Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts

Abstract

The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervosa we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervosa, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervosa falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.

Hybridisation has shaped a recent radiation of grass-feeding aphids

“…2018). Following the low-cost genome assembly approach set out in Mathers et al . (2020) we generated 23.9 Gb (62x coverage) of PCR-free Illumina genome sequence data and 14.8 Gb of strand-specific RNA-seq data for genome assembly scaffolding and genome annotation ( Supplementary Table 1 ).…”

“…We followed the procedures described in Mathers et al . (2020) to generate low-cost short-read de novo genome assemblies of S. avenae and M. dirhodum .…”

“…Erroneously duplicated content (i.e. haplotigs) in the initial draft assemblies was identified and removed using the K-mer based deduplication pipeline described in Mathers et al . (2020).…”

RNAi technology for management of banana bunchy top disease

“…The availability of annotated full genome and transcriptome sequence data will be a major advantage and a step in designing RNAi constructs targeting multiple gene families for optimal efficiency. A highly complete genome assembly of P. nigronervosa and its symbiotic bacteria Buchnera aphidicola and Wolbachia was recently published (Mathers, Mugford, Hogenhout, & Tripathi, 2020). The availability of the genome sequence of banana aphid would help to decipher the RNAi pathway gene(s).…”

Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

“…Around 100 out of approximately 5000 known aphid species are significant agricultural pests due to their feeding damages and/or disease transmission (Blackman & Eastop, 2020). Currently, studies on aphid genomes have mainly focused on the subfamily Aphidinae (International Aphid Genomics Consortium, 2010; Li, Zhao, et al, 2019; Li et al, 2019; Mathers, 2020; Mathers et al, 2017, 2020; Mathers, Wouters, et al, 2020; Nicholson et al, 2015; Thorpe et al, 2018; Wenger et al, 2016). Genome sequencing on species from other subfamilies that are distantly related to Aphidinae is relatively limited (Biello et al, 2021; Julca et al, 2020).…”