Abstract
BackgroundThe 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.FindingsThe 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.ConclusionsA 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.
Highlights
Reviewer Comments to Author: The authors reported a high-quality genome assembly of the corn leaf aphid, Rhopalosiphum maidis Fitch
Since this study is the most successful genome sequencing in aphids far, detailed procedures would be useful for readers
I list specific points as follows: * p.4: Around 50 ug of high molecular weight DNA was prepared ... : High molecular weight (HMW) genome preparation is key to a successful genome project
Summary
Title: Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch) Reviewer Comments to Author: The authors reported a high-quality genome assembly of the corn leaf aphid, Rhopalosiphum maidis Fitch. This is the first chromosome-level reference genome for aphids. I congratulate the authors on the excellent genome assembly generated by the combination of long-read sequencing and Hi-C technology.
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