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

  1. Wenbo Chen
  2. Sara Shakir
  3. Mahdiyeh Bigham
  4. Annett Richter
  5. Zhangjun Fei
  6. Georg Jander

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Abstract

Background

The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.

Findings

The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate–glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.

Conclusions

A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz033

    Wenbo Chen 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Wenbo ChenSara Shakir 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 148533Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liège, Gembloux, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sara ShakirMahdiyeh Bigham 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mahdiyeh BighamZhangjun Fei 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 148532US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zhangjun FeiGeorg Jander 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Georg JanderFor correspondence: gj32@cornell.edu

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101619 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101620 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101621

  2. Version published to 10.1093/gigascience/giz033
  3. Version published to 10.1101/438499v2 on bioRxiv
  4. Version published to 10.1101/438499v1 on bioRxiv