Tables and Figures
Figure 1 Overview of sequenced species and reference genome
assemblies generated in this study . (a) Photographs of the five
marsupial species sequenced. A yellow-footed antechinus
(Antechinus flavipes ), silver-headed antechinus (Antechinus
argentus ), and black-tailed dusky antechinus (Antechinus arktos )
from Australia; a black-tailed dasyure (Murexia melanurus ) from
Papua New Guinea. Antechinus spp. and M. melanurusphotographs are courtesy of A.M. Baker and John Hornbuckle,
respectively. (b) Circos plot of the reference genome assembly ofA. flavipes . The outermost segment represents chromosome
sequences, with the numbers on the external surface indicating genome
size in Mb. Chr7 in A. flavipes corresponds to the X chromosome.
The line plots, from outside to inside represent the distribution of CDS
density (from 0 to 0.15), GC content (from 0.30 to 0.65) and TE ratio
(from 0.2 to 1.0). Frequencies were calculated in 500-kb sliding
windows. (c) Circos plot showing shared synteny of Antechinus
flavipes (chr1-chr7) and Sarcophilus harrisii(NC_045426.1-NC_045432.1). Aligned using LASTZ. The synteny blocks are
linked using lines coloured in accordance with the A. flavipeschromosomes. Aligned blocks with length shorter than 20 kb are not
shown. Chr7 in A. flavipes corresponds to the X chromosome ofSarcophilus harrisii .
Figure 2 Evolutionary history of semelparous mammals. (a)
Inferred phylogeny of ten marsupials and the platypus (outgroup) based
on fourfold degenerate sites from 6,431 1:1 orthologs. Blue numbers at
nodes represent the estimated divergence time from present (million
years ago; Mya) between lineages. Semelparous lineages are indicated in
red. (b) Demography of the dasyurid subfamily Phascogalinae. Historic
population sizes (Ne ) were estimated using the
pairwise sequentially Markovian coalescent (PSMC) method (Li & Durbin,
2011) and diploid genome sequences. The x -axis shows the time
before present in years on a log scale; the dashed gray line shows human
arrival in Australia 59.3 to 65 kya (Clarkson et al., 2017); red dots
indicate the extinction times of 15 species of Pleistocene Sahul (Saltre
et al., 2016). The y -axis showsNe , with bootstrap estimates
indicated by lighter lines. Plots were scaled using a mutation rate
(μ ) of 1.37 × 10-9 substitutions
nucleotide-1 generation-1 and
species-specific generation times (g ) of one year. Two A.
flavipes individuals were interrogated (coloured in orange and blue).
(c) Map showing the location (coloured circles) and elevation (mamsl;
metres above sea level) of sampled dasyurids (see subfigure b).
Figure 3 Gene expression profiling of the Antechinus
flavipes breeding cycle. (a) Schematic overview of the yellow-footed
antechinus (Antechinus flavipes ) breeding season in Samford
Valley, Queensland, Australia. Free-CORT illustrates an increase in the
level of free (unbound) stress hormones (chiefly the corticosteroid
cortisol) in males during the breeding season of antechinuses (based on
three studies illustrated in (Naylor et al., 2008)). (b) Rapid
organismal senescence of male A. flavipes . Left, male
(~11 months of age) prior to the breeding season. Right,
late breeding stage male (~11.5 months of age). Note the
loss of fur clumps and deterioration of body condition. (c) In the
moribund state, when other energy stores have been depleted, skeletal
muscle catabolism generates amino acids for gluconeogenesis, induced by
the corticosteroid, cortisol. (d) Venn diagram for the overlap of
significantly up-regulated (left) or down-regulated (right) genes in
moribund male antechinuses. Called by limma v3.22.1 (≥1.5-fold change
and P ≤0.01). (e) Heat map of selected energy metabolism genes
differentially expressed in the skeletal muscle of moribund male
antechinuses. Moribund samples are indicated by a red bar below the map.
Scaled TMM-normalised read counts (denoted as the row Z score)
are plotted, with red indicating high expression and blue indicating low
expression. BPGM , 2,3-bisphosphoglycerate mutase; FBP2 ,
fructose-bisphosphatase 2; GPI , glucose-6-phosphate isomerase;LDHA , lactate dehydrogenase A; PFKM , phosphofructokinase,
muscle; PGK2 , phosphoglycerate kinase 2; PKM , pyruvate
kinase M1/2; GPD1 , glycerol-3-phosphate dehydrogenase 1;GPD2 , glycerol-3-phosphate dehydrogenase 2; SLC2A5 , solute
carrier family 2 member 5; SLC37A4 , solute carrier family 37
member 4; PRKAG3 , protein kinase AMP-activated non-catalytic
subunit gamma 3; STK11 , serine/threonine kinase 11. (f)
Expression pattern of the AMPK regulator LKB1 (STK11 ) in male
(left) and female (right) tissues throughout the breeding season. Counts
per million TMM-normalized counts, with standard error bars.
Table 1. Antechinus
flavipes genome assembly statistics