Introduction
The peach fruit moth (PFM), Carposina sasakii Matsumura
(Lepidoptera: Carposinidae, superfamily Copromorphoidea), is a major
phytophagous orchard pest of fruit such as apple, pear, peach, apricot
and jujube from the families of Rosaceae and Rhamnaceae (Fig.
1 ). The hatched larvae directly bore into fruit to feed, causing losses
in fruit production. PFM is one of the most severe borers on deciduous
fruit in northeast Asia. It is also considered a potential risk to fruit
production in most parts of the world, although PFM is currently
restricted to northeast Asia and far east Russia (D. Kwon, Kwon, Kim, &
Yang, 2018; Y. Z. Wang et al., 2017).
One possible of reason for the currently restricted distribution of PFM
is its sensitivity to environmental factors. PFM has evolved diapause to
cope with cold winter conditions and to synchronize its phenology with
host plants (Toshima, Honma, Masaki, & Zoology, 1961). Both long-day
and short-day photoperiods induce diapause in the last instar of PFM
larvae, resulting in a diapausing cocoon (B.-Z. Hua, Zeng, & Zhang,
1998; Huang, Wang, Ye, Zhang, & Zhang, 1976). The life cycle of PFM can
be univoltine or bivoltine, depending on photoperiods encountered and
environmental factors like humidity (Chiba & Kobayashi, 1985; D.-S.
Kim, Lee, & Yiem, 2000; Sato & Ishitani, 1976). Temperature also
affects the occurrence of PFM through effects on development rate and
the emergence of the overwintering generation from diapause (D. S. Kim,
Lee, & Yiem, 2001; B. Zhang et al., 2016).
The effects of environmental factors as well as photoperiod on the life
history of PFM provides an opportunity to investigate the genomic basis
of adaptation to temperate environments in the Copromorphoidea
superfamily and across Lepidoptera more generally. Candidate genes
involved in climatic adaptation could then also be investigated at the
geographic level, given that a combination of mtDNA and microsatellite
variation indicates strong genetic differentiation among populations of
the PFM among geographical populations across its native range in China
(Y. Z. Wang et al., 2017). The highly variable life history of PFM on
different host plants may reflect different host-associated biotypes as
supported by an analysis of esterase isozyme patterns (L. Hua & Hua,
1995) and random amplified polymorphic DNA (RAPD) (Xu & Hua, 2004),
although this is not yet been confirmed by direct studies on population
differentiation in PFM (D. H. Kwon, Kim, Kim, Lee, & Yang, 2017; J.
Wang et al., 2015).
Well-assembled genomes are increasingly becoming available as resources
for tracing evolutionary adaptation across the Lepidoptera. Already
there are substantial genomic resources for many moths (W. Chen et al.,
2019; Cheng et al., 2017; Kanost et al., 2016; Lange et al., 2018; Ma et
al., 2020; Pearce et al., 2017; Wan et al., 2019; Xia et al., 2004;
Xiang et al., 2018; Xiao et al., 2020; You et al., 2013; S. Zhang et
al., 2020) and butterflies (Ahola et al., 2014; Cong, Borek, Otwinowski,
& Grishin, 2015; Dasmahapatra et al., 2012; Lu et al., 2019; Nishikawa
et al., 2015; Zhan, Merlin, Boore, & Reppert, 2011) which are being
used in comparative analyses to link genomic changes to phenotypes like
the detoxification of compounds encountered in hosts (Rane et al.,
2019). Available genomes provide abundant reference points for
investigating evolution across the Lepidoptera, although most species
sequences so far are from the Papilionoidea, Noctuoidea, Bombycoidea and
Pyraloidea, with less genomic information available for the Carposinidae
(Copromorphoidea) despite the importance of this group as agricultural
pests.
In the present study, we report on a chromosome-level genome of PFM
which was de novo assembled based on sequences obtained from the
PacBio and Illumina platforms and assembled at the chromosome level with
the Hi-C technique. We compare features of the PFM genome with those of
eleven other moths, focusing particularly on detoxification gene
families important in host adaptation and pesticide resistance,
contributing to ecological niches occupied by species (Rane et al 2019).
As an initial study using the newly assembled genome, we investigate
transcriptomic changes induced by long-day and short-day photoperiods
that induce diapause in PFM larvae, and we identify genes involved in
these responses which are critical to climatic adaptation by PFM.