Displaying publications 21 - 40 of 8266 in total

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  1. Fulltext Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development
    Lee XW, Mat-Isa MN, Mohd-Elias NA, Aizat-Juhari MA, Goh HH, Dear PH, et al.
    PLoS One, 2016;11(12):e0167958.
    PMID: 27977777 DOI: 10.1371/journal.pone.0167958
    Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.
    Matched MeSH terms: Gene Expression Regulation, Plant/genetics; Angiosperms/genetics*; Flowers/genetics*; Transcriptome/genetics*
  2. Fulltext Population genomics of grey wolves and wolf-like canids in North America
    Sinding MS, Gopalakrishan S, Vieira FG, Samaniego Castruita JA, Raundrup K, Heide Jørgensen MP, et al.
    PLoS Genet, 2018 11;14(11):e1007745.
    PMID: 30419012 DOI: 10.1371/journal.pgen.1007745
    North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.
    Matched MeSH terms: Genetics, Population*; Wolves/genetics*; Coyotes/genetics*
  3. Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins
    Redjeki ES, Ho WK, Shah N, Molosiwa OO, Ardiarini NR, Kuswanto, et al.
    Genome, 2020 Jun;63(6):319-327.
    PMID: 32097026 DOI: 10.1139/gen-2019-0137
    A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
    Matched MeSH terms: Genetic Variation/genetics*; Microsatellite Repeats/genetics*; Polymorphism, Single Nucleotide/genetics*; Vigna/genetics*
  4. Electrotransformation of thermophilic bacterium Caldimonas manganoxidans
    Arai T, Aikawa S, Sudesh K, Kondo T, Kosugi A
    J Microbiol Methods, 2022 01;192:106375.
    PMID: 34793853 DOI: 10.1016/j.mimet.2021.106375
    Caldimonas manganoxidans is a Gram-negative, thermophilic, bioplastic-producing bacterium that is a promising strain to overcome the drawbacks of existing bioplastic manufacturing methods. However, genetic manipulation of this species has not previously been studied. Here, we developed an optimized electrotransformation protocol for C. manganoxidans by screening conditions, including the bacterial growth phase, electroporation buffer, pulse strength, and recovery time. The optimized transformation protocol obtained (3.1 ± 0.78) × 108 colony-forming units/μg DNA of plasmid pBBR1MCS-2. High transformation efficiency was observed when using plasmid DNA isolated from C. manganoxidans. The DNA methylases of Escherichia coli did not affect the transformation efficiency of C. manganoxidans. The electrotransformation technique proposed here will be beneficial for the genetic manipulation of thermophilic Caldimonas species.
    Matched MeSH terms: DNA, Bacterial/genetics; Plasmids/genetics; Transformation, Bacterial/genetics*; Comamonadaceae/genetics*
  5. The complete mitogenome of the minute mudskipper, Periophthalmus minutus Eggert, 1935 (Perciformes: Gobiidae: Oxudercinae)
    Gan HM, Tan MH, Lee YP, Hammer MP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4187-4188.
    PMID: 25600740
    The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.
    Matched MeSH terms: Perciformes/genetics*; RNA/genetics*; RNA, Transfer/genetics*; Mitochondrial Proteins/genetics*; Fish Proteins/genetics*
  6. Fulltext Population genetic structure of Aedes albopictus in Penang, Malaysia
    Zawani MK, Abu HA, Sazaly AB, Zary SY, Darlina MN
    Genet. Mol. Res., 2014;13(4):8184-96.
    PMID: 25299203 DOI: 10.4238/2014.October.7.13
    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.
    Matched MeSH terms: Aedes/genetics*; Electron Transport Complex IV/genetics; DNA, Mitochondrial/genetics; Genetics, Population*
  7. Fusion genes in malignant neoplastic disorders of haematopoietic system
    Saleem M, Yusoff NM
    Hematology, 2016 Oct;21(9):501-12.
    PMID: 26871368 DOI: 10.1080/10245332.2015.1106816
    OBJECTIVES: The new World Health Organization's (WHO) classification of haematopoietic and lymphoid tissue neoplasms incorporating the recurrent fusion genes as the defining criteria for different haematopoietic malignant phenotypes is reviewed. The recurrent fusion genes incorporated in the new WHO's classification and other chromosomal rearrangements of haematopoietic and lymphoid tissue neoplasms are reviewed.

    METHODOLOGY: Cytokines and transcription factors in haematopoiesis and leukaemic mechanisms are described. Genetic features and clinical implications due to the encoded chimeric neoproteins causing malignant haematopoietic disorders are reviewed.

    RESULTS AND DISCUSSION: Multiple translocation partner genes are well known for leukaemia such as MYC, MLL, RARA, ALK, and RUNX1. With the advent of more sophisticated diagnostic tools and bioinformatics algorithms, an exponential growth in fusion genes discoveries is likely to increase.

    CONCLUSION: Demonstration of fusion genes and their specific translocation breakpoints in malignant haematological disorders are crucial for understanding the molecular pathogenesis and clinical phenotype of cancer, determining prognostic indexes and therapeutic responses, and monitoring residual disease and relapse status.

    Matched MeSH terms: Hemoglobinopathies/genetics*; Leukemia/genetics*; Lymphoma/genetics*; Oncogene Proteins, Fusion/genetics*; Cytokines/genetics
  8. Characterization and expression of Xiphophorus maculatus microsatellite Msb069 full sequence in subgenus Poecilia
    Poh KB, Roslan ZM, Misnan R, Sinang SC
    J Genet, 2018 Sep;97(4):817-824.
    PMID: 30262693
    Msb069 primer pairs encompassed region is believed to be associated with a quantitative trait loci (QTL) of dorsal fin length in subgenus Poecilia. However, detailed investigation on Msb069 which originated from Xiphophorus on subgenus Poecilia remains unexplored. In this study, full sequence of Msb069 was characterized by sequencing bioinformatics analysis and gene expression. The sequence analysis of Msb069 primer pairs encompassed region on three species of Poecilia revealed higher number of microsatellite tandem repeats in Poecilia latipinna (ATG
    16
    ) compared to P. sphenops (ATG
    13-14
    ). There is no notable pattern of ATGtandem repeats discovered in the hybrids. The full sequence of Msb069 is 734 bp in length and showed a 233 bp conserved region between Xiphophorus and Poecilia. BLAST search performed on this sequence revealed no significant similarities. Nonquantitative RT-PCR exhibited the presence of Msb069 transcripts in three different tissues in subgenus Poecilia. Meanwhile, quantitative RTPCR expression on two different tissues showed relatively higher expression of Msb069 transcript in P. latipinna dorsal fin tissues in both male and female fishes, suggesting a repressive function of this transcript with respect to dorsal fin length. However the exact gene expression event of Msb069 is still unknown and requires further investigation.
    Matched MeSH terms: Cyprinodontiformes/genetics*; Poecilia/genetics*; Gene Expression/genetics; Microsatellite Repeats/genetics*; Quantitative Trait Loci/genetics
  9. The nearly complete mitogenome of the Southeast Asian firefly Pteroptyx tener (Coleoptera: Lampyridae)
    Cheng S, Mat-Isa MN, Sapian IS, Ishak SF
    Mol Biol Rep, 2021 Feb;48(2):1281-1290.
    PMID: 33582950 DOI: 10.1007/s11033-021-06189-0
    The estuarine firefly, Pteroptyx tener, aggregates in the thousands in mangrove trees lining tidal rivers in Southeast Asia where they engage one another in a nocturnal, pre-mating ritual of synchronised courtship flashes. Unfortunately, populations of the species by virtue of being restricted to isolated estuarine rivers systems in the region, are at risk of genetic isolation. Because of this concern we undertook the task of sequencing and characterising the mitochondrial DNA genome of P. tener, as the first step towards helping us to characterise and better understand their genetic diversity. We sequenced and assembled the mitochondrial DNA genome of P. tener from two male and female specimens from the district of Kuala Selangor in Peninsular Malaysia and announce the molecules in this publication. We also reconstructed the phylogenetic trees of all available lampyrids mitogenomes and suggest the need to re-examine our current understanding of their classification which have largely been based on morphological data and the cox1 gene. Separately, our analysis of codon usage patterns among lampyrid mitogenomes showed that the codon usage in a majority of the protein-coding genes were non-neutral. Codon usage patterns between mitogenome sequences of P. tener were, however, largely neutral. Our findings demonstrate the usefulness of mitochondrial genes/mitogenomes for analysing both inter- and intra- specific variation in the Lampyridae to aid in species discovery in this highly variable genus; and elucidate the phylogenetic relationships of Pteroptyx spp. from the region.
    Matched MeSH terms: Beetles/genetics; DNA, Mitochondrial/genetics*; Fireflies/genetics*; Genes, Mitochondrial/genetics; Genome, Mitochondrial/genetics*
  10. Role of the Tristetraprolin (Zinc Finger Protein 36 Homolog) Gene in Cancer
    Gupta G, Bebawy M, Pinto TJA, Chellappan DK, Mishra A, Dua K
    Crit Rev Eukaryot Gene Expr, 2018;28(3):217-221.
    PMID: 30311568 DOI: 10.1615/CritRevEukaryotGeneExpr.2018021188
    Cancer is a complicated transformational progression that fiercely changes the appearance of cell physiology as well as cells' relations with adjacent tissues. Developing an oncogenic characteristic requires a wide range of modifications in a gene expression at a cellular level. This can be achieved by activation or suppression of the gene regulation pathway in a cell. Tristetraprolin (TTP or ZFP36) associated with the initiation and development of tumors are regulated at the level of mRNA decay, frequently through the activity of AU-rich mRNA-destabilizing elements (AREs) located in their 3'-untranslated regions. TTP is an attractive target for therapeutic use and diagnostic tools due to its characteristic appearance in cancer tissue alone. Thus, the illumination of TTP in diverse types of cancer might deliver additional effective remedies in the coming era for cancer patients. The objective of this review is to familiarize the reader with the TTP proteins, focus on efficient properties that endow them with their effective oncogenic potential, describe their physiological role in cancer cells, and review the unique properties of TT, and of TTP-driven cancer.
    Matched MeSH terms: Neoplasms/genetics*; RNA, Messenger/genetics; Gene Expression Regulation, Neoplastic/genetics; RNA Stability/genetics; Tristetraprolin/genetics*
  11. Fulltext Geographic origin and individual assignment of Shorea platyclados (Dipterocarpaceae) for forensic identification
    Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.
    PLoS One, 2017;12(4):e0176158.
    PMID: 28430826 DOI: 10.1371/journal.pone.0176158
    The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases. A haplotype map was generated from chloroplast DNA sequencing for population identification, resulting in 29 multilocus haplotypes, based on 39 informative intraspecific variable sites. Subsequently, a DNA profiling database was developed from 15 STRs allowing for individual identification in Malaysia. Cluster analysis divided the 27 populations into two genetic clusters, corresponding to the region of Eastern and Western Malaysia. The conservativeness tests showed that the Malaysia database is conservative after removal of bias from population subdivision and sampling effects. Independent self-assignment tests correctly assigned individuals to the database in an overall 60.60-94.95% of cases for identified populations, and in 98.99-99.23% of cases for identified regions. Both the chloroplast DNA database and the STRs appear to be useful for tracking timber originating in Malaysia. Hence, this DNA-based method could serve as an effective addition tool to the existing forensic timber identification system for ensuring the sustainably management of this species into the future.
    Matched MeSH terms: DNA, Chloroplast/genetics; Microsatellite Repeats/genetics; Forensic Genetics*; Dipterocarpaceae/genetics*
  12. Fulltext Characterizing haploinsufficiency of SHELL gene to improve fruit form prediction in introgressive hybrids of oil palm
    Teh CK, Muaz SD, Tangaya P, Fong PY, Ong AL, Mayes S, et al.
    Sci Rep, 2017 06 08;7(1):3118.
    PMID: 28596562 DOI: 10.1038/s41598-017-03225-7
    The fundamental trait in selective breeding of oil palm (Eleais guineensis Jacq.) is the shell thickness surrounding the kernel. The monogenic shell thickness is inversely correlated to mesocarp thickness, where the crude palm oil accumulates. Commercial thin-shelled tenera derived from thick-shelled dura × shell-less pisifera generally contain 30% higher oil per bunch. Two mutations, sh MPOB (M1) and sh AVROS (M2) in the SHELL gene - a type II MADS-box transcription factor mainly present in AVROS and Nigerian origins, were reported to be responsible for different fruit forms. In this study, we have tested 1,339 samples maintained in Sime Darby Plantation using both mutations. Five genotype-phenotype discrepancies and eight controls were then re-tested with all five reported mutations (sh AVROS , sh MPOB , sh MPOB2 , sh MPOB3 and sh MPOB4 ) within the same gene. The integration of genotypic data, pedigree records and shell formation model further explained the haploinsufficiency effect on the SHELL gene with different number of functional copies. Some rare mutations were also identified, suggesting a need to further confirm the existence of cis-compound mutations in the gene. With this, the prediction accuracy of fruit forms can be further improved, especially in introgressive hybrids of oil palm. Understanding causative variant segregation is extremely important, even for monogenic traits such as shell thickness in oil palm.
    Matched MeSH terms: Chimera/genetics*; Fruit/genetics*; Plant Proteins/genetics*; Arecaceae/genetics*; Haploinsufficiency/genetics*
  13. FcgammaRIIa polymorphism in systemic lupus erythematosus
    Tan SY
    Kidney Blood Press Res, 2000;23(2):138-42.
    PMID: 10765117 DOI: 10.1159/000025967
    FcgammaRIIs are the most widely distributed of the Fcgamma receptor family and play an important role in the clearance of immune complexes. Evidence that the FcgammaRIIa-R131 allotype is less able to process and clear immune complexes effectively suggests that this may be a disease susceptibility factor for systemic lupus erythematosus (SLE). Data from studies published thus far do not agree on the potential role of FcgammaRIIa polymorphism in the genetics of SLE. Most studies in fact show no evidence for any correlation between polymorphism of FcgammaRIIa and risk for SLE. However, it remains to be determined whether FcgammaRIIa polymorphism may play a critical role in certain groups of patients, especially in those of differing ethnic background. Polymorphism of FcgammaRIIa may also be important in determining disease phenotype, and identification of this influence may have important implications in patient care and in identifying patients for more aggressive therapy.
    Matched MeSH terms: Lupus Erythematosus, Systemic/genetics*; Lupus Nephritis/genetics*; Polymorphism, Genetic/genetics*; Antigens, CD/genetics*; Receptors, IgG/genetics*
  14. Fulltext Inducible T7 RNA Polymerase-mediated Multigene Expression System, pMGX
    Hassan MI, McSorley FR, Hotta K, Boddy CN
    J Vis Exp, 2017 06 27.
    PMID: 28715370 DOI: 10.3791/55187
    Co-expression of multiple proteins is increasingly essential for synthetic biology, studying protein-protein complexes, and characterizing and harnessing biosynthetic pathways. In this manuscript, the use of a highly effective system for the construction of multigene synthetic operons under the control of an inducible T7 RNA polymerase is described. This system allows many genes to be expressed simultaneously from one plasmid. Here, a set of four related vectors, pMGX-A, pMGX-hisA, pMGX-K, and pMGX-hisK, with either the ampicillin or kanamycin resistance selectable marker (A and K) and either possessing or lacking an N-terminal hexahistidine tag (his) are disclosed. Detailed protocols for the construction of synthetic operons using this vector system are provided along with the corresponding data, showing that a pMGX-based system containing five genes can be readily constructed and used to produce all five encoded proteins in Escherichia coli. This system and protocol enables researchers to routinely express complex multi-component modules and pathways in E. coli.
    Matched MeSH terms: Escherichia coli/genetics*; Genetic Vectors/genetics*; Plasmids/genetics*; DNA-Directed RNA Polymerases/genetics*; Viral Proteins/genetics*
  15. Fulltext Protein profiling and histone deacetylation activities in somaclonal variants of oil palm (Elaeis guineensis Jacq.)
    Yaacob JS, Loh HS, Mat Taha R
    ScientificWorldJournal, 2013;2013:613635.
    PMID: 23844406 DOI: 10.1155/2013/613635
    Mantled fruits as a result of somaclonal variation are often observed from the oil palm plantlets regenerated via tissue culture. The mantling of fruits with finger-like and thick outer coating phenotypes significantly reduces the seed size and oil content, posing a threat to oil palm planters, and may jeopardize the economic growth of countries that depend particularly on oil palm plantation. The molecular aspects of the occurrence of somaclonal variations are yet to be known, possibly due to gene repression such as DNA methylation, histone methylation and histone deacetylation. Histone deacetylases (HDACs), involved in eukaryotic gene regulation by catalyzing the acetyl groups are removal from lysine residues on histone, hence transcriptionally repress gene expression. This paper described the total protein polymorphism profiles of somaclonal variants of oil palm and the effects of histone deacetylation on this phenomenon. Parallel to the different phenotypes, the protein polymorphism profiles of the mantled samples (leaves, fruits, and florets) and the phenotypically normal samples were proven to be different. Higher HDAC activity was found in mantled leaf samples than in the phenotypically normal leaf samples, leading to a preliminary conclusion that histone deacetylation suppressed gene expression and contributed to the development of somaclonal variants.
    Matched MeSH terms: Enzyme Activation/genetics; Fruit/genetics*; Plant Proteins/genetics*; Genetic Variation/genetics*; Arecaceae/genetics*
  16. Fulltext Speed breeding is a powerful tool to accelerate crop research and breeding
    Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey MD, et al.
    Nat Plants, 2018 Jan;4(1):23-29.
    PMID: 29292376 DOI: 10.1038/s41477-017-0083-8
    The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand 1 . This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.
    Matched MeSH terms: Hordeum/genetics*; Triticum/genetics*; Peas/genetics*; Brassica napus/genetics*; Cicer/genetics*
  17. Fulltext A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily
    Mirsafian H, Mat Ripen A, Singh A, Teo PH, Merican AF, Mohamad SB
    ScientificWorldJournal, 2014;2014:639682.
    PMID: 24707212 DOI: 10.1155/2014/639682
    Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin, α-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC) suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure.
    Matched MeSH terms: Albumins/genetics*; RNA, Messenger/genetics
  18. Fulltext Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach
    Yazid SN, Ahmad K, Razak MSFA, Rahman ZA, Ramachandran K, Mohamad SNA, et al.
    Braz J Biol, 2021;84:e248359.
    PMID: 34730685 DOI: 10.1590/1519-6984.248359
    Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.
    Matched MeSH terms: Plant Diseases/genetics; Disease Resistance/genetics
  19. Fulltext Molecular profiling of bacterial blight resistance in Malaysian rice cultivars
    Javed MA, Ali SW, Ashfaq M, Tabassam J, Ali M, IhsanUllah M, et al.
    Braz J Biol, 2022;82:e256189.
    PMID: 36541981 DOI: 10.1590/1519-6984.256189
    Bacteria blight is one of the most serious bacterial diseases of rice worldwide. The identification of genetic potential against bacterial blight in the existing rice resources is a prerequisite to develop multigenic resistance to combat the threat of climate change. This investigation was conducted to evaluate alleles variation in 38 Malaysian cultivars using thirteen Simple Sequences Repeats markers and one Sequence Tagged Sites (STS) marker which were reported to be linked with the resistance to bacterial blight. Based on molecular data, a dendrogram was constructed which classified the rice cultivars into seven major clusters at 0.0, 0.28 and 0.3 of similarity coefficient. Cluster 5 was the largest group comprised of ten rice cultivars where multiple genes were identified. However, xa13 could not be detected in the current rice germplasm, whereas xa2 was detected in 25 cultivars. Molecular analysis revealed that Malaysian rice cultivars possess multigenic resistance.
    Matched MeSH terms: Plant Diseases/genetics; Disease Resistance/genetics
  20. An endogenous lentivirus in the germline of a rodent
    Kambol R, Gatseva A, Gifford RJ
    Retrovirology, 2022 Dec 20;19(1):30.
    PMID: 36539757 DOI: 10.1186/s12977-022-00615-2
    Lentiviruses (genus Lentivirus) are complex retroviruses that infect a broad range of mammals, including humans. Unlike many other retrovirus genera, lentiviruses have only rarely been incorporated into the mammalian germline. However, a small number of endogenous retrovirus (ERV) lineages have been identified, and these rare genomic "fossils" can provide crucial insights into the long-term history of lentivirus evolution. Here, we describe a previously unreported endogenous lentivirus lineage in the genome of the South African springhare (Pedetes capensis), demonstrating that the host range of lentiviruses has historically extended to rodents (order Rodentia). Furthermore, through comparative and phylogenetic analysis of lentivirus and ERV genomes, considering the biogeographic and ecological characteristics of host species, we reveal broader insights into the long-term evolutionary history of the genus.
    Matched MeSH terms: Mammals/genetics; Rodentia/genetics
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