Displaying publications 1 - 20 of 34 in total

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  1. Fulltext Feature Selection for High-Dimensional and Imbalanced Biomedical Data Based on Robust Correlation Based Redundancy and Binary Grasshopper Optimization Algorithm
    Abdulrauf Sharifai G, Zainol Z
    Genes (Basel), 2020 06 27;11(7).
    PMID: 32605144 DOI: 10.3390/genes11070717
    The training machine learning algorithm from an imbalanced data set is an inherently challenging task. It becomes more demanding with limited samples but with a massive number of features (high dimensionality). The high dimensional and imbalanced data set has posed severe challenges in many real-world applications, such as biomedical data sets. Numerous researchers investigated either imbalanced class or high dimensional data sets and came up with various methods. Nonetheless, few approaches reported in the literature have addressed the intersection of the high dimensional and imbalanced class problem due to their complicated interactions. Lately, feature selection has become a well-known technique that has been used to overcome this problem by selecting discriminative features that represent minority and majority class. This paper proposes a new method called Robust Correlation Based Redundancy and Binary Grasshopper Optimization Algorithm (rCBR-BGOA); rCBR-BGOA has employed an ensemble of multi-filters coupled with the Correlation-Based Redundancy method to select optimal feature subsets. A binary Grasshopper optimisation algorithm (BGOA) is used to construct the feature selection process as an optimisation problem to select the best (near-optimal) combination of features from the majority and minority class. The obtained results, supported by the proper statistical analysis, indicate that rCBR-BGOA can improve the classification performance for high dimensional and imbalanced datasets in terms of G-mean and the Area Under the Curve (AUC) performance metrics.
  2. Fulltext Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes
    Al Yafei Z, Hajjej A, Alvares M, Al Mahri A, Nasr A, Mirghani R, et al.
    Genes (Basel), 2023 May 26;14(6).
    PMID: 37372339 DOI: 10.3390/genes14061159
    In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations.

    METHODS: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped for HLA class I (A, B, C) and class II (DRB1, DQB1) genes using reverse sequence specific oligonucleotide bead-based multiplexing. HLA haplotypes were assigned with certainty by segregation (pedigree) analysis, and haplotype frequencies were obtained by direct counting. HLA class I and class II frequencies in Emiratis were compared to data from other populations using standard genetic distances (SGD), Neighbor-Joining (NJ) phylogenetic dendrograms, and correspondence analysis.

    RESULTS: The studied HLA loci were in Hardy-Weinberg Equilibrium. We identified 17 HLA-A, 28 HLA-B, 14 HLA-C, 13 HLA-DRB1, and 5 HLA-DQB1 alleles, of which HLA-A*02 (22.2%), -B*51 (19.5%), -C*07 (20.0%), -DRB1*03 (22.2%), and -DQB1*02 (32.8%) were the most frequent allele lineages. DRB1*03~DQB1*02 (21.2%), DRB1*16~DQB1*05 (17.3%), B*35~C*04 (11.7%), B*08~DRB1*03 (9.7%), A*02~B*51 (7.5%), and A*26~C*07~B*08~DRB1*03~DQB1*02 (4.2%) were the most frequent two- and five-locus HLA haplotypes. Correspondence analysis and dendrograms showed that Emiratis were clustered with the Arabian Peninsula populations (Saudis, Omanis and Kuwaitis), West Mediterranean populations (North Africans, Iberians) and Pakistanis, but were distant from East Mediterranean (Turks, Albanians, Greek), Levantine (Syrians, Palestinians, Lebanese), Iranian, Iraqi Kurdish, and Sub-Saharan populations.

    CONCLUSIONS: Emiratis were closely related to Arabian Peninsula populations, West Mediterranean populations and Pakistanis. However, the contribution of East Mediterranean, Levantine Arab, Iranian, and Sub-Saharan populations to the Emiratis' gene pool appears to be minor.

  3. Fulltext Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation
    Asaduzzaman M, Igarashi Y, Wahab MA, Nahiduzzaman M, Rahman MJ, Phillips MJ, et al.
    Genes (Basel), 2019 12 30;11(1).
    PMID: 31905942 DOI: 10.3390/genes11010046
    The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.
  4. Fulltext Identification and Analysis of microRNAs in Chlorella sorokiniana Using High-Throughput Sequencing
    Azaman SNA, Satharasinghe DA, Tan SW, Nagao N, Yusoff FM, Yeap SK
    Genes (Basel), 2020 09 25;11(10).
    PMID: 32992970 DOI: 10.3390/genes11101131
    Chlorella is a popular microalga with robust physiological and biochemical characteristics, which can be cultured under various conditions. The exploration of the small RNA content of Chlorella could improve strategies for the enhancement of metabolite production from this microalga. In this study, stress was introduced to the Chlorella sorokiniana culture to produce high-value metabolites such as carotenoids and phenolic content. The small RNA transcriptome of C. sorokiniana was sequenced, focusing on microRNA (miRNA) content. From the analysis, 98 miRNAs were identified in cultures subjected to normal and stress conditions. The functional analysis result showed that the miRNA targets found were most often involved in the biosynthesis of secondary metabolites, followed by protein metabolism, cell cycle, and porphyrin and chlorophyll metabolism. Furthermore, the biosynthesis of secondary metabolites such as carotenoids, terpenoids, and lipids was found mostly in stress conditions. These results may help to improve our understanding of regulatory mechanisms of miRNA in the biological and metabolic process of Chlorella species. It is important and timely to determine the true potential of this microalga species and to support the potential for genetic engineering of microalgae as they receive increasing focus for their development as an alternative source of biofuel, food, and health supplements.
  5. Fulltext Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana
    Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, et al.
    Genes (Basel), 2020 12 09;11(12).
    PMID: 33317074 DOI: 10.3390/genes11121479
    Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
  6. Fulltext Eco-Friendly Formulated Zinc Oxide Nanoparticles: Induction of Cell Cycle Arrest and Apoptosis in the MCF-7 Cancer Cell Line
    Boroumand Moghaddam A, Moniri M, Azizi S, Abdul Rahim R, Bin Ariff A, Navaderi M, et al.
    Genes (Basel), 2017 Oct 20;8(10).
    PMID: 29053567 DOI: 10.3390/genes8100281
    Green products have strong potential in the discovery and development of unique drugs. Zinc oxide nanoparticles (ZnO NPs) have been observed to have powerful cytotoxicity against cells that cause breast cancer. The present study aims to examine the cell cycle profile, status of cell death, and pathways of apoptosis in breast cancer cells (MCF-7) treated with biosynthesized ZnO NPs. The anti-proliferative activity of ZnO NPs was determined using MTT assay. Cell cycle analysis and the mode of cell death were evaluated using a flow cytometry instrument. Quantitative real-time-PCR (qRT-PCR) was employed to investigate the expression of apoptosis in MCF-7 cells. ZnO NPs were cytotoxic to the MCF-7 cells in a dose-dependent manner. The 50% growth inhibition concentration (IC50) of ZnO NPs at 24 h was 121 µg/mL. Cell cycle analysis revealed that ZnO NPs induced sub-G₁ phase (apoptosis), with values of 1.87% at 0 μg/mL (control), 71.49% at IC25, 98.91% at IC50, and 99.44% at IC75. Annexin V/propidium iodide (PI) flow cytometry analysis confirmed that ZnO NPs induce apoptosis in MCF-7 cells. The pro-apoptotic genes p53, p21, Bax, and JNK were upregulated, whereas anti-apoptotic genes Bcl-2, AKT1, and ERK1/2 were downregulated in a dose-dependent manner. The arrest and apoptosis of MCF-7 cells were induced by ZnO NPs through several signalling pathways.
  7. Fulltext A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut
    Chai HH, Ho WK, Graham N, May S, Massawe F, Mayes S
    Genes (Basel), 2017 Feb 22;8(2).
    PMID: 28241413 DOI: 10.3390/genes8020084
    Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops.
  8. Fulltext Transcriptomic and Genomic Approaches for Unravelling Candida albicans Biofilm Formation and Drug Resistance-An Update
    Chong PP, Chin VK, Wong WF, Madhavan P, Yong VC, Looi CY
    Genes (Basel), 2018 Nov 07;9(11).
    PMID: 30405082 DOI: 10.3390/genes9110540
    Candida albicans is an opportunistic fungal pathogen, which causes a plethora of superficial, as well as invasive, infections in humans. The ability of this fungus in switching from commensalism to active infection is attributed to its many virulence traits. Biofilm formation is a key process, which allows the fungus to adhere to and proliferate on medically implanted devices as well as host tissue and cause serious life-threatening infections. Biofilms are complex communities of filamentous and yeast cells surrounded by an extracellular matrix that confers an enhanced degree of resistance to antifungal drugs. Moreover, the extensive plasticity of the C. albicans genome has given this versatile fungus the added advantage of microevolution and adaptation to thrive within the unique environmental niches within the host. To combat these challenges in dealing with C. albicans infections, it is imperative that we target specifically the molecular pathways involved in biofilm formation as well as drug resistance. With the advent of the -omics era and whole genome sequencing platforms, novel pathways and genes involved in the pathogenesis of the fungus have been unraveled. Researchers have used a myriad of strategies including transcriptome analysis for C. albicans cells grown in different environments, whole genome sequencing of different strains, functional genomics approaches to identify critical regulatory genes, as well as comparative genomics analysis between C. albicans and its closely related, much less virulent relative, C. dubliniensis, in the quest to increase our understanding of the mechanisms underlying the success of C. albicans as a major fungal pathogen. This review attempts to summarize the most recent advancements in the field of biofilm and antifungal resistance research and offers suggestions for future directions in therapeutics development.
  9. Fulltext Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis
    Fadzil NF, Wagiran A, Mohd Salleh F, Abdullah S, Mohd Izham NH
    Genes (Basel), 2018 Aug 12;9(8).
    PMID: 30103564 DOI: 10.3390/genes9080408
    The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues.
  10. Fulltext Expression of Genes Encoding Manganese Peroxidase and Laccase of Ganoderma boninense in Response to Nitrogen Sources, Hydrogen Peroxide and Phytohormones
    Ho PY, Namasivayam P, Sundram S, Ho CL
    Genes (Basel), 2020 10 26;11(11).
    PMID: 33114747 DOI: 10.3390/genes11111263
    Ganoderma produces lignolytic enzymes that can degrade the lignin component of plant cell walls, causing basal stem rot to oil palms. Nitrogen sources may affect plant tolerance to root pathogens while hydrogen peroxide (H2O2), salicylic acid (SA) and jasmonic acid (JA) play important roles in plant defense against pathogens. In this study, we examined the expression of genes encoding manganese peroxidase (MnP) and laccase (Lac) in Ganoderma boninense treated with different nitrogen sources (ammonium nitrate, ammonium sulphate, sodium nitrate and potassium nitrate), JA, SA and H2O2. Transcripts encoding MnP and Lac were cloned from G. boninense. Of the three GbMnP genes, GbMnP_U6011 was up-regulated by all nitrogen sources examined and H2O2 but was down-regulated by JA. The expression of GbMnP_U87 was only up-regulated by JA while GbMnP_35959 was up-regulated by ammonium nitrate but suppressed by sodium nitrate and down-regulated by H2O2. Among the three GbLac genes examined, GbLac_U90667 was up-regulated by ammonium nitrate, JA, SA and H2O2; GbLac_U36023 was up-regulated by JA and H2O2 while GbLac_U30636 was up-regulated by SA but suppressed by ammonium sulphate, sodium nitrate, JA and H2O2. Differential expression of these genes may be required by their different functional roles in G. boninense.
  11. Fulltext Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1
    Jabeen S, Yap HY, Abdullah FFJ, Zakaria Z, Isa NM, Tan YC, et al.
    Genes (Basel), 2019 01 25;10(2).
    PMID: 30691021 DOI: 10.3390/genes10020081
    Although more than 100 genome sequences of Pasteurella multocida are available, comprehensive and complete genome sequence analysis is limited. This study describes the analysis of complete genome sequence and pathogenomics of P. multocida strain PMTB2.1. The genome of PMTB2.1 has 2176 genes with more than 40 coding sequences associated with iron regulation and 140 virulence genes including the complete tad locus. The tad locus includes several previously uncharacterized genes such as flp2, rcpC and tadV genes. A transposable phage resembling to Mu phages was identified in P. multocida that has not been identified in any other serotype yet. The multi-locus sequence typing analysis assigned the PMTB2.1 genome sequence as type ST101, while the comparative genome analysis showed that PMTB2.1 is closely related to other P. multocida strains with the genomic distance of less than 0.13. The expression profiling of iron regulating-genes of PMTB2.1 was characterized under iron-limited environment. Results showed significant changes in the expression profiles of iron-regulating genes (p < 0.05) whereas the highest expression of fecE gene (281 fold) at 30 min suggests utilization of the outer-membrane proteins system in iron acquisition at an early stage of growth. This study showed the phylogenomic relatedness of P. multocida and improved annotation of important genes and functional characterization of iron-regulating genes of importance to the bacterial growth.
  12. Fulltext Clinical Investigation of Chemotherapeutic Resistance and miRNA Expressions in Head and Neck Cancers: A Thorough PRISMA Compliant Systematic Review and Comprehensive Meta-Analysis
    Jayaraj R, Polpaya K, Kunale M, Kodiveri Muthukaliannan G, Shetty S, Baxi S, et al.
    Genes (Basel), 2022 Dec 10;13(12).
    PMID: 36553594 DOI: 10.3390/genes13122325
    Background: Chemoresistance is a significant barrier to combating head and neck cancer, and decoding this resistance can widen the therapeutic application of such chemotherapeutic drugs. This systematic review and meta-analysis explores the influence of microRNA (miRNA) expressions on chemoresistance in head and neck cancers (HNC). The objective is to evaluate the theragnostic effects of microRNA expressions on chemoresistance in HNC patients and investigate the utility of miRNAs as biomarkers and avenues for new therapeutic targets. Methods: We performed a comprehensive bibliographic search that included the SCOPUS, PubMed, and Science Direct bibliographic databases. These searches conformed to a predefined set of search strategies. Following the PRISMA guidelines, inclusion and exclusion criteria were framed upon completing the literature search. The data items extracted were tabulated and collated in MS Excel. This spreadsheet was used to determine the effect size estimation for the theragnostic effects of miRNA expressions on chemoresistance in HNC, the hazard ratio (HR), and 95% confidence intervals (95% CI). The comprehensive meta-analysis was performed using the random effects model. Heterogeneity among the data collected was assessed using the Q test, Tau2, I2, and Z measures. Publication bias of the included studies was checked using the Egger's bias indicator test, Orwin and classic fail-safe N test, Begg and Mazumdar rank collection test, and Duval and Tweedie's trim and fill methods. Results: After collating the data from 23 studies, dysregulation of 34 miRNAs was observed in 2189 people. These data were gathered from 23 studies. Out of the 34 miRNAs considered, 22 were up-regulated, while 12 were down-regulated. The TaqMan transcription kits were the most used miRNA profiling platform, and miR-200c was seen to have a mixed dysregulation. We measured the overall pooled effect estimate of HR to be 1.516 for the various analyzed miRNA at a 95% confidence interval of 1.303-1.765, with a significant p-value. The null hypothesis test's Z value was 5.377, and the p-value was correspondingly noted to be less than 0.0001. This outcome indicates that the risk of death is determined to be higher in up-regulated groups than in down-regulated groups. Among the 34 miRNAs that were investigated, seven miRNAs were associated with an improved prognosis, especially with the overexpression of these seven miRNAs (miR15b-5p, miR-548b, miR-519d, miR-1278, miR-145, miR-200c, Hsa- miR139-3p). Discussion: The findings reveal that intricate relationships between miRNAs' expression and chemotherapeutic resistance in HNC are more likely to exist and can be potential therapeutic targets. This review suggests the involvement of specific miRNAs as predictors of chemoresistance and sensitivity in HNC. The examination of the current study results illustrates the significance of miRNA expression as a theragnostic biomarker in medical oncology.
  13. Fulltext Whole-Genome Profiles of Malay Colorectal Cancer Patients with Intact MMR Proteins
    Juhari WKW, Ahmad Amin Noordin KB, Zakaria AD, Rahman WFWA, Mokhter WMMWM, Hassan MRA, et al.
    Genes (Basel), 2021 09 20;12(9).
    PMID: 34573430 DOI: 10.3390/genes12091448
    BACKGROUND: This study aimed to identify new genes associated with CRC in patients with normal mismatch repair (MMR) protein expression.

    METHOD: Whole-genome sequencing (WGS) was performed in seven early-age-onset Malay CRC patients. Potential germline genetic variants, including single-nucleotide variations and insertions and deletions (indels), were prioritized using functional and predictive algorithms.

    RESULTS: An average of 3.2 million single-nucleotide variations (SNVs) and over 800 indels were identified. Three potential candidate variants in three genes-IFNE, PTCH2 and SEMA3D-which were predicted to affect protein function, were identified in three Malay CRC patients. In addition, 19 candidate genes-ANKDD1B, CENPM, CLDN5, MAGEB16, MAP3K14, MOB3C, MS4A12, MUC19, OR2L8, OR51Q1, OR51AR1, PDE4DIP, PKD1L3, PRIM2, PRM3, SEC22B, TPTE, USP29 and ZNF117-harbouring nonsense variants were prioritised. These genes are suggested to play a role in cancer predisposition and to be associated with cancer risk. Pathway enrichment analysis indicated significant enrichment in the olfactory signalling pathway.

    CONCLUSION: This study provides a new spectrum of insights into the potential genes, variants and pathways associated with CRC in Malay patients.

  14. Fulltext Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species
    Kaewdaungdee S, Sudmoon R, Tanee T, Lee SY, Chaveerach A
    Genes (Basel), 2022 Sep 22;13(10).
    PMID: 36292590 DOI: 10.3390/genes13101705
    In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997-152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.
  15. Fulltext Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus)
    Keating SE, Blumer M, Grismer LL, Lin A, Nielsen SV, Thura MK, et al.
    Genes (Basel), 2021 01 19;12(1).
    PMID: 33477871 DOI: 10.3390/genes12010116
    Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.
  16. Fulltext A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress
    Khan F, Chai HH, Ajmera I, Hodgman C, Mayes S, Lu C
    Genes (Basel), 2017 Apr 18;8(4).
    PMID: 28420201 DOI: 10.3390/genes8040121
    The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome.
  17. Fulltext Genomic Analysis to Elucidate the Lignocellulose Degrading Capability of a New Halophile Robertkochia solimangrovi
    Lam MQ, Oates NC, Leadbeater DR, Goh KM, Yahya A, Md Salleh M, et al.
    Genes (Basel), 2022 Nov 17;13(11).
    PMID: 36421811 DOI: 10.3390/genes13112135
    Robertkochia solimangrovi is a proposed marine bacterium isolated from mangrove soil. So far, the study of this bacterium is limited to taxonomy only. In this report, we performed a genomic analysis of R. solimangrovi that revealed its lignocellulose degrading ability. Genome mining of R. solimangrovi revealed a total of 87 lignocellulose degrading enzymes. These enzymes include cellulases (GH3, GH5, GH9 and GH30), xylanases (GH5, GH10, GH43, GH51, GH67, and GH115), mannanases (GH2, GH26, GH27 and GH113) and xyloglucanases (GH2, GH5, GH16, GH29, GH31 and GH95). Most of the lignocellulolytic enzymes encoded in R. solimangrovi were absent in the genome of Robertkochia marina, the closest member from the same genus. Furthermore, current work also demonstrated the ability of R. solimangrovi to produce lignocellulolytic enzymes to deconstruct oil palm empty fruit bunch (EFB), a lignocellulosic waste found abundantly in palm oil industry. The metabolic pathway taken by R. solimangrovi to transport and process the reducing sugars after the action of lignocellulolytic enzymes on EFB was also inferred based on genomic data. Collectively, genomic analysis coupled with experimental studies elucidated R. solimangrovi to serve as a promising candidate in seawater based-biorefinery industry.
  18. Fulltext Association Analysis of 14 Candidate Gene Polymorphism with Depression and Stress among Gestational Diabetes Mellitus
    Lee KW, Ching SM, Ramachandran V, Tusimin M, Mohd Nordin N, Chong SC, et al.
    Genes (Basel), 2019 11 30;10(12).
    PMID: 31801286 DOI: 10.3390/genes10120988
    The association of candidate genes and psychological symptoms of depression, anxiety, and stress among women with gestational diabetes mellitus (GDM) in Malaysia was determined in this study, followed by the determination of their odds of getting psychological symptoms, adjusted for socio-demographical background, maternal, and clinical characteristics. Single nucleotide polymorphisms (SNPs) recorded a significant association between SNP of EPHX2 (rs17466684) and depression symptoms (AOR = 7.854, 95% CI = 1.330-46.360) and stress symptoms (AOR = 7.664, 95% CI = 1.579-37.197). Associations were also observed between stress symptoms and SNP of OXTR (rs53576) and (AOR = 2.981, 95% CI = 1.058-8.402) and SNP of NRG1 (rs2919375) (AOR = 9.894, 95% CI = 1.159-84.427). The SNP of EPHX2 (rs17466684) gene polymorphism is associated with depression symptoms among Malaysian women with GDM. SNP of EPHX2 (rs17466684), OXTR (rs53576) and NRG1 (rs2919375) are also associated with stress symptoms.
  19. Fulltext Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters
    Lim HC, Habib A, Chen WJ
    Genes (Basel), 2021 11 29;12(12).
    PMID: 34946874 DOI: 10.3390/genes12121926
    A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman's center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters.
  20. Fulltext "Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus
    Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, et al.
    Genes (Basel), 2018 Oct 09;9(10).
    PMID: 30304855 DOI: 10.3390/genes9100485
    Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.
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