Genome of Russian wheat aphid an economically important cereal aphid

Abstract

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.

Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)

“…Here we report the genome sequence of R. maidis isolate BTI-1. Comparisons to six previously published aphid genomes [24][25][26][27][28][29][30][31] showed an improved assembly, with most of the sequences assembled into four scaffolds, consistent with the 2n = 8 karyotype of R. maidis.…”

Tracking genetic invasions: genome-wide SNPs reveal the source of pyrethroid-resistantAedes aegypti(yellow fever mosquito) incursions at international ports

“…For instance, Diuraphis noxia (Russian wheat aphid) was first detected in Australia in 2016, and successful control of this species now depends, in part, on identifying past and present sources of incursions (Yazdani et al, 2018). Although a recent genome assembly of D. noxia suggests that this species has low genetic variability (Burger & Botha, 2017), genome-wide SNPs may yet provide sufficient power to determine broad patterns of gene flow. Likewise, similar methodologies may help untangle the complexity of marine invasion narratives, in which many processes remain cryptic when analysed without the appropriate molecular tools (Ojaveer et al, 2014).…”

Partial characterization of the X chromosome of Diuraphis noxia (Hemiptera: Aphididae)

“…Finally, in the cellular component category, contribution of different components was similarly shared between protein complex (30%), nuclease (25%), cytoplasmic part (24%) and intracellular non-membrane bound organelles (21%). This is in stark contrast to that of the rest of the genome, where the largest components comprised of general function and signal transduction (Burger & Botha 2017). The distribution of enzyme codes derived from the PCGs suggested that hydrolases were the largest contributor to enzyme function on X chromosome, representing more than 50% of the total EC classes in the analysis (Fig.…”

“…These poor quality reads were filtered and trimmed by making use of FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_ toolkit/) to ensure that for a pair of paired-end reads each dataset had 90% or more bases with a phred score greater than or equal to Q20. Quality trimmed reads were aligned to the Russian wheat aphid (RWA) reference genome (SAM_Contigs_Version 1.1; GCA_0014 65515.1, Burger & Botha 2017;and GCA_0011 86385.1, Nicholson et al 2015) as well as to that of the pea aphid (Acyr_2.0; GCA_000142985.2, The International Aphid Genomics Consortium 2010) using the Burrows-Wheeler aligner with default parameters (Li & Durbin 2010). The quality of the alignments was assessed by using Qualimap (García-Alcalde et al 2012).…”

“…The mapping against the D. noxia reference genome produced a total of 13,799 PCGs, which represents roughly 43% of the PCGs present in the RWA genome as reported by Burger and Botha (2017) or 72% of that reported by Nicholson et al (2015) (Table 1). The Blast2GO analysis classified the PCGs into three broad functional categories (i.e.…”