The complete mitochondrial genome of marine gastropod Sydaphera spengleriana (Deshayes, 1830) (Neogastropoda: Cancellariidae)

Abstract

The complete mitochondrial genome of Sydaphera spengleriana was characterized for the first time. The total length of the mitogenome was 16,336 bp including a standard set of 13 protein-coding (PCGs), 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) genes. The overall nucleotides base composition of the heavy strand is A (26.44%), G (19.89%), C (13.25%), and T (40.41%), with an A + T bias (66.85%). With the exception of eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The mitogenomic phylogenetic relationships indicated that S. spengleriana was clustered with Bivetiella cancellata within the family Cancellariidae clade with a high bootstrap value.

Keywords:

• Mitogenome
• Sydaphera spengleriana
• phylogenetic analysis

Sydaphera spengleriana (Deshayes, 1830) belongs to Cancellariidae in Neogastropoda (Sowerby 1841; WoRMS 2021). The Cancellariidae is a diverse gastropod family containing ca. 300 living species around the world, which currently inhabiting mainly in tropical and temperate regions, from subtidal to bathyal depths (Petit and Harasewych 2005; Modica et al. 2011; Qu 2019). There is only one complete mitochondrial genome of the species Bivetiella cancellata in Cancellariidae recorded in the NCBI database. In this work, we have determined and described for the first time of the complete mitochondrial genome of S. spengleriana, which will provide a better insight into phylogenetic assessment and taxonomic classification.

One S. spengleriana individual was collected from Laizhou Bay (37.78°N, 119.33°E), China, during August 2020. Specimen (Voucher no. FIO-XLT-JH-002) was deposited in the Biodiversity Lab of the First Institute of Oceanography, MNR. The total genomic DNA was extracted from the muscle of the specimen using a QIAamp Fast DNA Tissue kit (Qiagen, Germany) following the manufacturer’s protocol. DNA libraries (350 bp insert) were constructed with the TruSeq NanoTM kit (Illumina, USA). The complete mitogenome of S. spengleriana was sequenced on the Illumina Novaseq 6000 sequencing platform (Illumina, USA) at Science Corporation of Gene, China. The clean data were then assembled using the NOVOPlasty (Dierckxsens et al. 2017). Gene annotation was performed by MITOS (Bernt et al. 2013). The information of this mitochondrial genome was submitted to Genbank and the accession number is MZ934412.

The circular mitochondrial genome of S. spengleriana was 16,336 bases long. Its genomic structure is as follows: There are 13 protein-coding (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes, which are the same as the other Cancellariidae species, B. cancellata (Cunha et al. 2009). The overall base composition of the mitogenome is estimated to be A 26.44%, T 40.41%, G 19.89%, and C 13.25%, with a high AT bias (66.85%). Most of the genes encoded on the heavy strand, except for the eight tRNA genes (tRNA-Gln, tRNA-Gly, tRNA-Glu, tRNA-Cys, tRNA-Tyr, tRNA-Met, tRNA-Trp, tRNA-Thr) encoded on the light strand. Most PCGs begin with ATG except for nd4 with GTG. The longest gene is nd5 (1719 bp) among the PCGs whereas the shortest is tRNA-His (64 bp). The rRNA genes, 12S rRNA (952 bp) and 16S rRNA (1344 bp) are located between the tRNA-Met (CAT) and tRNA-Leu (TAG) genes and are separated by the tRNA-Val (TAC) gene.

The phylogenetic distance was estimated using the concatenated set of the whole 13 PCGs of S. spengleriana mitogenome with 22 published Neogastropoda mitogenomes and Haliotis rubra mitogenome as an outgroup (Figure 1).

Figure 1. Maximum-likelihood tree showing phylogenetic relationships among 23 Neogastropoda species. Sequences from Haliotis rubra (AY588938) is used as outgroup. Numbers in the nodes correspond to ML bootstrap proportions. Only values above 70% are represented.

The phylogenetic analysis indicated that S. spengleriana was clustered with B. cancellata within the family Cancellariidae. Phylogenetic relationships within Neogastropoda were consistent with the phylogenetic analyses of Neogastropoda based on the entire Mitogenome (Cunha et al. 2009). Our data offered useful information for the studies of S. spengleriana on evolutionary characteristics, phylogenetic relationships as well as species identification.

Disclosure statement

The authors declare that they have no conflict of interest.

Data availability statement

The genome sequence data are deposited in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/under the accession no. MZ934412. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA761868, SRR15836237, and SAMN21365079, respectively.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [U1706217]. We appreciate the help of many lab members during the field sampling and laboratory analysis.