Browsing by Author "Burger, Nicolaas Francois Visser"

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    Diuraphis noxia biotypes ascribed through genotypic characterization and utilization of their endosymbiont, buchnera aphidicola
    (Stellenbosch : Stellenbosch University, 2022-11) Burger, Nicolaas Francois Visser; Oberholster, Anna-Maria; Stellenbosch University. Faculty of AgriSciences. Dept. of Forest and Wood Science. Genetics.
    ENGLISH ABSTRACT: The aphid Diuraphis noxia (more commonly known as the Russian wheat aphid), is a pest of wheat and other small grains which has successfully spread to all global wheat producing regions. Feeding damage of the aphid results in characteristic longitudinal streaking, leaf rolling, and head trapping which all contribute to a lowered crop yield. Although wheat cultivars resistant to the aphid have been successful in curbing yield losses, the aphid has overcome most of these resistant lines through the process of biotypification. As reproduction of the aphid is limited to cyclical parthenogenesis, and thus unable to generate genetic diversity through chromosomal crossover, the exact means of how biotypification occurs remains elusive. With the availability of the only known genealogically linked D. noxia biotypes SA1 and SAM, this study attempted to ascertain their genomic backgrounds to better understand how they could occupy the extremes of the virulence scale. Sequencing, assembly, and comparisons of the genomes of these biotypes revealed an unexpected number of genetic polymorphisms and an extremely AT rich genome. The roughly 400 Mb genome, containing just over 32,000 protein coding genes, appears to have many polymorphisms in genes responsible for protein expression and turnover, which supports previous results indicating that biotypes differ in their ability to regulate their transcription. The unexpected number of polymorphisms would indicate that there is a yet unknown mechanism that enables these aphids to induce genomic variation in the absence of sexual reproduction. Further analysis of the salivary protein genes shared between the biotypes indicates that copy number and polymorphisms in genes associated with defence against plant volatiles also play a role in how these biotypes interact with their wheat host. Through comparative transcriptomics with other aphid transcriptomes, this study was also able to identify genes preferentially expressed in aphid head and salivary tissue through a proof-of-concept comparison, thereby enabling the future discovery of D. noxia salivary effectors. Lastly, this study was able to assemble and compare the genome of the sole endosymbiont of D. noxia, Buchnera aphidicola, with that of nine other genomes. From this the overall importance of several genic features such as gene length and percentage GC content was found to be critical for the maintenance of Buchnera genes when compared to their closest free-living relative, Escherichia coli. It was also revealed that D. noxia contains multiple Buchnera isotypes and that their genes are polyadenylated which may indicate a mechanism for their regulation. With the availability of these datasets, the as of yet unanswered question of the process of biotypification within D. noxia is becoming clearer.
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    Genome of Russian wheat aphid an economically important cereal aphid
    (BioMed Central, 2017-12-28) Burger, Nicolaas Francois Visser; Botha, Anna-Maria
    Although the hemipterans ( Aphididae ) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, namely Acyrthosiphon pisum (pea aphid), Rhodnius prolixus (Kissing bug), Myzus persicae (Green peach aphid) and Diuraphis noxia (Russian wheat aphid). As a significant proportion of agricultural pests are phloem feeding aphids, it is crucial for sustained global food security that a greater understanding of the genomic and molecular functioning of this family be elucidated. Recently, the genome of US D. noxia biotype US2 was sequenced but its assembly only incorporated ~ 32% of produced reads and contained a surprisingly low gene count when compared to that of the model/first sequenced aphid, A. pisum . To this end, we present here the genomes of two South African Diuraphis noxia (Kurdjumov, Hemiptera : Aphididae ) biotypes (SA1 and SAM), obtained after sequencing the genomes of the only two D. noxia biotypes with documented linked genealogy. To better understand overall targets and patterns of heterozygosity, we also sequenced a pooled sample of 9 geographically separated D. noxia populations (MixIX). We assembled a 399 Mb reference genome ( PRJNA297165 , representing 64% of the projected genome size 623 Mb) using ± 28 Gb of 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SAM, whilst ± 13 Gb 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SA1 were generated to facilitate genomic comparisons between the two biotypes. Sequencing the MixIX sample yielded ±26 Gb 50 bp paired-end SOLiD reads which facilitated SNP detection when compared to the D. noxia biotype SAM assembly. Ab initio gene calling produced a total of 31,885 protein coding genes from the assembled contigs spanning ~ 399 Mb (GCA_001465515.1).