The genome of the oysterSaccostreaoffers insight into the environmental resilience of bivalves

Abstract

Oysters are keystone species in estuarine ecosystems and are of substantial economic value to fisheries and aquaculture worldwide. Contending with disease and environmental stress are considerable challenges to oyster culture. Here we report a draft genome of the Sydney Rock Oyster, Saccostrea glomerata, an iconic and commercially important species of edible oyster in Australia known for its enhanced resilience to harsh environmental conditions. This is the second reference genome to be reported from the family Ostreidae enabling a genus-level study of lophotrochozoan genome evolution. Our analysis of the 784-megabase S. glomerata genome shows extensive expansions of gene families associated with immunological non-self-recognition. Transcriptomic analysis revealed highly tissue-specific patterns of expression among these genes, suggesting a complex assortment of immune receptors provide this oyster with a unique capacity to recognize invading microbes. Several gene families involved in stress response are notably expanded in Saccostrea compared with other oysters, and likely key to this species’ adaptations for improved survival higher in the intertidal zone. The Sydney Rock Oyster genome provides a valuable resource for future research in molluscan biology, evolution and environmental resilience. Its close relatedness to Crassostrea will further comparative studies, advancing the means for improved oyster agriculture and conservation.

The Gene-Rich Genome of the ScallopPecten maximus

“…Levels of heterozygosity in P. maximus were higher than those found in the Sydney Rock Oyster Saccostrea (0.51%), or the Pacific oyster Crassostrea gigas (0.73%). Both of these oyster samples were derived from selective breeding programmes, which would reduce heterozygosity compared to wild populations [20].…”

“…We used RepeatModeler and RepeatMasker [45] to identify and mask regions of the genome containing previously identified or novel repetitive sequences [ maximus is large by scallop standards, its size is not due to large amounts of repetitive elements, as 27.0% is low compared to many other genome resources. For example, Crassostrea gigas has a repeat content of 36% [15] and Saccostrea glomerata 45.0% [20].…”

“…Scallops have been the subject of genome sequencing projects in the past, with genomes published for three species, Azumapecten farreri (as Chlamys [17]) and Mizuhopecten yessoensis (as Patinopecten; [18]) from the subfamily Pedinae, and Argopecten purpuratus from the subfamily Pectininae [19]. Other sequenced genomes for more distantly related bivalves include those of the Sydney Rock Oyster Saccostrea glomerata [20], Eastern oyster Crassostrea virginica [unpublished, but see 21], the Snout Otter Clam Lutraria rhynchaena [22], Blood Clam Scapharca broughtonii [23] and Manila Clam Ruditapes philippinarum [24]. There are also extant resources for the mussel Mytillus galloprovincialis [25] and the freshwater mussels Venustaconcha ellipsiformis [26], Limnoperna fortunei [27], Dreissena rostriformis [28] and Dreissena polymorpha [unpublished, but see 29].…”

The genome of a subterrestrial nematode reveals an evolutionary strategy for adaptation to heat

“…We note that the pacific oyster Crassostrea gigas has convergently expanded Hsp70 and AIG1 gene families 83 and activates the UPR in response to abiotic stress including heat 84 , so H. mephisto helps define a general evolutionary adaptive response to heat stress. While the oyster experiences considerable thermal fluctuation, H. mephisto does not, as described above.…”

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

“…The Pacific oyster has a reported genome size of between 545 and 637 Mb [ 95 ]. Meanwhile, the Sydney rock oyster ( S. glomerata ) has a reported genome size of 784 Mb [ 58 ]. In addition, the genome of the pearl oyster ( Pinctada fucata ) has a reported genome size of 990 Mb [ 82 ], but is not a species of true oyster, instead belonging to the family Pteriidae.…”