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Background: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods., Findings: The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species., Conclusions: We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.

The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to -1.8ºC over the past 30 million years, and the seawater had retained this cold temperature and isolated oceanic environment because of the Antarctic Circumpolar Current. Notothenioids dominate Antarctic fish, making up 90% of the biomass, and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled, and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6145 bp, and its N50 scaffold length 178 362 kb. The genome of P. charcoti is predicted to contain 32 712 genes, 18 455 of which have been assigned preliminary functions. A total of 8951 orthologous groups common to 7 species of fish were identified, while 333 genes were identified in P. charcoti only; 2519 orthologous groups were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to gene ontology enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes., (© The Author 2017. Published by Oxford University Press.)

Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i.e. arthropsins, peropsins, and melaopsins), suggesting potential regressive adaptation to the dark environment. However, A. bangokensis expressed conserved gene family sets, such as heat shock proteins and those related to key innate immunity pathways and antioxidant defense systems, at the transcriptional level, suggesting that this species has evolved adaptations involving molecular mechanisms of homeostasis. The transcriptomic information of A. bangokensis will be useful for investigating molecular adaptations and response mechanisms to subterranean environmental conditions. [ABSTRACT FROM AUTHOR]