Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae) Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu & Na Zhou To cite this article: Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu & Na Zhou (2015) Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae), Mitochondrial DNA, 26:5, 753-754, DOI: 10.3109/19401736.2013.850679 To link to this article: http://dx.doi.org/10.3109/19401736.2013.850679
Published online: 27 Jan 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California Santa Barbara]
Date: 05 November 2015, At: 21:58
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 753–754 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.850679
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae) Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu, and Na Zhou
Downloaded by [University of California Santa Barbara] at 21:58 05 November 2015
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, P. R. China
Abstract
Keywords
The complete mitochondrial genome sequence of Peronia verruculata is firstly described in the article. The mitogenome (13,861 bp) contains 22 tRNA genes, 2 ribosomal RNA genes and 13 protein-coding genes. The characteristic is the typical bivalvia mitochondrial gene composition.
Mitochondrial genome, Onchidiidae, Peronia verruculata, Pulmonata History Received 23 September 2013 Accepted 29 September 2013 Published online 24 January 2014
Introduction Onchidiidae is the only species of euthyneuran gastropods survived in the sea, the fresh water and on land, which has important research value in understanding macroevolutionary patterns of transitions from aquatic habitats to terrestrial habitats (Dayrat, 2009). The gill-bearing species are quite conspicuous and distinctive in the family of Onchidiidae. Peronia verruculata is link species, which connected Nudibranchia: Opisthobranchia with Pulmonata: Gastropoda. Its respiration takes place in the pulmonary cavity (Dayrat, 2010), meanwhile in mantle especially with branchial gills existed in the posterior of the notum. It is widely distributed in littoral areas of south China and other countries. In recent years, the wild resource of P. verruculata has sharply decreased because of over exploitation as seafood and utilization of coastal mudflats and coastal environment pollution (Shu et al., 2002; Wu et al., 2010).
This study will provide useful molecular evidence for management, conservation and sustainable exploitation of this species and be helpful in systematic identification and molecular evolutionary analysis. The complete mitochondrial genome of Peronia verruculata was sequenced and characterized particularly in this article. The sample was collected from Zhanjiang, Guangdong Province, China. Primers were designed according to the mitochondrial genome sequence of Onchidium struma (HQ452830) and Platevindex mortoni (GU475132) (Wei et al., 2010, 2011). The methods for PCR amplification and sequencing were same as described in Wei et al. (2010). The complete mitochondrial genome of Peronia verruculata was 13,861 bp in length and has been deposited in GenBank with accession No. HQ596407. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and as given in Table 1. Except the
Table 1. Mitochondrial genome characteristics of the P. verruculata. Position Locus COI tRNAval l-rRNA tRNALeu tRNAAla tRNAPro ND6 ND5 ND1 ND4L Cytb
From 67 1561 1617 2651 2700 2764 2869 3311 4941 5822 6168
Codon To 1560 1622 2649 2715 2763 2826 3285 4939 5822 6142 7215
Size (bp)
Start
Stop
1495 62 1033 65 64 63 417 1629 882 321 1048
ATT
TAG
Anti-codon TAC TAG TGC TGG
ATA ATA ATT ATG ATT
TAA TAG TAG TAG TAG
Intergenic nucleotidesa 0 6 52 16 0 2 25 1 0 25 0
Strandb H H H H H H H H H H H (continued )
Correspondence: H. D. Shen, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China. Tel: +86 21 61900446. Fax: +86 21 61900405. E-mail: [email protected]
754
C. Liu et al.
Mitochondrial DNA, 2015; 26(5): 753–754
Table 1. Continued.
Position Locus
Downloaded by [University of California Santa Barbara] at 21:58 05 November 2015
asp
tRNA tRNACys tRNAPhe COII tRNAtyr tRNATrp tRNAgly tRNAHis tRNAgln ATP8 tRNAAsn ATP6 tRNAArg tRNAGlu tRNAleu s-rRNA tRNAMet ND3 tRNAser tRNAser ND4 tRNAThr COIII tRNAIle ND2 tRNALys
Codon
From
To
Size (bp)
7216 7273 7334 7396 8068 8119 8179 8240 8360 8415 8567 8624 9270 9333 9512 9563 10,099 10,181 10,535 10,590 10,654 11,961 12,025 12,804 12,883 13,801
7278 7333 7395 8061 8126 8181 8245 8301 8419 8564 8628 9269 9330 9396 9562 10,096 10,162 10,459 10,588 10,645 12,012 12,023 12,802 12,866 13,813 13,861
63 61 62 666 59 63 65 62 60 150 62 645 61 64 51 534 64 279 54 56 1359 64 778 62 930 60
Start
Stop
Anti-codon GTC GCA GAA
TTG
TAA GTA TCA TCC GTG TTG
ATG
TAA
ATG
TAA
GTT TCG TTC TAA CAT ATT
TAG TGA GCT
ATT
TAA
ATG
T–
TTG
TAG
TGT GAT TTT
Intergenic nucleotidesa
Strandb
5 0 0 6 6 3 6 58 5 2 4 0 2 115 0 2 18 77 1 8 50 1 1 16 13 0
H H H H H H H H H L L L L L H H L H H H H L L H H H
a
Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. b H and L indicate genes transcribed on the heavy and light strand.
five tRNA genes and ATP8, ATP6 and COIII genes were encoded on the light strain, the remaining genes were all encoded on the heavy strain. The relative position and orientation of all the genes were similar to other species of Onchidiidae (Grande et al., 2008; Wei et al., 2010, 2011; White et al., 2011). In addition to the ATG, ATA, ATT and TTG are also used as the start codon, which is very common in invertebrates (Grande et al., 2008), but only ATP8 start with TTG. Except for COIII with an incomplete stop codon ‘‘T–’’, the remaining protein-coding genes stop with the TAG or TAA. Using the tRNA scan-SE 1.21 (Lowe & Eddy, 1997), 22 tRNA genes were found to fold into a typical cloverleaf secondary structure. 16S rRNA (1033 bp) gene was located between tRNAVal and tRNALeu(UAA) genes, 12S rRNA (534 bp) gene was located between tRNALeu(UAG) and tRNAMet genes. In all 19 non-coding regions, one usual non-coding region of 359 bp, with AT-rich and C-rich, is identified as a putative CR. The overall base composition of the heavy strand is 27.65% A, 37.24% T, 19.72% G and 15.38% C, with an AT content of 63.65%. The AT content is higher than the content of GC, as generally shown in bivalvia mitochondrial genomes (Wang et al., 2010).
Acknowledgements The authors appreciate anonymous reviewers for providing valuable comments on this article.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. The study was supported by the National Natural Science Foundation of China (No. 41276157), Shanghai Municipal Education Commission key innovation project funding (No. 12ZZ164) and Leading Academic Discipline
Project of Shanghai Municipal Education Commission, Project Number J50701 (Marine Biology).
References Dayrat B. (2009). Review of the current knowledge of the systematics of Onchidiidae (Mollusca: Gastropoda: Pulmonata) with a checklist of nominal species. Zootaxa 2068:1–26. Dayrat B. (2010). Comparative anatomy and taxonomy of Onchidium vaigiense (Gastropoda: Pulmonata: Onchidiidae). Molluscan Res 30: 87–101. Grande C, Templado J, Zardoya R. (2008). Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol 8:1–15. Lowe TM, Eddy SR. (1997). TRNAscan-SE 1.21. Available at: http:// lowelab.ucsc.edu/tRNAscan-SE/ (Accessed 5 April 2011). Shu TF, Luo L, Wen YM. (2002). Effects of mariculture on coastal ecological environment. Mar Environ Sci 21:74–9. Wang HX, Zhang SP, Li Y, Liu BZ. (2010). Complete mtDNA of Meretrix lusoria (Bivalvia: Veneridae) reveals the presence of an atp8 gene, length variation and heteroplasmy in the control region. Comp Biochem Physiol Part D 5:256–64. Wei LL, Shen B, Shen HD, Chen C, Fang L, Wu WJ. (2010). Analysis of complete mitochondrial genome of Platevindex mortoni of Onchidiidae (Mollusca: Gastropoda: Pulmonata). Biotechnol Bull 8: 188–94. Wei LL, Shen HD, Zhang Y, Fang L, Zhang KX, Chen C. (2011). Analysis of complete mitochondrial genome of Onchidium struma (Mollusca: Gastropoda: Pulmonata: Onchidiidae). J Fish China 35: 493–500. White TR, Conrad MM, Tseng R, Balayan S, Golding R, Martins AMD, Dayrat BA. (2011). Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evol Biol 11:1–15. Wu WJ, Shen B, Chen C, Shen HD, Wei LL, Wang L, Li K. (2010). Preliminary classification and phylogenetic relationship among Onchidiidae in China inferred from 18S rRNA partial sequence. Zool Res 31:381–6.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae) Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu & Na Zhou To cite this article: Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu & Na Zhou (2015) Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae), Mitochondrial DNA, 26:5, 753-754, DOI: 10.3109/19401736.2013.850679 To link to this article: http://dx.doi.org/10.3109/19401736.2013.850679
Published online: 27 Jan 2014.
Submit your article to this journal
Article views: 15
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California Santa Barbara]
Date: 05 November 2015, At: 21:58
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 753–754 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.850679
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Peronia verruculata (Gastropoda: Pulmonata: Systellommatophora: Onchidiidae) Chen Liu, Luanluan Wei, He Ding Shen, Hong Chai Zhu, and Na Zhou
Downloaded by [University of California Santa Barbara] at 21:58 05 November 2015
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, P. R. China
Abstract
Keywords
The complete mitochondrial genome sequence of Peronia verruculata is firstly described in the article. The mitogenome (13,861 bp) contains 22 tRNA genes, 2 ribosomal RNA genes and 13 protein-coding genes. The characteristic is the typical bivalvia mitochondrial gene composition.
Mitochondrial genome, Onchidiidae, Peronia verruculata, Pulmonata History Received 23 September 2013 Accepted 29 September 2013 Published online 24 January 2014
Introduction Onchidiidae is the only species of euthyneuran gastropods survived in the sea, the fresh water and on land, which has important research value in understanding macroevolutionary patterns of transitions from aquatic habitats to terrestrial habitats (Dayrat, 2009). The gill-bearing species are quite conspicuous and distinctive in the family of Onchidiidae. Peronia verruculata is link species, which connected Nudibranchia: Opisthobranchia with Pulmonata: Gastropoda. Its respiration takes place in the pulmonary cavity (Dayrat, 2010), meanwhile in mantle especially with branchial gills existed in the posterior of the notum. It is widely distributed in littoral areas of south China and other countries. In recent years, the wild resource of P. verruculata has sharply decreased because of over exploitation as seafood and utilization of coastal mudflats and coastal environment pollution (Shu et al., 2002; Wu et al., 2010).
This study will provide useful molecular evidence for management, conservation and sustainable exploitation of this species and be helpful in systematic identification and molecular evolutionary analysis. The complete mitochondrial genome of Peronia verruculata was sequenced and characterized particularly in this article. The sample was collected from Zhanjiang, Guangdong Province, China. Primers were designed according to the mitochondrial genome sequence of Onchidium struma (HQ452830) and Platevindex mortoni (GU475132) (Wei et al., 2010, 2011). The methods for PCR amplification and sequencing were same as described in Wei et al. (2010). The complete mitochondrial genome of Peronia verruculata was 13,861 bp in length and has been deposited in GenBank with accession No. HQ596407. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and as given in Table 1. Except the
Table 1. Mitochondrial genome characteristics of the P. verruculata. Position Locus COI tRNAval l-rRNA tRNALeu tRNAAla tRNAPro ND6 ND5 ND1 ND4L Cytb
From 67 1561 1617 2651 2700 2764 2869 3311 4941 5822 6168
Codon To 1560 1622 2649 2715 2763 2826 3285 4939 5822 6142 7215
Size (bp)
Start
Stop
1495 62 1033 65 64 63 417 1629 882 321 1048
ATT
TAG
Anti-codon TAC TAG TGC TGG
ATA ATA ATT ATG ATT
TAA TAG TAG TAG TAG
Intergenic nucleotidesa 0 6 52 16 0 2 25 1 0 25 0
Strandb H H H H H H H H H H H (continued )
Correspondence: H. D. Shen, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China. Tel: +86 21 61900446. Fax: +86 21 61900405. E-mail: [email protected]
754
C. Liu et al.
Mitochondrial DNA, 2015; 26(5): 753–754
Table 1. Continued.
Position Locus
Downloaded by [University of California Santa Barbara] at 21:58 05 November 2015
asp
tRNA tRNACys tRNAPhe COII tRNAtyr tRNATrp tRNAgly tRNAHis tRNAgln ATP8 tRNAAsn ATP6 tRNAArg tRNAGlu tRNAleu s-rRNA tRNAMet ND3 tRNAser tRNAser ND4 tRNAThr COIII tRNAIle ND2 tRNALys
Codon
From
To
Size (bp)
7216 7273 7334 7396 8068 8119 8179 8240 8360 8415 8567 8624 9270 9333 9512 9563 10,099 10,181 10,535 10,590 10,654 11,961 12,025 12,804 12,883 13,801
7278 7333 7395 8061 8126 8181 8245 8301 8419 8564 8628 9269 9330 9396 9562 10,096 10,162 10,459 10,588 10,645 12,012 12,023 12,802 12,866 13,813 13,861
63 61 62 666 59 63 65 62 60 150 62 645 61 64 51 534 64 279 54 56 1359 64 778 62 930 60
Start
Stop
Anti-codon GTC GCA GAA
TTG
TAA GTA TCA TCC GTG TTG
ATG
TAA
ATG
TAA
GTT TCG TTC TAA CAT ATT
TAG TGA GCT
ATT
TAA
ATG
T–
TTG
TAG
TGT GAT TTT
Intergenic nucleotidesa
Strandb
5 0 0 6 6 3 6 58 5 2 4 0 2 115 0 2 18 77 1 8 50 1 1 16 13 0
H H H H H H H H H L L L L L H H L H H H H L L H H H
a
Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. b H and L indicate genes transcribed on the heavy and light strand.
five tRNA genes and ATP8, ATP6 and COIII genes were encoded on the light strain, the remaining genes were all encoded on the heavy strain. The relative position and orientation of all the genes were similar to other species of Onchidiidae (Grande et al., 2008; Wei et al., 2010, 2011; White et al., 2011). In addition to the ATG, ATA, ATT and TTG are also used as the start codon, which is very common in invertebrates (Grande et al., 2008), but only ATP8 start with TTG. Except for COIII with an incomplete stop codon ‘‘T–’’, the remaining protein-coding genes stop with the TAG or TAA. Using the tRNA scan-SE 1.21 (Lowe & Eddy, 1997), 22 tRNA genes were found to fold into a typical cloverleaf secondary structure. 16S rRNA (1033 bp) gene was located between tRNAVal and tRNALeu(UAA) genes, 12S rRNA (534 bp) gene was located between tRNALeu(UAG) and tRNAMet genes. In all 19 non-coding regions, one usual non-coding region of 359 bp, with AT-rich and C-rich, is identified as a putative CR. The overall base composition of the heavy strand is 27.65% A, 37.24% T, 19.72% G and 15.38% C, with an AT content of 63.65%. The AT content is higher than the content of GC, as generally shown in bivalvia mitochondrial genomes (Wang et al., 2010).
Acknowledgements The authors appreciate anonymous reviewers for providing valuable comments on this article.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. The study was supported by the National Natural Science Foundation of China (No. 41276157), Shanghai Municipal Education Commission key innovation project funding (No. 12ZZ164) and Leading Academic Discipline
Project of Shanghai Municipal Education Commission, Project Number J50701 (Marine Biology).
References Dayrat B. (2009). Review of the current knowledge of the systematics of Onchidiidae (Mollusca: Gastropoda: Pulmonata) with a checklist of nominal species. Zootaxa 2068:1–26. Dayrat B. (2010). Comparative anatomy and taxonomy of Onchidium vaigiense (Gastropoda: Pulmonata: Onchidiidae). Molluscan Res 30: 87–101. Grande C, Templado J, Zardoya R. (2008). Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol 8:1–15. Lowe TM, Eddy SR. (1997). TRNAscan-SE 1.21. Available at: http:// lowelab.ucsc.edu/tRNAscan-SE/ (Accessed 5 April 2011). Shu TF, Luo L, Wen YM. (2002). Effects of mariculture on coastal ecological environment. Mar Environ Sci 21:74–9. Wang HX, Zhang SP, Li Y, Liu BZ. (2010). Complete mtDNA of Meretrix lusoria (Bivalvia: Veneridae) reveals the presence of an atp8 gene, length variation and heteroplasmy in the control region. Comp Biochem Physiol Part D 5:256–64. Wei LL, Shen B, Shen HD, Chen C, Fang L, Wu WJ. (2010). Analysis of complete mitochondrial genome of Platevindex mortoni of Onchidiidae (Mollusca: Gastropoda: Pulmonata). Biotechnol Bull 8: 188–94. Wei LL, Shen HD, Zhang Y, Fang L, Zhang KX, Chen C. (2011). Analysis of complete mitochondrial genome of Onchidium struma (Mollusca: Gastropoda: Pulmonata: Onchidiidae). J Fish China 35: 493–500. White TR, Conrad MM, Tseng R, Balayan S, Golding R, Martins AMD, Dayrat BA. (2011). Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evol Biol 11:1–15. Wu WJ, Shen B, Chen C, Shen HD, Wei LL, Wang L, Li K. (2010). Preliminary classification and phylogenetic relationship among Onchidiidae in China inferred from 18S rRNA partial sequence. Zool Res 31:381–6.
