Complete Mitochondrial Genome of<i>Diuraphis noxia</i>(Hemiptera: Aphididae) from Nine Populations, SNP Variation between Populations, and Comparison with Other Aphididae Species

Jager, Laura-Ellen De; Burger, N. Francois V.; Botha, Anna‐Maria

doi:10.4001/003.022.0409

Cited by 9 publications

(7 citation statements)

References 52 publications

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“…scutellata; and ±115 bp for the hybrids. Variation in mitogenome size is typically the consequence of variation in the non-coding regions in insects 45 , which is consistent with our observations of A . mellifera mitogenomes.…”

Section: Discussionsupporting

confidence: 92%

“…De Jager et al . 45 found that the greatest variation in the Diuraphis noxia (Hemiptera: Aphididae) was observed in the ND5 nucleotide gene but the causal effects of variation in ND5 was not fully understood. These results suggest that the degree of stabilizing selection differs on different genes within the mitochondria, and that this likely also differs among different taxonomic groups.…”

Section: Discussionmentioning

confidence: 99%

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Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Eimanifar

Kimball

Braun

2018

Sci Rep

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Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Eimanifar

Kimball

Braun

2018

Sci Rep

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“…The cornicles above the cauda give the aphid the appearance of having two tails and it is believed that these structures help aphids with predator defense [ 3 ]. Alignments using whole mitochondrial genomes [ 19 ] indicate that the closest relative of D. noxia is Acyrthosiphon pisum (Fig. 2 ).…”

Section: Organism Informationmentioning

confidence: 99%

“…Genomic DNA from adult aphids of the South African D. noxia biotypes SAM [ 11 ] and SA1 [ 16 ], and that of the pooled MixIX sample, was used for next generation sequencing (NGS) during the study. The genomic DNA extraction of aphid DNA was conducted as follows; whole aphids were flash frozen in liquid nitrogen, ground and DNA extracted using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer’s protocol [ 19 ]. The MixIX sample consisted of 2 μg of genomic DNA for each D. noxia representative, which consisted of three field collected South African D. noxia populations (SA1 < SA2 < SA3 in order of increasing virulence); one field collected Czech D. noxia population; two insectary reared US D. noxia populations (US1 < US2 in order of increasing virulence); one field collected Syrian D. noxia population; and two field collected Argentinian D. noxia populations.…”

Section: Genome Sequencing Informationmentioning

confidence: 99%

“…Raw sequences obtained from the Illumina HiSeq2000 sequencing of the D. noxia SAM biotype, and from the SOLiD system for the MixIX sample, were trimmed and filtered so that all bases had a minimum Phred score of 20. Reads mapping to 10.1601/nm.3113 of D. noxia [ CP013259 .1] and that of the mitochondrion of D. noxia [ 19 ] were removed from further analysis. Optimal k -mer length for the D. noxia biotype SAM assembly was determined using KMERGENIE [ 23 ], while using DSK [ 24 ] to estimate the optimal k -mer frequency cut-off.…”

Section: Genome Sequencing Informationmentioning

confidence: 99%

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Genome of Russian wheat aphid an economically important cereal aphid

Burger

Botha

2017

Stand in Genomic Sci

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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).Electronic supplementary materialThe online version of this article (10.1186/s40793-017-0307-6) contains supplementary material, which is available to authorized users.

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Comparison of full mitochondrial genomes for the rice weevil, Sitophilus oryzae and the maize weevil, Sitophilus zeamais (Coleoptera: Curculionidae)

et al. 2016

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Complete Mitochondrial Genome ofDiuraphis noxia(Hemiptera: Aphididae) from Nine Populations, SNP Variation between Populations, and Comparison with Other Aphididae Species

Cited by 9 publications

References 52 publications

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Genome of Russian wheat aphid an economically important cereal aphid

Comparison of full mitochondrial genomes for the rice weevil, Sitophilus oryzae and the maize weevil, Sitophilus zeamais (Coleoptera: Curculionidae)

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