Mengenalpasti kepelbagaian spesies hidupan akuatik menggunakan analisis taksonomi di Tasik Ghazali, UKM

Kajian mengenai kepelbagaian hidupan akuatik air tawar adalah penting untuk memelihara dan memulihara ekosistem mereka. Pelbagai pembangunan infrastruktur telah dijalankan di sekitar kawasan UKM sejak kebelakangan tahun ini boleh menjejaskan keseimbangan ekosistem dan kawasan persekitaran tersebut. Tujuan kajian ini dilakukan adalah untuk mengenalpasti taburan hidupan akuatik di Tasik Ghazali, UKM yang ditangkap menggunakan tiga alatan tangkapan ikan aktif dan pasif. Sebanyak 1,268 sampel hidupan akuatik air tawar berjaya dikumpulkan pada lima aktiviti persampelan yang berbeza. Hasil pencerapan morfologi mengkategorikan hasil tangkapan ini kepada lapan spesies iaitu Poecilia reticulata, Gambusia affinis, Puntius sp., Betta pugnax, Clarias batrachus, Macrobrachium lanchesteri, Macrobrachium malayanum dan Gyraulus sp. Daripada jumlah ini, spesies ikan yang paling banyak ditangkap adalah Puntius sp.(464) manakala Clarias batrachus merupakan spesies ikan yang paling kurang ditangkap (7). Akhir sekali, jumlah tangkapan hidupan akuatik lain adalah Macrobrachium sp. (294) dan Gyraulus sp. (7)

Pencirian jujukan genom mitokondria spesies Rafflesia (Rafflesiaceae) di Semenanjung Malaysia

Rafflesia terkenal sebagai tumbuhan yang menghasilkan bunga tunggal yang terbesar di dunia. Namun, ia semakin jarang ditemui dan ialah spesies dalam bahaya. Sistem pengelasan spesies Rafflesia ialah komponen penting dalam usaha pemuliharaan lazimnya bergantung kepada pencirian morfologi bunga. Walau bagaimanapun, pendekatan molekul, termasuk yang berasaskan kepada jujukan genom mitokondria (mtDNA), berupaya menyediakan kaedah pengelasan yang lebih berkesan. Untuk meneroka kemungkinan ini, jujukan mtDNA empat spesies Rafflesia di Semenanjung Malaysia, iaitu R. cantleyi, R. azlanii, R. kerrii dan R. sharifah-hapsahiae telah dihimpun dan dicirikan dalam kajian ini. Bacaan jujukan mtDNA untuk setiap spesies kajian pada mulanya telah ditentukan masing-masing daripada set data genom keseluruhan menggunakan pendekatan pemetaan berbantukan rujukan. Proses penghimpunan secara de novo dan perancahan kemudiannya telah dijalankan ke atas bacaan jujukan yang telah dikenal pasti untuk menghasilkan jujukan mtDNA bagi R. cantleyi (441,992 pb), R. azlanii (472,723 pb), R. kerrii (500,932 pb) dan R. sharifah-hapsahiae (453,747 pb). Seterusnya, anotasi mtDNA bagi setiap spesies telah mengenal pasti sekurang-kurangnya 31 gen pengekodan protein, enam gen tRNA dan tiga rRNA. Perbandingan gen mitokondria mendapati bahawa beberapa gen seperti cob, rpl10, mttB dan ccmB mempamerkan orientasi yang berbeza dalam spesies Rafflesia yang tertentu manakala analisis penjajaran jujukan berganda menunjukkan jujukan gen nad1 adalah berbeza antara keempat-empat spesies Rafflesia yang dikaji. Analisis filogenetik dengan menggunakan jujukan bagi tujuh gen pengekodan protein yang terpelihara berupaya membezakan spesies Rafflesia yang dikaji. Kesimpulannya, hasil pencirian jujukan mDNA menunjukkan bahawa jujukan gen mitokondria yang khusus berupaya membezakan spesies Rafflesia yang dikaji dan berpotensi untuk digunakan bagi tujuan pengenalpastian serta pengelasan spesies Rafflesia dalam usaha pemuliharaan organisma yang unik ini

The Genomic Basis of Adaptation in the Barley Fungal Pathogen Rhynchosporium Commune

Plant fungal pathogens cause significant damage, jeopardize modern agricultural ecosystems and global food security. Fungal pathogens possess a high evolutionary potential that enables rapid evolution to environmental changes. Despite many evidence pointing to local adaptations in fungal pathogens, the genetic basis underpinning the adaptation processes remains poorly understood. The main objective of this PhD thesis is to study the genetic basis of adaptation in Rhynchosporium commune, the causal agent of the devastating barley scald disease. In this study, we resequenced the whole genome of 125 R. commune isolates collected from nine global populations: Iceland, Norway, Finland, Switzerland, Spain, Ethiopia, USA, New Zealand, and Australia. These populations represent a wide range of climatic conditions and agricultural practices with evident of selection acting on quantitative traits of virulence, thermal adaptation, and fungicide sensitivity. The analysis of population structures using single nucleotide polymorphisms (SNPs) spanning the whole genome grouped these isolates into three main clusters with evidence of gene flow among clusters. We performed a genome-wide association study (GWAS) to investigate the genetic basis of fungal resistance to the widely used azole class of fungicides. We found significant associations with SNPs located in conserved genes encoding a vacuolar cation channel YVC1, a transcription activator, and a saccharopine dehydrogenase. The YVC1 gene is involved in a conserved pathway critical to azole resistance in human pathogenic fungi. We found evidence for fitness trade-offs in the isolates accumulating resistance mutations suggesting azole resistance evolutions impose costs. We also performed genome-wide selection scans to identify footprints of recent selection that shaped the genetic variation in R. commune populations. Our analyses revealed widespread signals of selective sweeps across the genomes with little overlaps between the genetic clusters, suggesting that ecological differences drive divergent selection among these clusters. The strongest selective sweeps identified in our study encoded protein associated with various functions in response to abiotic and biotic stresses. Finally, we performed a comparative genomic analysis to investigate the evolution of a known R. commune effector, namely necrosis-inducing protein 1 (NIP1) and its association with host adaptation. In addition to the 125 genome sequences of R. commune, this study also included the whole genome assemblies of nine, eight, and four R. secalis, R. agropyri, and R. orthosporum strains, respectively. We found that the NIP1 effector gene shows presenceabsence polymorphism in all the four species. The phylogenetic analysis revealed a clear division of NIP1 into two major clades we named NIP1A and NIP1B. We found recent duplications of NIP1A and NIP1B following the speciation of R. commune with statistical evidence for the association with fungal virulence. Selection analyses suggest that NIP1A experienced a strong positive selection, while NIP1B experienced a relaxed purifying selection in R. commune. This suggests that selection pressures exerted by the host plant led to the rapid diversification of at least one paralog of the NIP1 effector gene. This study demonstrates the importance of nucleotide polymorphisms and structural variations in the evolution and rapid adaptation of NIP1 effector gene. Overall, these studies demonstrate the potential applications of multiple genomics approaches to substantially enhance our understanding of adaptive evolution in plant fungal pathogen

The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses

ISSN:1462-2912ISSN:1462-292

Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen

Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.ISSN:1759-665

The population genetics of adaptation through copy number variation in a fungal plant pathogen

Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.ISSN:0962-1083ISSN:1365-294

Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.ISSN:1664-462

Compositional Dynamics of Gastrointestinal Tract Microbiomes Associated with Dietary Transition and Feeding Cessation in Lake Sturgeon Larvae

Compromised nutritional conditions associated with dietary transitions and feeding cessation in the wild and during fish aquaculture operations are common and can impact growth and survival. These effects are especially prevalent during early ontogenetic stages. We quantified phenotypic and GI tract microbial community responses with an emphasis on protease-producing bacteria of lake sturgeon (Acipenser fulvescens) larvae, a species of aquacultural and conservational importance. To quantify responses associated with experimental food transition and feeding cessation, we performed a 36-day feeding experiment using two treatments: control and diet transition. However, larvae in the diet transition treatment failed to undergo transition and ceased feeding. Larvae in the diet transition treatment exhibited lower growth (total length and body weight) and survival than control larvae. Treatment had a greater effect than ontogenetic changes on taxonomic composition and diversity of the GI tract microbial community. Proteobacteria dominated the GI tract microbial community of the diet transition larvae whereas Firmicutes dominated the GI tracts of control larvae. Most of the 98 identified protease-producing isolates in both treatments were from genera Pseudomonas and Aeromonas: taxonomic groups that include known fish pathogens. Overall, failing to transition diets affected responses in growth and GI tract microbiome composition and diversity, with the later dysbiosis being an indicator of morbidity and mortality in larval lake sturgeon. Thus, microbiological interrogations can characterize responses to dietary regimes. The results can inform fish culturalists and microbiologists of the importance of dietary practices consistent with the establishment and maintenance of healthy GI tract microbiota and optimal growth during early ontogeny

In Vitro Activity, Stability and Molecular Characterization of Eight Potent Bacteriophages Infecting Carbapenem-Resistant <i>Klebsiella pneumoniae</i>

Background: Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment, including bacteriophage therapy. Bacteriophages are considered very safe and effective in treating bacterial infections. In this study, we characterize eight lytic bacteriophages that were previously isolated by our team against carbapenem-resistant Klebsiella pneumoniae. Methods: The one-step-growth curves, stability and lytic ability of eight bacteriophages were characterized. Restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD) typing analysis and protein profiling were used to characterize the microbes at the molecular level. Phylogenetic trees of four important proteins were constructed for the two selected bacteriophages. Results and conclusions: All eight bacteriophages showed high efficiency for reducing bacterial concentration with high stability under different physical and chemical conditions. We found four major protein bands out of at least ten 15–190 KDa bands that were clearly separated by SDS-PAGE, which were assumed to be the major head and tail proteins. The genomes were found to be dsDNA, with sizes of approximately 36–87 Kb. All bacteriophages reduced the optical density of the planktonic K. pneumoniae abruptly, indicating great potential to reduce K. pneumoniae infection. In this study, we have found that tail fiber protein can further distinguished closely related bacteriophages. The characterised bacteriophages showed promising potential as candidates against carbapenem-resistant Klebsiella pneumoniae via bacteriophage therapy

Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations

The oil palm-pollinating weevil (Elaeidobius kamerunicus Faust) was introduced from Cameroon, West Africa, to Malaysia in 1981, and subsequently, to other oil palm-growing countries as well. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of the weevil populations. A total of 19,148 SNP and 223,200 SSR were discovered from 48 weevils representing three origins (Peninsular Malaysia, Sabah, and Riau) using RAD tag sequencing. Subsequent filtering steps further reduced these to 1000 SNP and 120 SSR. The selected 220 SNP exhibited a polymorphism information content (PIC) of 0.2387 (&plusmn;0.1280), and 8 SSR had the PIC of 0.5084 (&plusmn;0.1928). These markers were found to show sufficient polymorphism, making it possible to assign 180 weevils into three major clusters from Ghana, Cameroon, and Southeast Asia (mainly in Malaysia and Indonesia). These DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, the presence of null alleles in the SSR markers, due to limited flexibility of the probe design on the short RAD tags, led to an underestimation of heterozygosity within the populations. Hence, the developed SNP markers turned out to be more efficient than the SSR markers in the genetic diversity assessment of the E. kamerunicus populations. The genetic information provides useful insight into developing guidelines for the genetic monitoring and conservation planning of E. kamerunicus