Draft genome of the cotton aphid Aphis gossypii

Quan, Qingmei; Hu, Xiao; Pan, Bohu; Zeng, Baosheng; Wu, Ningning; Fang, Gangqi; Cao, Yanghui; Chen, Xiao‐Ya; Li, Xuan; Huang, Yongping; Zhan, Shuai

doi:10.1016/j.ibmb.2018.12.007

Cited by 59 publications

(59 citation statements)

References 69 publications

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“…They are also important models used to study plant-insect interactions (Hogenhout and Bos 2011;Ferry et al 2004), speciation genomics (Pecoud and Simon 2010;Peccoud et al 2009;Hawthorne and Via 2001) and sex chromosome evolution (Jaquiéry et al 2018(Jaquiéry et al , 2013. Despite their importance, only a small number of the approximately 5,000 described aphid species have had their genomes sequenced (IAGC 2010;Nicholson et al 2015;Wenger et al 2017;Mathers et al 2017;Chen et al 2019;Jiang et al 2019;Quan et al 2019; Thorpe et al 2018), limiting genomic insights into their diversity and evolution. Furthermore, although highly contiguous assemblies have recently been published for two aphid species (Jiang et al 2019;Chen et al 2019), the majority of publicly available aphid genomes were sequenced using second-generation short-read sequencing technology, resulting in fragmented assemblies that contain thousands of genomic scaffolds.…”

Section: Introductionmentioning

confidence: 99%

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

Mathers

2019

Preprint

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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.

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Section: Introductionmentioning

confidence: 99%

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

Mathers

2019

Preprint

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“…The screening of a large number of candidate genes by RNAi could greatly enhance the mortality and promote the application of RNAi‐based pest control . Based on the currently sequenced aphid genomes, there are approximately 10 249 to 19 182 genes; therefore, our test of only seven genes represents a tiny fraction of the whole gene set that could be explored. Thus, a large number of candidate genes should be tested for toxicity by RNAi and the easy‐to‐adapt topical RNAi method developed in this study would be ideal for this work; (ii) herbivorous arthropods have co‐evolved with host plants for millions of years.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, research on some of these agriculturally important species, such as pea aphid ( Acyrthosiphon pisum ), M. persicae , Russian wheat aphid ( Diuraphis noxia ), Ap. gossypii , and soybean aphid ( Aphis glycines ), has been greatly enhanced owing to their sequenced genomes. In addition, transcriptome analyses have identified large amounts of gene expression information .…”

Section: Introductionmentioning

confidence: 99%

Topical dsRNA delivery induces gene silencing and mortality in the pea aphid

Niu

Yang

Tian

et al. 2019

Pest Management Science

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BACKGROUND: With the growing number of available aphid genomes and transcriptomes, an efficient and easy-to-adapt tool for gene function study is urgently required. RNA interference (RNAi), as a post-transcriptional gene silencing mechanism, is important as a research tool for determining gene functions and has potential as a novel insect control strategy. However, these applications have been hampered by the lack of effective dsRNA delivery approaches in aphids. RESULTS:Here, we developed a convenient and efficient dsRNA delivery method, topical RNAi, in aphids. An investigation of its dose and time-dependent RNAi efficiencies revealed that with as little as 60 ng dsRNA per adult pea aphid (Acyrthosiphon pisum), the indicator gene, Aphunchback, could be significantly silenced within 2 h of exposure. The method was further validated by successfully silencing other different genes, and it was also efficient toward two other aphid species, Aphis citricidus and Myzus persicae. Furthermore, a noticeable mortality was also observed in pea aphids using topical RNAi-mediated gene silencing, within 4 days post-dsRNA application for four out of seven tested genes. CONCLUSION: Compared with the currently used dsRNA delivery methods in aphids, microinjection and ingestion, topical RNAi is time-and cost-effective, which could greatly influence RNAi-based gene functional studies and potential candidate gene selection for developing RNAi-based aphid control strategies in the future.

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“…Currently there are 12 publicly available genomes of agricultural aphid pests which differ in genome size, life history patterns, geographic distribution and impact as pests: Ap. gossypii (Quan et al, 2019), Myzus persicae (Mathers et al, 2017), M. cerasi (Aphid-Base; https://bipaa.genouest.org/is/aphidbase/), Acyrthosiphon pisum (The International Aphid Genomics Consortium, 2010), Diuraphis noxia (Nicholson et al, 2015), Melanaphis sacchari (NCBI; PRJNA413550), Rhopalosiphum maidis (NCBI; PRJNA480062), R. padi (AphidBase; https://bipaa.genouest.org/is/aphidbase/), Schizaphis graminum, and Sipha slava (NCBI; PRJNA472250), including the genome of Ap. glycines obtained by sequencing specimens from laboratory colonies and field specimens from six geographic localities in the Midwest U.S. (Wenger et al, 2017) and the genome of the strain of Ap.…”

Section: Introductionmentioning

confidence: 99%

Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Giordano

Donthu

Zimin

et al. 2020

Insect Biochemistry and Molecular Biology

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The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.

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Draft genome of the cotton aphid Aphis gossypii

Cited by 59 publications

References 69 publications

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

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

Topical dsRNA delivery induces gene silencing and mortality in the pea aphid

Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

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