Pharaoh Cuttlefish, Sepia pharaonis, Genome Reveals Unique Reflectin Camouflage Gene Set

Weiwei Song,Chunlin Wang,Michaël Bekaert,Ronghua Li,Yun Zhao,Herve Migaud

doi:10.3389/fmars.2021.639670

Weiwei Song, Chunlin Wang + Show 4 more

Open Access

https://doi.org/10.3389/fmars.2021.639670

Copy DOI

Abstract

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. Research efforts to develop linkage mapping, or marker-assisted selection have been hampered by the absence of a high-quality reference genome. To address this need, we produced a hybrid reference genome of S. 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. The genome was assembled into 5,642 scaffolds with a total length of 4.79 Gb and a scaffold N50 of 1.93 Mb. Annotation of the S. 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. This new reference genome for S. pharaonis provides an essential resource for future studies into the biology, domestication and selective breeding of the species.

Highlights

Sepia pharaonis Ehrenberg, 1,831 is commonly distributed in the Indo-Pacific from 35◦N to 30◦S and from 30◦E to 140◦E 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)
We report the first draft genome assembly for S. pharaonis using a hybrid assembly technique, with Oxford Nanopore Technologies PromethION, a long-read platform for genome assembly, and Illumina HiSeq X Ten short-read for precise correction of sequence errors
The S. pharaonis used in this work was obtained from a male S. pharaonis (Body length 21.5 cm, Weight 1.205 kg) cultured in a farm located along the coast of Ningbo City, China (29◦35 N, 121◦59 E)

Summary

Introduction

Sepia pharaonis Ehrenberg, 1,831 (pharaoh cuttlefish) is commonly distributed in the Indo-Pacific from 35◦N to 30◦S and from 30◦E to 140◦E 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). S. 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). This remarkable ability depends on their skin structure and a unique protein, the reflectin, expressed exclusively in cephalopods (Crookes, 2004; Cai T. et al, 2019). The population is scattered into five groups (Anderson et al, 2011) forming a species complex. Population structure, size and extent of the potential species complex is unknown

Methods

Results

Conclusion