Improved genome assembly and annotation of the soybean aphid (Aphis glycinesMatsumura)

Abstract

Aphids are an economically important insect group due to their role as plant disease vectors. Despite this economic impact, genomic resources have only been generated for a small number of aphid species. The soybean aphid (Aphis glycines Matsumura) was the third aphid species to have its genome sequenced and the first to use long-read sequence data. However, version 1 of the soybean aphid genome assembly has low contiguity (contig N50 = 57 KB, scaffold N50 = 174 KB), poor representation of conserved genes and the presence of genomic scaffolds likely derived from parasitoid wasp contamination. Here, I use recently developed methods to reassemble the soybean aphid genome. The version 2 genome assembly is highly contiguous, containing half of the genome in only 40 scaffolds (contig N50 = 2.00 Mb, scaffold N50 = 2.51 Mb) and contains 11% more conserved single copy arthropod genes than version 1. To demonstrate the utility this improved assembly, I identify a region of conserved synteny between aphids and Drosophila containing members of the Osiris gene family that was split over multiple scaffolds in the original assembly. The improved genome assembly and annotation of A. glycines demonstrates the benefit of applying new methods to old data sets and will provide a useful resource for future comparative genome analysis of aphids.

Genome Sequence of the Banana Aphid,Pentalonia nigronervosaCoquerel (Hemiptera: Aphididae) and Its Symbionts

“…The Wolbachia WolPenNig assembly was more fragmented (1.46 Mb total length, 182 scaffolds, N50 = 15.5kb). Despite this, the WolPenNig assembly is likely highly complete as it is similar in size to both a more contiguous long-read assembly of a strain found in the soybean aphid (1.52 Mb total length, 9 contigs, N50 = 841 Kb [Mathers 2020]) and to the reference assembly of Wolbachia wRi (Klasson et al 2009) from Drosophila simulans (1.44 Mb total length, 1 contig). Furthermore, BUSCO analysis using the proteobacteria gene set (n = 221) reveals that WolPenNig has similar gene-level completeness to these high-quality assemblies, with 81% of BUSCO genes found as complete, single copies (Supplementary Figure 4).…”

“…To investigate the phylogenetic position of P. nigronervosa within aphids we carried out orthology clustering of 223,889 protein sequences from P. nigronervosa, our improved M. cerasi annotation, and seven previously published aphid genomes (Nicholson et al 2015;Thorpe et al 2018;Chen et al 2019;Mathers 2020;Mathers et al 2020). Although the number of aphid species with sequenced genomes is still low, the included species span three aphid tribes (Macrosphini, Aphidini and Lachnini) and approximately 100 million years of aphid evolution (Kim et al 2011;Hardy et al 2015;Julca et al 2019).…”

“…To date, genome sequencing efforts have focused on members of the aphid tribe Macrosiphini (within subfamily Aphidinae), including the widely studied aphids Acyrthosiphon pisum (pea aphid) (IAGC 2010; Li et al 2019;Mathers et al 2020) and Myzus persicae (green peach aphid) (Mathers et al 2017(Mathers et al , 2020, as well as other important pest species such as Diuraphis noxia (Russian wheat aphid) (Nicholson et al 2015). Recently, additional genome sequences have become available for members of the tribe Aphidini (also in the subfamily Aphidinae) (Wenger et al 2017;Thorpe et al 2018;Chen et al 2019;Quan et al 2019;Mathers 2020) and the subfamily Lanchinae (Julca et al 2019), broadening the phylogenetic scope of aphid genomic resources. However, many clades of the aphid phylogeny are still missing or underrepresented in genomic studies.…”

Novel genetic basis of resistance to Bt toxin Cry1Ac inHelicoverpa zea

“…2019; Wan et al 2019; Ferguson et al . 2020; Jaworski et al 2020; Ma et al 2020; Mathers 2020; Schmidt et al 2020; Xu et al 2021). For the short-read assembly, we collected and sequenced 30 GA-R larvae as described below.…”

The Resistant Soybean-Aphis glycines Interaction: Current Knowledge and Prospects

“…Although this mini review does not discuss the biology of the soybean aphid itself, ongoing studies to genetically distinguish the four biotypes are critical to determine distinguishing factors that make certain aphid biotypes virulent on resistant soybean. Publication of the updated version of the Aphis glycines genome provides a reliable reference and enhances the ability to detect biotype variability, advancing biotype-specific genetic studies ( Giordano et al., 2020 ; Mathers, 2020 ). Future studies should also examine virulence of aphid biotypes on resistant soybean and utilization of additional sources of resistance to develop soybean cultivars that confer resistance to the most virulent aphid biotype 4.…”