Genomic Variation of Five Indonesian Cacao (Theobroma Cacao L.) Varieties Based on Analysis Using Next Generation Sequencing

Indonesian cacao productivity is still low mainly due to the lack availability of superior cacao planting materials. A new breeding method is necessary to expedite cacao yield improvement programs. To date, no study has yet been done to characterize Indonesian cacao varieties at the whole genome level. The objective of this study was to characterize genomic variation of five superior Indonesian cacao varieties using next-generation sequencing. Genetic materials used were five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4, SUL2 and ICS13. Genome sequences were mapped to the cacao reference genome sequence of Criollo variety. Sequence alignment and genomic variation discovery were done using Bowtie2 and mpileup software of Samtools, respectively. A total of 2,326,088 single nucleotide polymorphisms (SNPs) and 362,081 insertions and deletions (Indels) were obtained from this study. In average, a DNA variant was identified in every 121 nucleotides of the genome sequence. Most of the DNA variants were located outside the genes. Only 347,907 SNPs and Indels (13.18%) were located within protein coding region (exon). Among the DNA variations within exon, 188,949 SNPs caused missense mutation and 1,535 SNPs induced nonsense mutation. Unique gene-based SNPs were also discovered from this study that can be used as fingerprints for the particular cacao variety. The DNA variants obtained were excellent DNA marker resources to support cacao breeding programs. The SNPs discovered are useful as materials for genome-wide SNP chip development to be used for gene and QTL tagging of important traits for expediting national cacao breeding program

Revealing the molecular signatures of host-pathogen interactions.

Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary co-existence

MHC-I genotype drives early immune selection of oncogenic mutations.

MHC-I exposes the intracellular contents to immune cells for surveillance of cellular health. Due to high genomic variation, individuals' immune systems differ in their ability to expose and eliminate cancer-causing mutations. These personalized immune blind spots create specific oncogenic mutation predispositions within patients and influence their prevalence across populations

Genomic variation in rotaviruses

The rotaviruses are a recently defined ubiquitous group of viruses responsible for causing acute-gastroenteritis in human infants and young animals. Biochemical studies have shown that the rotavirus genome consists of 11 segments of double-stranded RNA (dsRNA). This thesis concerns an investigation of the nature and extent of genomic variation in rötaviruses. A rapid and sensitive method for analyzing the genome profiles of rotavirus field isolates was developed. This is based on the direct extraction of dsRNA from faecal samples followed by radiolabelling with [32P3 pCp using T4 RNA ligase. This procedure has been further developed to produce a method for generating diagnostic fingerprints from individual species of dsRNA. A detailed structural study making use of this fingerprinting method has been undertaken on bovine, porcine and human rotavirus isolates. These analyses show that genome segment mobility variations are always associated with detectable changes in nucleotide sequence. They also show that corresponding genome segments with no mobility variation can have sequence-changes at least as great as those found in segments showing electrophoretic mobility variation. These results also revealed evidence for genome segment specific regions of terminal sequence conservation. Evidence for the occurrence of genome segment reassortment between viruses in the field was obtained. Finally evidence for the existence of a 'new' porcine rotavirus which is antigenically unrelated to previously described rotaviruses and has an unusual pattern for it's 11 genome segments is presented

Designing probiotic therapies with broad-spectrum activity against a wildlife pathogen

Host-associated microbes form an important component of immunity that protect against infection by pathogens. Treating wild individuals with these protective microbes, known as probiotics, can reduce rates of infection and disease in both wild and captive settings. However, the utility of probiotics for tackling wildlife disease requires that they offer consistent protection across the broad genomic variation of the pathogen that hosts can encounter in natural settings. Here we develop multi-isolate probiotic consortia with the aim of effecting broad-spectrum inhibition of growth of the lethal amphibian pathogen Batrachochytrium dendrobatidis (Bd) when tested against nine Bd isolates from two distinct lineages. Though we achieved strong growth inhibition between 70 and 100% for seven Bd isolates, two isolates appeared consistently resistant to inhibition, irrespective of probiotic strategy employed. We found no evidence that genomic relatedness of the chytrid predicted similarity of inhibition scores, nor that increasing the genetic diversity of the bacterial consortia could offer stronger inhibition of pathogen growth, even for the two resistant isolates. Our findings have important consequences for the application of probiotics to mitigate wildlife diseases in the face of extensive pathogen genomic variation

A molecular diagnostic for tropical race 4 of the banana

This study analysed genomic variation of the translation elongation factor 1 (TEF-1) and the intergenic spacer region (IGS) of the nuclear ribosomal operon of Fusarium oxysporum f. sp. cubense (Foc) isolates, from different banana production areas, representing strains within the known races, comprising 20 vegetative compatibility groups