1. INTRODUCTION
For every animal species, the most critical activity is mating and the
raising of offspring. Reproduction is a costly process, and animals
invest energy into strategies that maximize the number and survival of
offspring (Collett, Baker, & Fisher, 2018). Broadly, these strategies
span the so-called iteroparity-semelparity continuum – from a single
(semel ) to repeated (itero ) reproductive episode(s) before
death [reviewed in (Hughes, 2017; Krajewski, Woolley, & Westerman,
2000)]. In mammals, semelparity is observed in Australian dasyurids
(males-only) and South American didelphids (both sexes) (Fisher,
Dickman, Jones, & Blomberg, 2013; Leiner, Setz, & Silva, 2008).
Obligate male semelparity is the most extreme form of semelparity,
occurring in the marsupial subfamilies Phascogalinae (15Antechinus species and three Phascogale species (A. J.
Bradley, 2003; Naylor, Richardson, & McAllan, 2008)) and Dasyurinae
(the kaluta, Dasykaluta rosamondae (Hayes et al., 2019)). In
these dasyurid species, all males die soon after a 1-3 week mating
period (‘die-off’ at 11.5 months of age), and a proportion of females
survive to breed in the subsequent year (A. Baker & Dickman, 2018).
Breeding is a stressful life-history event, but the stress response
enables most animals to cope and to mobilise energy (Romero, 2004).
Hormones play a vital role in this process. While in antechinus, both
sexes have elevated stress hormone levels (chiefly the corticosteroid
cortisol) during breeding, males also exhibit surging plasma
testosterone levels (A. J. Bradley, 2003; Braithwaite & Lee, 1979;
Croft, 2003; McAllan, 2006; Naylor et al., 2008). This interferes with
negative feedback mechanisms and reduces levels of corticosteroid
binding globulin (CBG), increasing the levels of free (i.e., unbound),
active corticosteroids in the blood (A. J. Bradley, 2003; Naylor et al.,
2008). As the breeding season progresses, corticosteroid levels continue
to rise; ultimately contributing to systemic collapse and death of all
males. Corticosteroids are anti-inflammatory and, at high
concentrations, immunosuppressive, triggering a decline of body
condition (Manoli et al., 2007; Perogamvros, Ray, & Trainer, 2012).
Stress, combined with malnutrition, results in a significant negative
energy balance and is associated with numerous comorbidities (Argiles,
Campos, Lopez-Pedrosa, Rueda, & Rodriguez-Manas, 2016). Cortisol is
also elevated in females throughout the short breeding season, but in
the absence of elevated testosterone, free cortisol levels remain
relatively constant.
There is mounting evidence that testosterone and cortisol contribute to
differences in ageing and related diseases (Austad & Fischer, 2016;
Gems, 2014; Lemaitre et al., 2020; Martocchia et al., 2016). Moreover,
ageing (Childs et al., 2017; Froy et al., 2019) and obligate semelparity
manifest as a decline in immune function – immunosenescence. In
contrast to current mammal models of ageing, antechinuses are ‘natural’
models of physiological senescence (see (Diamond, 1982; McAllan, 2006)).
For example, the brain of the ageing wild-type mouse and rat does not
accumulate amyloid-beta (Aβ) (Jucker, 2010). Aβ plaques, which are
associated with chronic stress and elevated cortisol levels [e.g., see
(Lesuis, Weggen, Baches, Lucassen, & Krugers, 2018)], accumulate at
the end of the antechinus lifespan in antechinuses – mirroring
Alzheimer’s disease neuropathology and potentially making them a
suitable disease model (McAllan, 2006; Naylor et al., 2008). A
high-quality genome assembly is critical for future genetic experiments
(e.g., CRISPR). Moreover, considering the strong effects of cortisol and
testosterone on male obligate semelparity, identifying the expression of
genes associated to these hormones and its consequences may help to
understand the evolution of this extreme reproductive strategy.
Recent work has uncovered several new antechinus species, bringing the
total number of species to 15 (Mutton, Phillips, Fuller, Bryant, &
Baker, 2019). In 2018, A. arktos and A. argentus were
listed as Endangered on the Australian Government’s threatened species
list and were included in the 20 Australian mammals most likely to go
extinct in the next two decades (Geyle et al., 2018). Moreover, areas of
their habitat were recently ravaged by extensive wildfires and drought.
Genomic resources are urgently required to support research on the
population structure, speciation, and recovery of antechinus species.
To investigate the phylogeny, demographic history, and genomic diversity
of A. flavipes and to pave the way to understanding the evolution
of semelparity, high-quality genomic data is required. A genome assembly
of the brown antechinus (A. stuartii ) was recently reported
(Brandies, Tang, Johnson, Hogg, & Belov, 2020a). However, a
chromosome-level genome is not yet available. PacBio long-read
sequencing combined with the chromosome conformation capture method Hi-C
resolves complex regions (such as repeat regions) and can greatly
improve downstream analyses (Schloissnig et al., 2021). Here, we
employed third-generation sequencing technologies to generate the first
chromosome-level genome of an antechinus, that of the yellow-footed
antechinus (A. flavipes ), as well as draft genomes of three
related dasyurids (Figure 1a ). We highlight genome features,
phylogeny and historical demography, and the gene expression profile ofA. flavipes male die-off.