The complete mitochondrial genome of Saccostrea malabonensis (Ostreida: Ostreidae): characterization and phylogenetic position

Abstract

The taxonomy of the genus Saccostrea is very confused, however, there is relatively little molecular information available on Saccostrea. In this study, we determined and described for the first time the complete mitochondrial genome of Saccostrea malabonensis. The complete mitogenome of S. malabonensis is 16,204 bp in length, containing 12 protein-coding genes (lack of atp8 gene), two rRNA genes, 23 tRNA genes. The overall nucleotide composition of S. malabonensis has an AT content of 61.94% (26.29% A, 15.71% C, 22.35% G, 35.65% T). Phylogenetic analyses showed that S. malabonensis is first clustered with S. cucullata then united with Saccostrea kegaki.

Keywords:

• Saccostrea malabonensis
• mitochondrial genome
• phylogenetic analysis

Oysters are bivalve mollusks widely distributed in world estuaries and oceans, performing important roles in mitigating turbidity and improving water quality (Powell et al. 2018). They are sessile and benthic filter-feeders playing important roles in estuary ecology (Ren et al. 2010). Species in the genus Saccostrea are well known for high plasticity in shell with different habitat conditions, which leads to taxonomic problems (Lam and Morton 2006; Sekino and Yamashita 2016). The complete mitochondrial genome can provide useful information for species identification and studying phylogenetic relationships (Lei et al. 2010; Ma et al. 2012). Here we first sequenced the complete mitochondrial genome of Saccostrea malabonensis Faustino, 1932, and examined the phylogenetic position of S. malabonensis within Ostreidae.

The specimens of S. malabonensis were collected from Beihai, Guangxi province (21°0′55.9″N, 109°6′31.5″E), and preserved in 95% ethanol. Voucher specimens are deposited in the Fourth Institute of Oceanography, Ministry of Natural Resources, and the deposited numbers are IDNW8 (Wendan Mu, [email protected]). Total genomic DNA was extracted from the ethanol-preserved tissue using TIANGEN marine animal DNA kit (TIANGEN, China). The complete mitochondrial genome of S. malabonensis was sequenced by Illumina NovaSeq6000 platform with 350 bp paired-end. The reads were assembled using SPAdes (v3.14.1). ORFfinder (http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi) and BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) were used to identify protein encoding genes and rRNA genes. The tRNA genes were identified by the program MITOS webserver (Bernt et al. 2013) and tRNAscan-SE 1.21 (Lowe and Eddy 1997). Sequences of twelve-partitioned amino acid sequences of protein-coding genes (excluding atp8) were aligned by MAFFT v7.037b (Katoh and Standley 2013). Poorly aligned sites were objectively eliminated with Gblocks ver. 0.91b (Castresana 2000). The appropriate evolutionary models for each data partition were selected using ProtTest version 3.4 (Darriba et al. 2011). Phylogenetic reconstruction was performed using Maximum Likelihood (ML) and Neighbor-Joining (NJ) with MEGA 5.0 (Tamura et al. 2011). The assessments of node reliability in the ML and NJ analyses were done by using 1000 bootstrap replicates.

The complete mitogenome of S. malabonensis is 16204 bp in length, containing 12 protein-coding genes (lack of atp8 gene), two rRNA genes and 23 tRNA genes on the same strand (GenBank accession: ON649706). Previous studies on oysters (Ren et al. 2010; Volatiana et al. 2016; Wu JH et al. 2019; Li et al. 2021) showed the missing atp8 gene, which is also confirmed in the present study. In contrast to the typical metazoan mitogenome, the large subunit rRNA gene (rrnL) is split into two fragments that occurs only in Ostreidae. S. malabonensis has an AT content of 61.94% (26.29% A, 15.71% C, 22.35% G, 35.65% T). Phylogenetic trees were constructed using the concatenated set of 12 protein-coding gene amino acid sequences of S. malabonensis and 20 published complete mitogenomes of mollusca. Aplysia californica was used as outgroup. Phylogenetic analyses showed that S. malabonensis is first clustered with S. cucullata then united with S.kegaki (Figure 1). Our phylogenetic analysis supports the current established taxonomic framework among the three genera of Crassostrea, Ostrea and Saccostrea in Ostreidae, and the relationships have also been verified by other molecular phylogenetic studies (Volatiana et al. 2016; Wu JH et al. 2019; Li et al. 2021). In conclusion, we expect that the complete mitogenome of S. malabonensis will provide important genome information for molecular phylogenetic studies on Bivalvia.

Figure 1. The branch length is determined with NJ analysis. NJ/ML bootstrap values are given for each branch. Saccostrea mytiloides NC_036479, Saccostrea glomerata NC_036483, Saccostrea echinata NC_036478, Saccostrea kegaki NC_030533, Saccostrea cucullata NC_027724 (Volatiana et al. 2016), Saccostrea malabonensis ON649706 (This study), Saccostrea mordax NC_013998, Ostrea lurida NC_022688 (Xiao et al. 2015), Ostrea denselamellosa NC_015231 (Yu and Li 2011), Crassostrea virginica NC_007175, Crassostrea iredalei NC_013997 (Wu X et al. 2010), Crassostrea dianbaiensis NC_018763 (Wu X et al. 2012), Crassostrea gigas NC_001276, Crassostrea angulata NC_012648 (Ren et al. 2010), Crassostrea sikamea NC_012649 (Ren et al. 2010), Crassostrea nippona NC_015248 (Yu and Li 2011), Crassostrea hongkongensis NC_011518 (Ren et al. 2009), Crassostrea ariakensis NC_012650, Mytilus galloprovincialis NC_006886 (Cao et al. 2004), Mytilus edulis NC_006161 (Boore et al. 2004), Aplysia californica NC_005827 (Knudsen et al. 2006).

Ethical approval

This study was conducted with the guidelines of the Council of China and animal welfare requirements. The study does not involve the study of vertebrates or regulated invertebrates, and samples are collected in areas available for collection in public areas, in accordance with guidelines provided by the authors’ institutions and national or international regulations (Standers for sampling, detecting and preserving specimen). All the research meets ethical guidelines and adheres to the legal requirements of the study country.

Authors contributions

Wendan Mu was involved in the conception and design, or analysis and interpretation of the data; the drafting of the paper, revising it critically for intellectual content; and the final approval of the version to be published; and the author agrees to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study will be available in GenBank at https://www.ncbi.nlm.nih.gov/. The GenBank accession No. (reference number) is ON649706. The associated Bio-Sample, SRA, and BioProject numbers are SAMN28772344, SRR19514085, and PRJNA844164, respectively, and all of the accession numbers are activated.

Additional information

Funding

The work was supported by Funding for Doctoral Research of the Fourth Institute of Oceanography, Ministry of Natural Resources [202002], Guangxi Science and Technology Base and talent Special project [2019AC20290], Youth Science Fund project of Guangxi Natural Science Foundation [2021GXNSFBA220041].