A chromosome-level genome of Semiothisa cinerearia provides insights into its genome evolution and control

Abstract

Background: Semiothisa cinerearia belongs to Geometridae, which is one of the most species-rich families of lepidopteran insects. It is also one of the most economically significant pests of the Chinese scholar tree (Sophora japonica L.), which is an important urban greenbelt trees in China due to its high ornamental value. A genome assembly of S. cinerearia would facilitate study of the control and evolution of this species.

Results: We present a reference genome for S. cinerearia; the size of the genome was ~ 580.89 Mb, and it contained 31 chromosomes. Approximately 43.52% of the sequences in the genome were repeat sequences, and 21,377 protein-coding genes were predicted. Some important gene families involved in the detoxification of pesticides (P450) have expanded in S. cinerearia. Cytochrome P450 gene family members play key roles in mediating relationships between plants and insects, and they are important in plant secondary metabolite detoxification and host-plant selection. Using comparative analysis methods, we find positively selected gene, Sox15 and TipE, which may play important roles during the larval-pupal metamorphosis development of S. cinerearia.

Conclusion: This assembly provides a new genomic resource that will aid future comparative genomic studies of Geometridae species and facilitate future evolutionary studies on the S. cinerearia.

Keywords: Cytochrome P450; Geometridae; Semiothisa cinerearia; tipE.

Fig. 1

Chromosome-level assembly of Semiothisa cinerearia. A The genome‐wide Hi‐C interaction maps of 31 chromosomes in the S. cinerearia genome. Calculated interaction frequency distribution of Hi-C links between and within chromosomes. B Circos graph of characteristics of the S. cinerearia genome. From the outer ring to inner circle: marker distribution on 31 chromosomes at the megabase scale (I), gene distribution (II), tandem repeat (TRP) (III), long terminal repeat (LTR) (IV), long interspersed nuclear element (LINE) (V), short interspersed nuclear element (SINE) (VI), DNA elements (VII), and guanine-cytosine (GC) content (VIII)

Fig. 2

Comparison of TEs insertion history among species. The x-axis indicates the inferred insertion time (unit: million years ago) of TEs. The y-axis indicates the length of different TEs elements

Fig. 3

Orthology and evolutionary analysis among species. A Species phylogenetic tree and gene family expansion/contraction. The phylogenetic relationships of S. cinerearia with other insects were characterized using a maximum likelihood analysis of a concatenation of single‐copy orthologous protein sequences and 100 bootstrap replicates. The numbers of gene families that underwent expansion (red) or contraction (green) are shown on branches with predicted species divergence times plotted at each node. B Orthologous genes distribution. The bars are subdivided to indicate different orthologous relationships. Single-copy and multiple-copy orthologs are families in which each species has only one or more than one copy, respectively. Other orthologs are genes with matches with other species that could not be placed into other ortholog categories. Unclustered genes are genes in each species that could not be associated with the gene predictions in any of the other lineages. Unique paralogs show species-specific families. C Relative evolutionary rates of these species. The analysis was performed using single-copy protein-coding genes with S. cinerearia as the reference species and P. bianor as the outgroup species. The x-axis indicates the relative evolutionary rates of the species

Fig. 4

Positively selected sites of sox15 and tipE in various insect species. A Positively selected sites in sox15 gene. The left panel is the phylogenetic tree of these species, and the right panel is the amino acids sequences of sox15 gene. B Positively selected sites in tipE gene. The left panel is the phylogenetic tree of these species, and the right panel is the amino acids sequences of tipE gene

Fig. 5

Number of cytochrome P450 gene, HSP70, HSP90, and sHSP genes in various insect species. The left panel is the phylogenetic tree of these species, the right panel is the gene number of P450, HSP70, HSP90, and sHSP genes