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Genome of Russian wheat aphid an economically important cereal aphid

dc.contributor.authorBurger, Nicolaas Francois Visseren_ZA
dc.contributor.authorBotha, Anna-Mariaen_ZA
dc.date.accessioned2018-01-05T10:07:21Z
dc.date.available2018-01-05T10:07:21Z
dc.date.issued2017-12-28
dc.identifier.citationBurger, N. F. V. & Botha, A.-M. 2017. Genome of Russian wheat aphid an economically important cereal aphid. Standards in Genomic Sciences, 12:90, doi:10.1186/s40793-017-0307-6.
dc.identifier.issn1944-3277 (online)
dc.identifier.otherdoi:10.1186/s40793-017-0307-6
dc.identifier.urihttp://hdl.handle.net/10019.1/103026
dc.descriptionCITATION: Burger, N. F. V. & Botha, A.-M. 2017. Genome of Russian wheat aphid an economically important cereal aphid. Standards in Genomic Sciences, 12:90, doi:10.1186/s40793-017-0307-6.
dc.descriptionThe original publication is available at https://standardsingenomics.biomedcentral.com
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.
dc.description.abstractAlthough 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).
dc.description.urihttps://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-017-0307-6
dc.format.extent12 pages
dc.language.isoen
dc.publisherBioMed Central
dc.subjectDiuraphis noxiaen_ZA
dc.subjectAphidsen_ZA
dc.subjectArthropod pestsen_ZA
dc.subjectGenomicsen_ZA
dc.titleGenome of Russian wheat aphid an economically important cereal aphiden_ZA
dc.typeArticle
dc.date.updated2017-12-31T04:18:23Z
dc.description.versionPublisher's version
dc.rights.holderAuthors retain copyright


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