Abstract
The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid’s apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.
Highlights
The genomes of M. persicae clones G006 and O were derived from the sequencing of a single aphid clone, whereas the A. glycines genome, currently available in Genbank and referred as a “hybrid” genome, derived from the simultaneous sequencing of assembling of both laboratory colonies and natural populations collected from soybean fields [10]
Clone O showed 30.5% of genes involved in clone-specific deletions, 57.2% had an orthologue in the two M. persicae clones, and 4.3% of genes were duplicated
M. persicae clone O was sampled in the UK from Chinese cabbage plants, Brassica rapa [26], whereas clone G006 was collected from pepper, Capsicum, annuum in Geneva, Switzerland [26] making the comparison of their genomes useful in evaluating the extant of genome conservation in clones collected in very different habitats [18,27]
Summary
In the last few decades several insect genomes have been sequenced, assembled and annotated covering six different orders belonging to both holometabolous and hemimetabolous species [1,2,3,4,5,6].current genomic data are not limited to highly studied ‘model’ insects such as Drosophila melanogaster and Anopheles gambiae, and other species, like the honey bee Apis mellifera [1], the red flour beetle Tribolium castaneum [3], the yellow fever mosquito Aedes aegypti [7], the mosquito Culex quinquefasciatus [4], and the blood-sucking bug, Rhodnius prolixus [6].In view of their relevance as serious pests of a variety of crops of agricultural and horticultural importance , several aphid species (Hemiptera: Aphididae) have been studied to date, whilst economic resources are available for the pea aphid, Acyrthosiphon pisum [8], the Russian wheat aphid, Diuraphis noxia [9], the soybean aphid, Aphis glycines (from a composite of multiple North American populations) [10], the cotton aphid Aphis gossypii [11], as well as for additional species whose genomesInsects 2019, 10, 368; doi:10.3390/insects10100368 www.mdpi.com/journal/insectsInsects 2019, 10, 368 are available in Aphidbase, even if their papers are still unpublished: i.e. Aphis glycines biotype 1, the black cherry aphid, Myzus cerasi; the peach potato aphid, Myzus persicae; and the bird cherry-oat aphid, Rhopalosiphum padi.Genomic resources have prompted several comparisons among species and this approach has allowed, for instance, the identification of the molecular pathways evolving in each aphid species, sometimes fast, and/or the study of gene families, the functions of which are related to environmental adaptation [11,12], together with the identification of species-specific gene expansions or losses [12].Interestingly, even if aphid genomic resources include genome assemblies of biotypes/clones belonging to a same species [10], aphid intra-specific variability has been very largely neglected, despite the usefulness of this comparison. Current genomic data are not limited to highly studied ‘model’ insects such as Drosophila melanogaster and Anopheles gambiae, and other species, like the honey bee Apis mellifera [1], the red flour beetle Tribolium castaneum [3], the yellow fever mosquito Aedes aegypti [7], the mosquito Culex quinquefasciatus [4], and the blood-sucking bug, Rhodnius prolixus [6]. Intra-specific comparative analysis could be useful to validate genomic data, more especially considering the fact that aphid genomes are currently scattered in thousands of contigs, thereby making the evaluation of their quality difficult
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