De novo assembly and annotation of Popillia japonica's genome with initial clues to its potential as an invasive pest

Abstract

Background: The spread of Popillia japonica in non-native areas (USA, Canada, the Azores islands, Italy and Switzerland) poses a significant threat to agriculture and horticulture, as well as to endemic floral biodiversity, entailing that appropriate control measures must be taken to reduce its density and limit its further spread. In this context, the availability of a high quality genomic sequence for the species is liable to foster basic research on the ecology and evolution of the species, as well as on possible biotechnologically-oriented and genetically-informed control measures.

Results: The genomic sequence presented and described here is an improvement with respect to the available draft sequence in terms of completeness and contiguity, and includes structural and functional annotations. A comparative analysis of gene families of interest, related to the species ecology and potential for polyphagy and adaptability, revealed a contraction of gustatory receptor genes and a paralogous expansion of some subgroups/subfamilies of odorant receptors, ionotropic receptors and cytochrome P450s.

Conclusions: The new genomic sequence as well as the comparative analyses data may provide a clue to explain the staggering invasive potential of the species and may serve to identify targets for potential biotechnological applications aimed at its control.

Keywords: Beetles; Cytochrome P450; Gustatory receptors; Invasive species; Ionotropic receptors; Japanese beetle; Odorant receptors.

Fig. 1

Adult specimen of P. japonica. Photo courtesy of Mr. Luciano Gollini

Fig. 2

Phylogenetic relationships among Coleoptera based on high-quality aligned single-copy orthologs derived from the BUSCO analysis. All the nodes have a bootstrap value of 1. Each species is coupled with the corresponding BUSCO graphic. The two available genomes of P. japonica (from the CanSeq150 project as well as this study) are highlighted in red. Higher ranking categories are indicated at relevant nodes with green shades

Fig. 3

Relative abundance, as percentages, of transposable elements in the P. japonica’s genome. TE classes are based on RepeatMasker annotation. Despite the high quantity of unclassified repetitive regions, the vast majority (~ 57.56%) is represented by DNA elements and LINEs. Classes are color coded

Fig. 4

Phylogenetic reconstruction of gustatory receptors (including splicing isoforms) observed in the genome of P. japonica as well as T. castaneum, L. decemlineata, D. ponderosae and A. planipennis. Relevant clades are color coded. The large number of non-annotated branches reflects current limitations in knowledge of this receptors. Putative orthologs in P. japonica are highlighted in red. The tree is rooted with the clade of conserved sugar GRs. Supported nodes (SH-aLRT >  = 70, UFB >  = 85) are identified with a dark gray dots along the branch

Fig. 5

Phylogenetic reconstruction of odorant receptors (including splicing isoforms) in the genome of P. japonica as well as A. glabripennis, L. decemlineata and T. castaneum. Relevant clades, following the classification in [15], are color coded. Putative orthologs in P. japonica are highlighted in red. Eighteen JB outliers were not recovered within orthologous clades and hence considered as outliers. The tree is rooted on the conserved Orco group. Supported nodes (SH-aLRT >  = 70, UFB >  = 85) are identified with a dark gray dot along the branch

Fig. 6

OR gene counts (excluding splicing variants) in the genome of P. japonica as well as A. glabripennis, L. decemlineata and T. castaneum. Subfamilies were defined following the phylogenetic reconstruction of ORs (Fig. 5). Group 2B, 3 and 4 show a strong expansion in P. japonica’s genome (from 1.2x to 21x) in comparison to other species. Instead, Group 1 and 5A apparently experienced a gene contraction in JB genome. Species are color-coded

Fig. 7

Phylogenetic reconstruction of ionotropic receptors (including splicing isoforms) in the genome of P. japonica, as well as T. castaneum, L. decemlineata, D. ponderosae, A. planipennis. The two annotated clades (antennal and divergent) are color coded. Putative orthologs in P. japonica are highlighted in red. Fine scale subfamily level annotation of groups is provided in the outer most circle. The different density of subfamilies level annotation reflects the current limited knowledge of gene divergent IR subfamilies. The tree is rooted on the conserved IR8a and IR25a clades. Supported nodes (SH-aLRT >  = 70, UFB >  = 85) are shown with a dark gray dot along the branch

Fig. 8

IR gene counts (excluding splicing variants) in the genome of P. japonica as well as T. castaneum, L. decemlineata, D. ponderosae, A. planipennis. Subfamilies were defined following the phylogenetic reconstruction of IRs (Fig. 7). IRs which did not belong to any family were cataloged as “divergent IRs”, while the well clustered monophyletic paralogous clade of P. japonica is classified as “JB IR basal group”. Species are color-coded

Fig. 9

Phylogenetic reconstruction of CYP 450 (including splicing isoforms) in the genome of P. japonica as well as D. ponderosae, N. vespilloides and T. castaneum. Clans are color coded following [14]. Putative orthologs in P. japonica are highlighted in red. All CYP clans were found as monophyletic clades. The tree is mid-point rooted. Supported nodes (SH-aLRT >  = 70, UFB >  = 85) are identified with a dark gray dot along the branch

Fig. 10

CYP 450 gene counts (excluding splicing variants) in the genome of P. japonica as well as D. ponderosae, N. vespilloides and T. castaneum. Subfamilies were defined following the phylogenetic reconstruction of cytochrome P450 (Fig. 9). An apparent gene expansion is retrieved in P. japonica’s clan 3 and 4. On the contrary, clan 2 and mito clan gene number of the JB are in line with other coleopteran species. Species are color-coded