The complete mitochondrial genome of Thryssa kammalensis (Clupeiformes: Engraulidae)

Abstract

In this study, the complete mitochondrial genome (mitogenome) sequence of Thryssa kammalensis has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16 968 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence (TAS) domain, the central conserved sequence block domains (CSB-F, CSB-E and CSB-D) and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3). There are eight copies of tandem repeats of 38 bp in the control region, which contain TAS.

Thryssa kammalensis, which belongs to order Clupeiformes, family Engraulidae, genus Thryssa is a warm-temperature species. It is mainly distributed along the coasts of Indo-West Pacific Ocean, as well as also common in China (Whitehead et al. 1988). There are few specific genetic research about T. kammalensis, only some phylogenetic studies involved T. kammalensis (Ma et al. 2010; Bloom and Lovejoy 2012). To provide useful genetic resource that could be used in future research of population genetics, phylogenetics and taxology, the complete mitochondrial genome of T. kammalensis was sequenced.

In the present study, one T. kammalensis specimen chosen for mitochondrial genome analysis was collected from the coastal of Fujian Province in China. The complete mitogenome of T. kammalensis was sequenced to be 16 968 bp in length (GenBank accession No. KT985048). It consisted of 13 typical vertebrate protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions. The encoding genes of mitogenome were located on H-strand with the exception of ND6 and eight tRNA genes that were transcribed from L-strand (Table 1). The overall nucleotide composition of T. kammalensis mitogenome was estimated to be 26.6% T, 26.7% C, 30.1% A and 16.6% G, with anti-G bias and a slight excess of AT as other most fishes (Miya et al. 2001, 2003). The 13 protein-coding genes were totally 11 419 bp in size, accounting for 67.3% of the whole mitogenome and contained 3797 amino acids for protein coding. Like other mitochondrial genomes (Zardoya et al. 1995; Inoue et al. 2000), 22 tRNA genes interspersed between the rRNA and protein-coding genes were identified, ranging in size from 66 bp to 75 bp. The T. kammalensis mitogenome also contained a small subunit rRNA (12S rRNA) and a large subunit rRNA (16S rRNA), which were 954 and 1691 bp in length, respectively. The origin of light strand replication (O_L) was observed between the tRNA^Asn and tRNA^Cys in WANCY region and it could form a stable stem-loop secondary structure, with 11 paired nucleotides in the stem and 11 nucleotides in the loop. The largest non-coding region (control region) located between the tRNA^Pro and tRNA^Phe genes is determined to be 1320 bp in length. The T. kammalensis control region included a termination-associated motif sequence (TAS), a central conserved domain (CSB-F, CSB-E and CSB-D) and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3) (Walberg and Clayton 1981). There are eight copies of tandem repeats of 38 bp in the control region, which contain TAS. The mechanism of gene replication needs to be further studied and analyzed.

Table 1.

Characteristics of the mitochondrial genome of Thryssa kammalensis.

Sequence	Position		Size (bp) Nucleotide	Amino acid	Gap	Codon		Strand
	From	To				Initial	Terminal
tRNAPhe	1	69	69		0			H
12S rRNA	70	1023	954		0			H
tRNAVal	1024	1095	72		0			H
16S rRNA	1096	2786	1691		0			H
tRNALeu(UUR)	2787	2861	75		0			H
ND1	2862	3836	975	324	0	ATG	TAA	H
tRNAIle	3837	3908	72		−1			H
tRNAGln	3908	3978	71		−1			L
tRNAMet	3978	4046	69		0			H
ND2	4047	5091	1045	348	0	ATG	T	H
tRNATrp	5092	5162	71		2			H
tRNAAla	5165	5233	69		1			L
tRNAAsn	5235	5307	73		30			L
tRNACys	5338	5403	66		0			L
tRNATyr	5404	5474	71		1			L
CO I	5476	7020	1545	514	0	GTG	TAA	H
tRNASer(UCN)	7021	7091	71		5			L
tRNAAsp	7097	7165	69		11			H
CO II	7177	7867	691	230	0	ATG	T	H
tRNALys	7868	7940	73		1			H
ATPase8	7942	8109	168	55	−10	ATG	TAA	H
ATPase6	8100	8783	684	227	−1	ATG	TAA	H
CO III	8783	9567	785	261	0	ATG	TA	H
tRNAGly	9568	9639	72		0			H
ND3	9640	9988	349	116	0	ATG	T	H
tRNAArg	9989	10 057	69		0			H
ND4L	10 058	10 354	297	98	−7	ATG	TAA	H
ND4	10 348	11 728	1381	460	0	ATG	T	H
tRNAHis	11 729	11 797	69		1			H
tRNASer(AGY)	11 799	11 865	67		0			H
tRNALeu(CUN)	11 866	11 937	72		0			H
ND5	11 938	13 773	1836	611	−4	ATG	TAA	H
ND6	13 770	14 291	522	173	0	ATG	TAG	L
tRNAGlu	14 292	14 360	69		7			L
Cyt b	14 368	15 508	1141	380	0	ATG	T	H
tRNAThr	15 509	15 578	70		0			H
tRNAPro	15 579	15 648	70		0			L
Control region	15 649	16 968	1320					H

The phylogenetic tree among 10 Engraulidae species based on 12 H-strand protein-coding genes (Figure 1) was visualized using Mrbayes (Ronquist & Huelsenbeck 2003). C. nasus, C. mystus and C. grayii were used to root the trees. The NJ tree showed that the genus of Pellona firstly clustered together with Brevoortia, then grouped with Engraulis and Thryssa species, and finally gathered with Setipinna, with high value of posterior probability.

Figure 1.

Phylogenetic relationships using Bayesian analysis among 10 Engraulidae species based on 12 H-strand mitochondrial protein-coding genes of Thryssa kammalensis, Thryssa baelama (AP009616), Engraulis japonicas (AB040676), Engraulis encrasicolus (AP009137), Brevoortia tyrannus (AP009618), Pellona flavipinnis (AP009619), Setipinna taty (KC439458), Coilia nasus (KM363243), Coilia mystus (KJ710625), Coilia grayii (KP317088). C. nasus, C. mystus and C. grayii were used to root the trees. Bayesian posterior probabilities are shown at nodes.

Declaration of interest

This study was supported by the Scientific Startup Foundation of Zhejiang Ocean University (Q1505) and National Programme on Global Change and Air-Sea Interaction (GASI-02-SCS-YSWaut, GASI-02-SCS-YSWspr). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.