The complete mitochondrial DNA genome of Chinese Daphnia carinata (Clasocera: Daphniidae)

Abstract

In this paper, we determined the complete mitochondrial genome of Chinese Daphnia carinata for the first time by the long and accurate polymerase chain reaction and primer-walking methods. It was 15,245 bp in length, with an A + T content of 70.35%, containing 37 typical animal mitochondrial genes and an A + T-rich region. The COI gene started with ACTA. All the 22 typical tRNA genes had a classical cloverleaf structure except for trnS1, in which the D-stem pairings in the DHU arm were absent.

Water fleas are an important component of the microcrustacean zooplankton, their habitats are mostly continental fresh and saline waters (Forró et al. 2008). Daphnia carinata has become a well-known model species in studying evolutionary biology, environmental biology and ecology (Miner et al. 2013). Only the complete mitochondrial DNA of North American Daphnia pulex (GenBank accession no. AF117817) and the Chinese Daphnia pulex (GenBank accession no. KT003819) and the Chinese Daphnia magna (GenBank accession no. KP296147) have been released in Genbank database. And other partial mitochondrial genome DNA of Daphnia has also been published; however, this is far from enough. Gu et al. (2013) had named Daphnia similoides sinensis for this D. carinata, by comparing the sequences of COI with the similarity of 99%. So the standard of morphology species identification could not meet taxonomy studies. It is, thus, worthy to do the further researches for molecular biology of Daphnia so far, advancing our understanding of Cladoceran diversity and evolution.

Using the long and accurate polymerase chain reaction and primer-walking methods, we sequenced and characterized the complete mitochondrial genome of Chinese D. carinata (sampled from Chaohu, Anhui province in China) for the first time (GenBank accession no. KP721459). The total length is 15,245 bp with an A + T content of 70.35%. Table 1 provides detailed information about the mitogenome. The D. carinata mitogenome including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes for the small and large subunits (rrnS and rrnL) and a putative control region. The ATN initiation codon are used in all protein-coding genes except ATP8 (GTG) and COI (ACTA). The TAN termination codon are used in all protein-coding genes except COI, COII, ND4 and ND5 used the incomplete stop codon T. The assignment of incomplete termination codon on these genes could avoid overlapping nucleotides between their adjacent genes (Gong et al. 2012), which is commonly reported in other invertebrates (Masta & Boore 2004). And then they would produce functional stop codons via posttranscriptional polyadenylation (Ojala et al. 1981). Fourteen overlaps were found between adjacent genes (80 bp in total), the longest is 23 bp located rrnL and trnL1; and including eight intergenic spacers ranged from 1 to 30 bp (58 bp in total), of which only two spacer span longer than 10 bp (Figure 1).

Table 1.

Organization of the Chinese Daphnia carinata mitogenome.

No.	Gene name	Start	End	Stranda	Length	Overlap/intergenicb	Start codon	Stop codon
1	trnI	1	66	J	66
2	trnQ	121	188	N	68	54
3	trnM	190	254	J	65	1
4	ND2	255	1241	J	987		ATG	TAG
5	trnW	1240	1303	J	64	−2
6	trnC	1303	1366	N	64	−1
7	trnY	1368	1432	N	65	1
8	COI	1430	2967	J	1538	−3	(A)CTA	T––
9	trnL2	2968	3035	J	68
10	COII	3037	3715	J	679	1	ATG	T––
11	trnK	3716	3785	J	70
12	trnD	3786	3850	J	65
13	ATP8	3851	4021	J	171		GTG	TAG
14	ATP6	4015	4689	J	675	−7	ATG	TAA
15	COIII	4689	5477	J	789	−1	ATG	TAG
16	trnG	5480	5541	J	62	2
17	ND3	5542	5895	J	354		ATT	TAG
18	trnA	5894	5956	J	63	−2
19	trnR	5957	6020	J	64
20	trnN	6021	6087	J	67
21	trnS1	6088	6152	J	65
22	trnE	6153	6217	J	65
23	trnF	6217	6280	N	64	−1
24	ND5	6281	7994	N	1714		ATA	T––
25	trnH	7989	8051	N	63	−6
26	ND4	8052	9369	N	1318	1	ATG	T––
27	ND4L	9369	9647	N	279	−1	ATT	TAA
28	trnT	9678	9740	J	63	30
29	trnP	9741	9804	N	64
30	ND6	9822	10,313	J	492	17	ATT	TAA
31	Cytb	10,313	11,446	J	1134	−1	ATG	TAG
32	trnS2	11,446	11,514	J	69	−1
33	ND1	11,505	12,440	N	936	−10	ATG	TAA
34	trnL1	12,444	12,510	N	67	3
35	rrnL	12,488	13,849	N	1362	−23
36	trnV	13,828	13,899	N	72	−22
37	rrnS	13,898	14,644	N	747	−2
38	D-loop	14,644	15,245	J	601

^aJ and N refer to the majority and the minority strand, respectively.

^bPositive numbers indicate the number of intergenic nucleotides. Negative numbers indicate that adjacent genes overlap.

Figure 1.

Phylogenetic tree obtained by the maximum-likelihood (ML) method based on amino acid sequences of ND5 gene.

All 22 tRNA genes are ranged from 62 bp to 72 bp in size, showing the typical cloverleaf secondary structures except for trnS1, in which its DHU arm simply formed a loop. Generally speaking, the aberrant loop in trnS is a common theme in metazoan mitochondrial genomes. Whether or not the aberrant tRNAs lose their respective functions is still unknown, however, these shortage may be modified by RNA-editing mechanisms (Masta & Boore 2004; Li et al. 2012). The rrnL and rrnS are 1362 bp and 747 bp, respectively. The rRNA genes with A + T content of 72.69%.

The putative control region is located between rrnS and trnI with a sequenced length of 601 bp, with the A + T content of 72.54%. This region was usually believed to play an important role in the transcription and replication of mitogenome (Clayton 1992; Delarbre et al. 2001; Delport et al. 2002; Yu et al. 2013).

The complete mitogenome of the Chinese Daphina carinata reported here is expected to supply more molecular information for further studies of the daphnia phylogeny and for analyses on the taxonomic status of the Cladocera.