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.