Poecilia picta genome assembly and analysis of tissue-specific dosage compensation. (A) Phylogeny of Poecila species depicting the diversity of XY heteromorphism between P. reticulata, P. picta, and M. parae and the ∼3.7-Myr interval (shaded in red) for when the Y Chromosome degenerated and dosage compensation arose in the common ancestor of P. picta and P. parae. The phylogeny and divergence times are taken from The Fish Tree of Life (Rabosky et al. 2018) and adapted from Sandkam et al. (2021) and Metzger et al. (2021). (B) Sequence synteny between the female P. picta and the female P. reticulata genomes. Chromosomes are labeled 1–23 and are differentiated by color around the outer ring with P. picta chromosomes on the left and P. reticulata chromosomes on the right. The color of the connecting lines indicates the chromosomal origin of the sequence from the P. picta genome. The X Chromosome is Chromosome 12 and is highlighted in green. (C) Chromosome 12 alignments between the female P. reticulata (red horizontal line) (Künstner et al. 2016), our P. picta (green horizontal line), and the male P. reticulata (blue horizontal line) (Fraser et al. 2020) genome assemblies. Gray segments connecting horizontal lines represent syntenic regions. Orange segments connecting horizonal lines indicate inverted regions. (D) Comparison of autosomal (A; gray) and X Chromosome (X; red or blue fill) gene expression values in female (red) and male (blue) gonad, head, liver, and muscle tissues. Gene expression levels are presented as log2 counts per million (cpm) normalized to sequencing library size. The horizontal line of the box and whisker plot is the median; the box denotes the 25th and 75th percentile; and “whiskers” are 1.5 times the interquartile range. A significant difference (P < 0.05) in gene expression between groups is indicated by an asterisk, as determined by Bonferroni-corrected Wilcoxon rank-sum test. Complete list of P-values are available in Supplemental Table 2. (E) Comparison of gene expression levels between autosomal and X Chromosome genes in female and male gonad, head, liver, and muscle tissues in four expression quantiles. Colors and expression units are the same as in panel B. The complete list of P-values is available in Supplemental Table 3.
