The complete mitogenome of clam Corbicula fluminea determined usingnext-generation and PacBio sequencing

Abstract

Corbicula fluminea is an important aquatic commercial species in China. In this study, we present the complete mitogenome and a phylogenetic analysis of C. fluminea, determined using next-generation and PacBio long read sequencing. The mitogenome of C. fluminea is 17,423 bp in size, including 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region, all located on the same strand. The base composition of the entire mitogenome showed a conspicuous A + T bias of 70.5 %. The entire mitogenome data produced in this study provides the genomic resources available for future evolutionary studies.

Keywords:

• Corbicula fluminea
• mitogenome
• next-generation sequencing
• PacBio sequencing
• aquatic commercial species

Corbicula fluminea (Müller, 1774) is a species of bivalve mollusks. The extant native distribution of this freshwater suspension feeder is Asia, the Middle East, Africa, and Australia (Mcmahon 1982). Since the early 20th century, it spreads over the world through commercialization, occupies the benthic sediment in rivers, lakes and estuaries, and becomes an invasive alien species (IAS) to American and European ecosystems (Counts 1981; Phelps 1994; Mouthon 2001; Schmidlin and Baur 2007; Sousa et al. 2008; Caffrey et al. 2011; Beghelli et al. 2014; Ilarri et al. 2014; Molina et al. 2015). As an edible aqua-cultural shellfish, over 12 million tons C. fluminea is output per year (Chen et al. 2013), making it to be one of the most important aquatic commercial species in China.

In this study, we characterized the complete mitogenome sequence of C. fluminea using Illumina next-generation and Pacific Biosciences (PacBio) sequencing technology and performed an analysis of the phylogenetic relationships among Veneroida.

We collected the clam (NO. HX_HZ092701) from Hongze Lake (33.2443 N and 118.4566 E) on 27 September 2017. Purified mitochondria were extracted from muscle tissue homogenate by differential centrifugation, and subsequently, DNA was isolated following Sambrook and Russell (2001). The specimen was stored in the herbarium of Freshwater Fisheries Research Institute of Jiangsu Province.

Mitochondrial genome was sequenced and reconstructed based on both Illumina Hiseq (Borgström et al. 2011) and the Pacbio Sequel (English et al. 2012) data. 5,545,482,944 clean reads were generated and assembly was performed using ABySS (Simpson et al. 2009). Genes were annotated using MITOS (Matthias et al. 2013) and AUGUSTUS (http://bioinf.uni-greifswald.de/augustus/). tRNA and rRNA genes were predicted using tRNAscan-SE (Lowe and Eddy 1997) and rRNAmmer 1.2 (Lagesen et al. 2007), respectively.

The mitogenome of C. fluminea (HX_HZ092701) is 17,423 bp long (GenBank accession no. MK392334), has a 29.5% G + C content, and encodes 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. All genes located on the same strand, compared with the majority of bivalves. Most protein-coding genes have ATG as the start codon, while two PCGs (cox1 and nad5) use ATT and nad4L uses ATA. TAA and TAG stop codons are used in most genes, excepted for four genes, nad1-4, which have incomplete stop codon TA.

To investigate the phylogenetic relationships of C. fluminea and other 36 species from nine superfamilies in Veneroida, phylogenetic trees were obtained using Maximum-Likelihood (ML) and Bayesian inference (BI) analyses based on entire PCGs sequences. Two species in the order Lucinoida were used as outgroup (Figure 1). The consensus topology of phylogeny trees for 38 Veneroida species shows that Corbiculoidea and Arcticoidea is a sister group. Each superfamily in Veneroida is monophyly. It is worth noting that a classical barcoding fragment (cox1) shows an obvious genetic divergency between a partial genome of C. fluminea (KX254564) and our sequences. Further investigation will be needed to reveal the reason for this genetic divergency.

Figure 1. Phylogenetic tree in Veneroida using the complete mitochondrial PCGs sequences. The complete mitogenome is downloaded from GenBank and the phylogenic tree is constructed by maximum-likelihood (ML) and Bayesian inference (BI) method. The bootstrap values and posteriori probability were presented as the proportion of gray and white circles, respectively. The dotted lines indicated the structure of the BI tree differing from that of ML tree. The genomic sequences obtained in this study were shown by bold type.

Acknowledgements

The authors would like to thank Yan Cheng and Cun Jing for their helpful suggestions.

Disclosure statement

The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by Major Project of Hydro Bios Resources in Jiangsu Province [ZYHB16-3].