Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes

Abstract

Ostreid oysters (the 'true oysters') represent a large and commercially important family of bivalve molluscs. Several species, such as the Pacific oyster (Magallana gigas), the American oyster (Crassostrea virginica), the European oyster (Ostrea edulis) and the Sydney rock oyster (Saccostrea glomerata), are currently farmed at a large scale. However a number of other species may also be suitable for commercial-scale aquaculture. One such species is the 'black-lip oyster', a large Saccostrea species of uncertain taxonomic affinity found in northern Australia. Here, phylogenetic analysis of the COI gene places this oyster within a clade identified in a previous study of Japanese Saccostrea species, 'Saccostrea lineage J'. To facilitate comparisons between this oyster and the better-studied S. glomerata, de novo transcriptomes were generated from larval stages and adult tissues of both species. Patterns of orthology indicated an expansion of repetitive elements within Saccostrea genomes when compared to M. gigas and C. virginica, which may be reflected in increased evolutionary rates and/or genome sizes. The generation of high-quality transcriptomes for these two commercially relevant oysters provides a valuable resource for gene identification and comparison of molecular processes in these and other mollusc species.

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.

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.

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.