Research Article |
Corresponding author: Pei Wang ( wangpei601@126.com ) Corresponding author: Hong-Mu Ai ( aihongmu@yahoo.com.cn ) Academic editor: Frank Köhler
© 2016 Jun-Hong Lin, Weichuan Zhou, Hong-Li Ding, Pei Wang, Hong-Mu Ai.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Lin J-H, Zhou W-C, Ding H-L, Wang P, Ai H-M (2016) The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys 589: 55-69. https://doi.org/10.3897/zookeys.589.7637
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The land snail Cernuella virgata (da Costa, 1778) is widely considered as a pest to be quarantined in most countries. In this study, the complete mitochondrial genome of C. virgata is published. The mitochondrial genome has a length of 14,147 bp a DNA base composition of 29.07% A, 36.88% T, 15.59% C and 18.46% G, encoding 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The complete nucleotide composition was biased toward adenine and thymine, A+T accounting for 69.80%. Nine PCGs and 14 tRNA genes are encoded on the J strand, and the other four PCGs and eight tRNA genes are encoded on the N strand. The genome also includes 16 intergenic spacers. All PCGs start strictly with ATN, and have conventional stop codons (TAA and TAG). All tRNAs fold into the classic cloverleaf structure, except tRNAArg, tRNASer(UCN), tRNASer(AGN) and tRNAPro. The first three lack the dihydrouridine arm while the last lacks the TψC arm. There are 502 bp long noncoding regions and 418bp long gene overlaps in the whole mitochondrial genome, accounting for 3.54% and 2.95% of the total length respectively. Phylogenetic analyses based on the sequences of the protein coding genes revealed a sister group relationship between the Hygromiidae and the Helicidae.
DNA sequencing, phylogeny, plant quarantine, secondary structure, white snail
The land snail Cernuella virgata (da Costa, 1778), also known as the Mediterranean white snail or Common white snail, is endemic to the Mediterranean and western Europe, and has been introduced to America, Australia and Morocco (
The metazoan mitochondrial (mt) genome usually comprise 37 genes and some noncoding regions, such as 13 protein coding genes (PCGs) (COI−COIII, Cytb, ND1−ND6, ND4L, ATP6 and ATP8), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and the AT-rich region or control region (Wolstenholme 1992;
Adult snail was intercepted from barley shipments imported to China from southern Australia on 1 March 2012 and stored at -20 °C in the Key Laboratory of Molluscan Quarantine and Identification of AQSIQ, Fujian Entry-Exit Inspection & Quarantine Bureau, Fuzhou, Fujian, China (FJIQBC). Voucher specimens (FJIQBC000123) were deposited in FJIQBC. Total genomic DNA was obtained from approximately 50 mg fresh foot tissue, using the DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
The entire genome was successfully amplified by polymerase chain reaction (PCR) in overlapping fragments with four pairs of mitochondrial universal primers chosen from previous works (
No. of fragment | Primer name | Nucleotide sequence (5’ – 3’) and location | Size (bp) | Reference |
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1 | LCO-1490 | GGTCAACAAATCATAAAGATATTGG |
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HCO-2198 | TAAACTTCAGGGTGACCAAAAAATCA |
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2 | F1231 | GAACGGGTTAGTTTGTTTGTCT(490–511) | 1763 | Present study |
R1231 | TAGGGTCTTCTCGTCTATTATGGT(2229–2252) | Present study | ||
3 | 16Sar-L | CGCCTGTTTATCAAAAACAT |
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16Sbr-H | CCGGTCTGAACTCAGATCACGT |
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4 | 123F116 | TGTAACCATAATAGACGAGAAGACC(2225–2249) | 4545 | Present study |
123R1b | TAGGAGCAAAAAATACTACCAGAAA(6745–6769) | Present study | ||
5 | 144F | TGAGSNCARATGTCNTWYTG |
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272R | GCRAANAGRAARTACCAYTC |
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6 | 123Fb | CTTTTCACCCCTACTTTAC(6683–6701) | 1044 | Present study |
123RII | ACTCCCTTTCAGGTGTTAT(7708–7726) | Present study | ||
7 | FCOII | AAATAATGCTATTTCATGAYCAYG |
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RCOII | GCTCCGCAAATCTCTGARCAYTG |
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8 | F1233 | AGTTACATTGGCCCTCCCTAGTCTTCGC(7560–7587) | 6930 | Present study |
R1233 | GTAAACGGTTCAACCTGTACCAGCTCCC(315–342) | Present study |
The BigDye Terminator Sequencing Kit (Applied Biosystems, San Francisco, CA, USA) and the ABI PRIMERTM 3730XL DNA Analyzer (PE Applied Biosystems) were used to sequence short fragments from both directions after purification. For the long fragments, the shotgun libraries of C. virgata were constructed, and the positive clones were then sequenced using the above kit and sequenator with vector-specific primers BcaBest primer M13-47 and BcaBest Primer RV-M.
To control sequencing errors, each partial sequence was evaluated at least twice. Annotations and editing procedures of the mitochondrial genomes of C. virgata were performed in MEGA5.0. Mitochondrial PCGs and rRNA genes were identified by BLAST searches at NCBI against other Eupulmonata sequences (
The base composition and codon usage were analyzed with MEGA 5.0 (Tamura et al. 2007). AT skew and GC skew were used to describe strand asymmetry according to the formulae AT = [A−T]/[A+T] and GC = [G−C]/[G+C] (
Phylogenetic analyses were performed based on 15 complete mt genomes of gastropods from GenBank (Table
Subclass /order | Family | Species | Accession number | Reference |
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Stylommatophora | Hygromiidae | Cernuella virgata | KR736333 | Present study |
Camaenidae | Camaena cicatricosa | KM365408 |
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Camaena sp. | KT001074 | Ding et al. 2015 (submitted) | ||
Bradybaenidae | Euhadra herklotsi | Z71693 – Z71701 |
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Mastigeulota kiangsinensis | KM083123 | Deng et al. 2014 | ||
Aegista diversifamilia | KR002567.1 | Huang et al. 2015 | ||
Dolicheulota formosensis | KR338956.1 | Huang et al. 2015 | ||
Helicidae | Cornu aspersum | JQ417195 |
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Cepaea nemoralis | CMU23045 |
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Cylindrus obtusus | JN107636 |
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Succineidae | Succinea putris | JN627206 |
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Clausiliidae | Albinaria caerulea | X83390 |
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Achatinidae | Achatina fulica | NC024601 |
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Basommatophora | Lymnaeidae | Galba pervia | JN564796 | Liu et al. 2012 |
Opisthobranchia | Aplysiidae | Aplysia californica | AY569552 | Knudsen et al. 2006 |
The entire circular genome was 14,147 bp in length (GenBank: KR736333), containing 13 PCGs, 22 tRNA genes and two rRNA genes (Figure
The mt genome of Cernuella virgata. The tRNA genes are labeled based on the IUPACIUB single letter amino acid codes. Genes with underline illustrate the direction of transcription from 3’ to 5’, and without underline revealing from 5’ to 3’. Numbers and overlapping lines within the circle indicate PCR fragments amplified for sequencing (see Table
Gene | Direction | Location | Size (bp) | Anticodon | Start codon | Stop codon | Intergenic nucleotides |
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COI | F | 1–1497 | 1497 | ATT | TAA | 26 | |
tRNA Val | F | 1494–1554 | 61 | 1524–1526 TAC | –4 | ||
lrRNA | F | 1555–2567 | 1013 | 0 | |||
tRNA Leu(CUN) | F | 2568–2628 | 61 | 2597–2599 TAG | 0 | ||
tRNA Pro | F | 2629–2685 | 57 | 2655–2657 TGG | 0 | ||
tRNA Ala | F | 2687–2748 | 62 | 2718–2720 TGC | 1 | ||
ND6 | F | 2767–3222 | 456 | ATA | TAA | 18 | |
ND5 | F | 3227–4888 | 1662 | ATT | TAA | 4 | |
ND1 | F | 4804–5769 | 966 | ATG | TAG | –85 | |
ND4L | F | 5847–6215 | 369 | ATT | TAA | 77 | |
CytB | F | 6151–7167 | 1017 | ATA | TAG | –65 | |
tRNA Asp | F | 7157–7214 | 58 | 7188–7190 GTC | –11 | ||
tRNA Cys | F | 7215–7276 | 62 | 7245–7247 GCA | 0 | ||
tRNA Phe | F | 7283–7341 | 59 | 7313–7315 GAA | 6 | ||
COII | F | 7387–8031 | 645 | ATT | TAA | 45 | |
tRNA Tyr | F | 8015–8083 | 69 | 8046–8048 GTA | –17 | ||
tRNA Trp | F | 8071–8132 | 62 | 8102–8104 TCA | –13 | ||
tRNA Gly | F | 8282–8341 | 60 | 8311–8313 TCC | 149 | ||
tRNA His | F | 8338–8398 | 61 | 8369–8371 GTG | –4 | ||
tRNA Gln | R | 8400–8457 | 58 | 8427–8429 TTG | 1 | ||
tRNA Leu(UUR) | R | 8457–8513 | 57 | 8485–8487 TAA | –1 | ||
ATP8 | R | 8485–8754 | 270 | ATG | TAA | –29 | |
tRNA Asn | R | 8743–8804 | 62 | 8771–8773 GTT | –12 | ||
ATP6 | R | 8807–9472 | 666 | ATG | TAA | 2 | |
tRNA Arg | R | 9458–9517 | 60 | 9489–9491 TCG | –15 | ||
tRNA Glu | R | 9518–9578 | 61 | 9547–9549 TTC | 0 | ||
SrRNA | R | 9579–10277 | 699 | 0 | |||
tRNA Met | R | 10278–10343 | 66 | 10306–10308 CAT | 0 | ||
ND3 | R | 10304–10735 | 432 | ATA | TAA | –40 | |
tRNA Ser(UCN) | R | 10691–10743 | 53 | 10723–10725 TGA | –45 | ||
tRNA Ser(AGN) | F | 10820–10880 | 61 | 10844–10846 GCT | 76 | ||
ND4 | F | 10904–12178 | 1275 | ATT | TAG | 23 | |
tRNA Thr | R | 12182–12246 | 65 | 12210–12212 TGT | 3 | ||
COIII | R | 12170–13051 | 882 | ATG | TAA | –77 | |
tRNA Ile | F | 13068–13127 | 60 | 13096–13098 GAT | 16 | ||
ND2 | F | 13182–14060 | 879 | ATA | TAG | 54 | |
tRNA Lys | F | 14062–14121 | 60 | 14090–14092 TTT | 1 |
The total length of all PCGs was 10, 977 bp, accounting for 77.59% of the entire mt genome (Table
Proportion of nucleotides | ||||||||
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Feature | %A | %T | %G | %C | %A+T | AT Skew | GC Skew | No. of nucleotides |
Whole genome | 29.07 | 36.88 | 18.46 | 15.59 | 69.80 | –0.12 | 0.08 | 14147 |
Protein coding genes | 26.39 | 39.31 | 18.43 | 15.87 | 69.26 | –0.20 | 0.07 | 10977 |
Protein coding genes (J) | 26.08 | 39.96 | 18.70 | 15.26 | 69.17 | –0.21 | 0.10 | 8739 |
Protein coding genes (N) | 27.61 | 36.77 | 17.38 | 18.23 | 69.67 | –0.14 | –0.02 | 2034 |
tRNA genes | 31.46 | 34.23 | 18.73 | 15.58 | 71.41 | –0.04 | 0.09 | 1335 |
tRNA genes (J) | 29.82 | 34.77 | 20.30 | 15.10 | 70.77 | –0.08 | 0.15 | 788 |
tRNA genes (N) | 33.82 | 33.46 | 16.45 | 16.27 | 72.54 | 0.01 | 0.01 | 547 |
rRNA genes | 32.83 | 35.63 | 17.00 | 14.54 | 72.42 | –0.04 | 0.08 | 1712 |
Codon usage could reveal nucleotide bias. NNA and NNU as codons were used frequently in most PCGs. Additionally, the codons TTT (phenylalanine), TTA (leucine) and ATT (isoleucine) composing A and T were used widely (Figure
The length of tRNA genes ranged from 53 to 69 bp.The 22 tRNA genes typically found in metazoan mt genomes were also discovered in C. virgata; eleven of them were determined by tRNAscan-SE and eight of them were determined by DOGMA. Another three tRNA genes that could not be detected by the above two programs were identified and passed through comparisons with known patterns of previous research Fourteen tRNA genes were encoded on the J strand and the remainder on the N strand. Most tRNA genes could be folded into classic clover leaf structures except for tRNAArg, tRNASer(UCN) and tRNASer(AGN), which lack the dihydrouridine arm. The gene tRNAPro has a loop in its TψC arm (Figure
In some tRNA genes, non-Watson-Crick matches and aberrant loops had been found. For example, a total of 41 unmatched base pairs existed in some tRNAs, and 18 of them were G-U non-classical pairs, most of which existed in Discriminator nucleotide, anticodon arm and Dihydrouridine arm (Figure
The rRNA genes of C. virgata encompassed the lrRNA and srRNA genes with a length of 1,013 bp and 699 bp, repsectively. The former was situated between tRNAVal and tRNALeu(CUN) and the latter was located between tRNAGlu and tRNAMet (Table
In the mitochondrial genome of C. virgata, there are 16 noncoding regions with total 502 bp length, accounting for 3.54%. The longest was 149bp, between tRNATrp and tRNAGly. The shortest was 1 bp existing three regions, respectively locating tRNAPro and tRNAAla, tRNAHis and tRNAGln, ND2 and tRNALys (Table
The ML tree (Figure
The length of mt genome of C. virgata was 304 bp longer than Camaena cicatricosa and 97 bp longer than Cornu aspersum. All gene directions showed similarity to the sequenced mt genome of C. cicatricosa, but gene order was different, especially with respect to the positions between CYTB and ATP8 genes (
In the study of mt genome of C. cicatricosa, GTG is the start codon of the COII gene, and COI and ND6 genes of C. aspersum start with TTG (
Usually, in the tRNA, the Acceptor arm (7 bp) and Anticodon arm (5 bp) were conservative in size (
Noncoding regions are assumed to splice recognition sites during the process of transcription (
Three species in the Helicidae were sister groups and consistent with previous works (
We sincerely thank professor De-Niu Chen of Institute of Zoology, Chinese Academy of Science for helpful comments on the manuscript. We thank the reviewers and the subject editor for their very helpful suggestions on the manuscript. This research is supported by National Natural Science Foundation of China (31372162), Natural Science Foundation in Fujian Province (2015J05076) and Public Science and Technology Research Funds Projects of General Administration of Quality Supervision, Inspection and Quarantine of the People’s Republic of China (201410076, 2015IK042).