| This study is the first report about the complete mitochondrial genome sequence offour species of cuttlefish, including Sepia pharaonis, Sepia aculeata, Sepia lycidas andSepiella inermis. After sequenced these four kinds of cuttlefish and annotated all thefunctional genes, we analyzed their structure and characteristics, then we madecomparative genomic studies of four cuttlefish, finally, four different kinds of phylogenetictrees are used to analyze the phylogenetic relationships of ten species of cuttlefish. Themain results were summarized as follows:1. The length of the complete mitochondrial genome of S. pharaonis, S. aculeata, S.lycidas and S. inermis are16,208bp,16,219bp,16,228bp and16,191bp, respectively.They all display a typical gene composition found in Sepioidea mitogenomes, including13protein-coding genes,22tRNAgenes,2rRNAgenes and2long-noncoding regions.2. It is common to find the intergenic regions and overlap regions in those fourcuttlefish. The complete length of intergenic regions is between147-182bp, and thecomplete length of overlap regions is between51-104bp. The mitogenome basecomposition: Acontent is around40%, T content is between32-39%, C content is between12-17%, G content is between7-9%. The overall A+T content is between74-77%. Thewhole mitogenome shows a highly A+T bias which is generally observed among thecuttlefish in Sepiidae.3. Among the13protein-coding genes, COIII、ND2、COI、COII、ATP8、ATP6andND3genes are encoded by the Light-strand, and ND1、ND5、ND4、ND4L、CYTB and ND6genes are encoded by the Heavy-strand. Most of the protein-coding genes start with aninitiation codon of ATG, except for ND4, which starts with an initiation codon of ATA. Thetermination codons are far more complex, in which exist incomplete termination codon.4. Most of the tRNA genes fold into a typical cloverleaf structure, and the secondarystructure includes the acceptor arm, TΨC arm, DHU arm, anticodon arm, TΨC loop, DHUloop and anticodon loop. Meanwhile, structure deletion and nucleotide mismatch are alsoordinary. 5. The two ribosomal RNA genes,16SrRNA is located between tRNALeuand tRNAValgene,12SrRNAis located between tRNAValand tRNACysgene.6. The mitogenomes of four cuttlefish species each have two non-coding regions, andboth are control regions which contain termination-associated sequences and conservedsequence blocks. The whole lengths are1,114bp,1,112bp,1,154bp,1,110bp separately.One is located between tRNAGlyand tRNAAsn, and another one is located between tRNAGluand protein-coding gene COX3. Compared with other cuttlefish, we came to theconclusion that the difference in the control region length is the main cause for thedifference in the mitochondrial genome length.7. Four species of methods, including Maximum Likelihood, Neighbor Joining,Minimum Evolution and Maximum Parsimony are used to build the phylogenetic tree often species of cuttlefishes. The results show that the four kinds of cuttlefish in this studyand two other species absolutely support their traditional morphological classificationresults, but among other six species, three of them appear divergence. Sepia officinalis,which belongs to the genus Sepia, are being partition into Sepiella. It is thought that S.officinalis exists as a kind of transitional species; the classification results of Sepialatimanus and Sepia apama are slightly chaotic in this study. It is inferred that there mightstill exist another unknown genus or subgenus in Sepiidae.This work is the first report about the complete mitochondrial genomes of S.pharaonis, S. aculeata, S. lycidas and S. inermis. The properties of the organization andstructure of these four mitochondrial genomes are analysed. All these data have enrichedthe NCBI GenBank genome database. Also in this work the whole mitochondrial genomesare used to analyse the phylogenetic relationships of Sepiidae. Our results will lay a goodfoundation for the further research of higher order phylogenetic relationship ofCephalopoda. |
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