Fig 1.
Morphology of the black-lip oyster.
The sample has been stored in ethanol, causing some shift in colour within the internal soft tissues. A. Upper surface of the right valve, showing intense dark pigmentation. The outer shell layer has been chipped away at the umbo (arrowhead). B. Inner surface of the right valve. The dark outer shell margin is sharply separated from the white internal surface by large, obvious chomata (ch). The mantle edge is darkly pigmented (m). C. Outer surface of the deeply-cupped left valve. D. Inner surface of the left valve, showing a dark outer shell margin and obvious chomata, and dark pigmentation in the mantle E. Inner surface of the left valve of a second specimen, with soft tissues removed to display the adductor scar (arrowhead). Scale bar = 10mm.
Fig 2.
Maximum likelihood phylogenetic analysis of Saccostrea COI sequences.
Bootstrap values >50 are given on branches, and the scale bar indicates the number of substitutions per site. The clade containing Striostrea, Dendostrea, Magallana and Crassostrea COI sequences is used as an outgroup. Lineages have been designated (where possible) following Lam and Morton [11] and Sekino and Yamashita [12]. The Bowen black-lip COI sequence (circled in inset) falls within ‘Lineage J’ with strong support.
Table 1.
Assembly statistics for S. lin. J and S. glomerata transcriptomes.
Table 2.
BUSCO results for both Saccostrea species compared to Crassostreinae whole-genome data.
Fig 3.
Patterns of gene orthology in oyster species.
Number of orthogroups shared between Saccostrea lineage J, Saccostrea glomerata, Magallana gigas, and Crassostrea virginica. 15117 orthogroups are shared between all four species, and 5719 orthogroups are shared exclusively between the two Saccostrea species.
Table 3.
GO categories enriched in Saccostrea-specific orthogroups.
Fig 4.
Repetitive element content of oyster genomes as assessed by searches against RepBase.
Saccostrea species possess a greater proportion of retroelements within their genomes, particularly within the SINE, LINE, and Penelope classes. Additional expansion of the Gypsy/DIRS1 LTR class is evident in S. glomerata.