resulted in the highest microspore viability of 58.33% and callus initiation rate of 9.33%. The microspore isolation protocol was also optimised in the present study. The filtration sieve engagement with a pore size of 80 µm and further suspension centrifugation at 800 rpm for 5 min produced the highest microspore viability percentage and callus initiation rate. The incorporation of 3.0 mg/L kinetin in conjunction with 0.5 mg/L 2,4-D greatly enhanced the callus initiation rate, with 11.33%. The callus proliferation capacity, with the formation of 481.67 mg callus, was significantly promoted by the addition of 1.0 mg/L kinetin and 0.5 mg/L 2,4-D into the growth medium. Moreover, a higher green plantlet regeneration frequency of 2.83% was induced by the supplementation of 8% sucrose, which produced an average of 3.50 green plantlets.
Although plants and animals are evolutionarily distant, the structure and function of their chrom... more Although plants and animals are evolutionarily distant, the structure and function of their chromosomes are largely conserved. This allowed the establishment of a human-Arabidopsis hybrid cell line in which a neo-chromosome was formed by insertion of segments of Arabidopsis chromosomes into human chromosome 15. We used this unique system to investigate how the introgressed part of a plant genome was maintained in human genetic background. The analysis of the neo-chromosome in 60-and 300-day-old cell cultures by next-generation sequencing and molecular cytogenetics suggested its origin by fusion of DNA fragments of different sizes from Arabidopsis chromosomes 2, 3, 4, and 5, which were randomly intermingled rather than joined end-to-end. The neo-chromosome harbored Arabidopsis centromeric repeats and terminal human telomeres. Arabidopsis centromere wasn't found to be functional. Most of the introgressed Arabidopsis DNA was eliminated during the culture, and the Arabidopsis genome in 300-day-old culture showed significant variation in copy number as compared with the copy number variation in the 60-day-old culture. Amplified Arabidopsis centromere DNA and satellite repeats were localized at particular loci and some fragments were inserted into various positions of human chromosome. Neo-chromosome reorganization and behavior in somatic cell hybrids between the plant and animal kingdoms are discussed. The unique structure of eukaryotic chromosomes played important roles in genome evolution, speciation, and transmission of genetic information to progenies. The study of chromosome functions, including replication, segregation, gene expression, and inheritance, is necessary to reveal the differences between plant and animal chromosome organization and function. Understanding chromosome conservation among different organisms can contribute not only to genetics, but also to studies of the biosynthesis and genome evolution of the organisms. Cell fusion is a useful technique commonly used in biomedical research for gene mapping 1, 2. It has also been used to produce hybridoma cells through fusion of murine myeloma cells with human lymphocytes to produce monoclonal antibodies 3. However, cell fusion often induces chromosomal instability. Production of somatic hybrid cell lines is often accompanied by chromosome loss whose mechanism is not clear. Human-rodent somatic cell hybrids are useful tools for mapping human chromosomes and understanding gene functions. Human-mouse hybrid cell lines 4 showed preferential loss of human chromosomes and at least 75% of the human component was lost. The clones had a relatively stable karyotype, and to some extent, the human chromosome content was found to be dependent on the culture conditions. After the hybrid population was formed, Weiss and Green 4 noted that continued subculture resulted in slow elimination of the human chromosome component. However, no evidence of chromosomal rearrangement was found in a majority of hybrid cell lines. In a mouse chimeric line, several human chromosome fragments were retained and expressed in chimeric mice 5. A human chromosome fragment of about 1-2 Mb carrying human Ig genes was maintained as an independent chromosome in the chimeric mice, and chromosomal rearrangement occurred in some of the clones.
bioRxiv (Cold Spring Harbor Laboratory), Jun 22, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Uploads
Papers by Chee How Teo