To keep up with global demand and to fight disease and environmental stress, appropriate management of wild stocks and farmed S. The lack of genomic resources coupled with limited understanding of the population structure and size, molecular basis of gene expression and phenotypic variation have limited advancements in environmental conservation and aquaculture-based development.
The development of farming protocols to breed, feed, ensure good health and welfare of farmed stocks requires a good understanding of the species biology, behavior and adaptations. pharaonis species have been successfully cultivated in China since 2012 the rearing methods include cement pond culture, pond culture and tank culture ( Li et al., 2019). Efforts have been made over the last few years to develop S. pharaonis is still classified as “Data Deficient” ( Barratt and Allcock, 2012), only Yemen have an annual fishing quota ( Reid et al., 2005). pharaonis fisheries are in constant increase while the real conservation status of S. pharaonis is the largest, most abundant, and exploited species of cuttlefish in the Gulf of Thailand and Andaman Seas, accounting for 16% of the annual offshore cephalopods trawled and 10% of the offshore fixed net catches ( Iglesias et al., 2014). As a giant cuttlefish species, it can grow up to 42 cm in mantle length and 5 kg in weight. It is also economically important along the southeast coast of China, with an annual catch of approximately 150,000 tonnes. Sepia pharaonis is also an important species economically for local fisheries, especially in the Yemeni Sea, Suez Canal, Gulf of Thailand and the northern Indian Ocean ( Al Marzouqi et al., 2009).
Population structure, size and extent of the potential species complex is unknown. No extensive population genetic study has, to date, been conducted. pharaonis subclades depending of the geographical locations: Western Indian Ocean, North-eastern Australia, Iran, Western Pacific Ocean and Central Indian Ocean. The population is scattered into five groups ( Anderson et al., 2011) forming a species complex.
CUTTLEFISH CAMOUFLAGE SKIN
This remarkable ability depends on their skin structure and a unique protein, the reflectin, expressed exclusively in cephalopods ( Crookes, 2004 Cai T. pharaonis exhibit behaviors beyond those of ordinary aquatic animals, such as inkjet, camouflage, clustering, sudden changes of color in reaction to excitement and escape ( Hanlon et al., 2009 How et al., 2017). Sepia pharaonis Ehrenberg, 1,831 (pharaoh cuttlefish) is commonly distributed in the Indo-Pacific from 35°N to 30°S and from 30☎ to 140☎ and is present in shallow waters to a depth of 100 m ( Minton et al., 2001 Al Marzouqi et al., 2009 Anderson et al., 2011). pharaonis provides an essential resource for future studies into the biology, domestication and selective breeding of the species. pharaonis genome assembly identified a total of 51,541 genes, including 12 copies of the reflectin gene, that enable cuttlefish to control their body coloration. The genome was assembled into 5,642 scaffolds with a total length of 4.79 Gb and a scaffold N 50 of 1.93 Mb. pharaonis using a long-read platform (Oxford Nanopore Technologies PromethION) to assemble the genome and short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing errors. To address this need, we produced a hybrid reference genome of S. Research efforts to develop linkage mapping, or marker-assisted selection have been hampered by the absence of a high-quality reference genome. Sepia pharaonis, the pharaoh cuttlefish, is a commercially valuable cuttlefish species across the southeast coast of China and an important marine resource for the world fisheries. 3Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom.2Collaborative Innovation Centre for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China.1Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.Weiwei Song 1,2, Ronghua Li 1,2,3, Yun Zhao 1,2, Herve Migaud 1,2,3, Chunlin Wang 1,2* and Michaël Bekaert 3*
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