http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003833
MITOGENOME ANNOUNCEMENT
Sequencing and analysis of the complete mitochondrial genome of Eriocheir sinensis Gaopeng Li, Yingjie Zheng, Xiaowei Mao, Yan Xu, Xueli Chen, Shoubao Yang, and Lanlan Jia
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/19/15 For personal use only.
College of Life Sciences, Shaoxing University, Shaoxing, PR China
Abstract
Keywords
The Chinese mitten crab Eriocheir sinensi belongs to the family Decapoda, Varunidae, Eriocheir. In this study, the full length of mitochondrial genome of an ovulated Chinese mitten crab was first sequenced and analyzed. It was determined to be 16,353 bp in length, and consists of 13 protein coding genes (PCDs), 22 tRNA genes, 2 rRNA genes and 1 control region.
Chinese mitten crab, Eriocheir sinensis, mitochondrial genome, sequencing History Received 17 November 2014 Accepted 5 December 2014 Published online 28 January 2015
The Chinese mitten crab Eriocheir sinensis, which belongs to the family Decapoda, Varunidae, Eriocheir, is one of the main cultural crabs in China (Xu et al., 1991; Zhao et al., 1988). The Chinese mitten crab performs a special growth and aging mechanisms; after mating and ovulation, the male and some female crabs will die, but to date, the detailed mechanism of maturation and aging of crab E. sinensis remains undiscovered (Ying et al., 2004). Mutations in mitochondrial DNA could accelerate the processes of aging and death of the organism (Nan et al., 2006; Zhang et al., 2001). Therefore, sequencing and
comparative analysis of the complete mitochondrial genome sequence could provide important information for species identification, and analyze the mechanisms of aging and death in Chinese mitten crab E. sinensis. In the present study, the complete mitochondrial genome of an ovulated individual of Chinese mitten crab E. sinensis was sequenced, it was determined to be 16,353 bp in length (GenBank accession no. KP126617). This ovulated crab was sampled from a commercial farm (Dalian city, Liaoning province, China). The genomic DNA was extracted from leg muscle of Chinese mitten
Table 1. Organization of the mitochondrial genome of Eriocheir sinensis. Position Locus Gln
tRNA tRNACys tRNATyr tRNALys tRNAAsp tRNAGlu tRNAPhe ND4 ND4L ND6 Cyt b tRNASer(UCN) tRNAIle tRNAMet ND2 tRNATrp COX I
Abbreviations Q C Y K D E F nd4 nd4L nd6 cytb S I M nd2 W cox1
From 1 80 143 226 295 376 452 541 1872 2256 2780 3915 4060 4141 4209 5218 5300
To 69 142 206 296 360 441 516 1878 2174 2780 3914 3980 4126 4208 5219 5286 6833
Codon SizeNucleotide (bp) 69 63 64 71 66 66 65 1338 303 525 1135 66 67 68 1011 69 1534
Start
ATG ATG ATT ATG
Stop
TAA TAA TAG T– –
Aminoacid
Anti-codon
Intergenicnucleotide
Strand
TTG GCA GTA TTT GTC TTC GAA
10 0 19 2 15 10 24 7 81 1 0 80 14 0 2 13 0
L H L H H H L L L H H H H H H H H
460 98 173 380 TGA GAT CAT
ATC
TAG
348
ATG
T– –
516
TCA
(continued )
Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, PRChina. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
G. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/19/15 For personal use only.
Leu(UUR)
tRNA COX II ATP8 ATP6 COX III tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer(AGY) tRNAThr tRNAPro ND1 tRNALeu(CUN) 16S rRNA 12S rRNA tRNAHis ND5 tRNAVal Control region
Codon
Abbreviations
From
To
SizeNucleotide (bp)
L cox2 atp8 atp6 cox3 G nd3 A R N S T P nd1 L 16S 12S H nd5 V CR
6834 6907 7661 7816 8490 9281 9344 9696 9761 9823 9890 10,007 10,077 10,160 11,130 11,198 12,564 13,456 13,563 15,386 15,459
6900 7602 7822 8490 9281 9343 9694 9758 9823 9887 9957 10,075 10,141 11,095 11,196 12,508 13,455 13,524 15,293 15,458 16,353
67 696 162 675 792 63 351 63 63 65 68 69 65 936 67 1311 892 69 1731 73 895
crab E. sinensis using a DNA extraction kit (Simgen, China) according to the manufacturer’s instructions. 11 primer pairs were designed and used, the total volume of PCR amplification is 30 ml including: 0.2 ml Ex-Taq DNA polymerase (5U/ml), 2.0 mM MgCl2, 2 mM dNTP, 50 ng genomic DNA, and 10 pM of each primers. The characteristics of the mitogenome are presented in Table 1. The mitogenome content (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes), gene arrangement and gene coding strand of E. sinensis mitogenome is similar to the crustacean consensus. The overall base composition is 36.37% T; 17.63% C; 35.3% A; and 10.7% G. The AT content (71.67%) is higher than GC content (28.33%), which is similar to other crustacean. Of the 37 genes, 4 PCGs (ND1, ND4, ND4L, and ND5) and 7 tRNA genes (tRNAGln, tRNATyr, tRNAPhe, tRNAPro, tRNALeu (CUN) , tRNAHis, and tRNAVal) are on the light strand (L-strand), and 26 genes are on the heavy strand (H-strand). The proteincoding genes were determined to be 11,189 bp in length. Eight PCGs begin with an ATG start codon (ND4, ND4L, ND5, Cyt b, COX I, COX II, COX III, and ATP8), ND6 and ATP6 begin with ATT, ND2 and ND3 begin with ATC, and ND1 begins with ATA (Table 1). Eight PCGs (ND1, ND4, ND4L, ND5, COX II, COX III, ATP6, and ATP8) stop with TAA; 3 PCGs (ND2, ND3, and ND6) use TAG as a stop codon, while the Cytb and COX I genes use an incomplete stop codon of T (Table 1). The tRNA genes was 1466 bp in length varying from 63 bp (tRNACys, tRNAGly, tRNAAla, and tRNAArg) to 73 bp (tRNAVal). Two rRNA genes,
Start
Stop
Aminoacid
ATG ATG ATT ATG
TAA TAA TAA TAA
230 54 227 261
ATC
TAG
116
Anti-codon
Intergenicnucleotide
Strand
TAA
6 58 7 1 1 0 1 2 1 2 59 1 18 34 1 55 0 48 92 0
H H H H H H H H H H H H L L L H H L L L –
TCC TGC TCG GTT TGT TGG ATA
TAA
324 TAG GTG
ATG
TAA
611 TAC
12S rRNA gene (rrnS) and 16S rRNA gene (rrnL), had 2203 bp length, both of which are encoded on the H-strand, and there is no intervention between them. The control region was determined to be 895 bp in length. This study will provide useful data for species identification, and analysis of the mechanisms of aging and death in Chinese mitten crab E. sinensis.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We thank the Young & Middle-aged Academic Backbone Project of Shaoxing University (2014) for financial support.
References Nan TZ, Chen YX, Wu XY. (2006). Comparison of Eriocheir sinensis embryos and larvae of Z1 quality of the first and two incubation. J Shanghai Fish Univ 15:41–6. Xu XC. (1991). Discussion on the problems of Chinese Mitten Crab quality retention. Fish Sci Technol Inform 18:17–19. Ying XP, Luo YY, Zhang YP. (2004). A comparative study on the composition of faminoacid and fatty acid in the fertilized eggs and lost eggs of Eriocheir sinensis. Acta Hydrobiol Sin 28:802–8. Zhang LS, Xu QY. (200l). Natural and aquaculture water crab sex maturation and precocious puberty study. Sci Technol Inform 28: 106–11. Zhao NG, Du NS, Bao XS. (1988). Artificial propagation and aquaculture of Chinese Mitten Crab. Hefei: Anhui Science and Technology Press.
MITOGENOME ANNOUNCEMENT
Sequencing and analysis of the complete mitochondrial genome of Eriocheir sinensis Gaopeng Li, Yingjie Zheng, Xiaowei Mao, Yan Xu, Xueli Chen, Shoubao Yang, and Lanlan Jia
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/19/15 For personal use only.
College of Life Sciences, Shaoxing University, Shaoxing, PR China
Abstract
Keywords
The Chinese mitten crab Eriocheir sinensi belongs to the family Decapoda, Varunidae, Eriocheir. In this study, the full length of mitochondrial genome of an ovulated Chinese mitten crab was first sequenced and analyzed. It was determined to be 16,353 bp in length, and consists of 13 protein coding genes (PCDs), 22 tRNA genes, 2 rRNA genes and 1 control region.
Chinese mitten crab, Eriocheir sinensis, mitochondrial genome, sequencing History Received 17 November 2014 Accepted 5 December 2014 Published online 28 January 2015
The Chinese mitten crab Eriocheir sinensis, which belongs to the family Decapoda, Varunidae, Eriocheir, is one of the main cultural crabs in China (Xu et al., 1991; Zhao et al., 1988). The Chinese mitten crab performs a special growth and aging mechanisms; after mating and ovulation, the male and some female crabs will die, but to date, the detailed mechanism of maturation and aging of crab E. sinensis remains undiscovered (Ying et al., 2004). Mutations in mitochondrial DNA could accelerate the processes of aging and death of the organism (Nan et al., 2006; Zhang et al., 2001). Therefore, sequencing and
comparative analysis of the complete mitochondrial genome sequence could provide important information for species identification, and analyze the mechanisms of aging and death in Chinese mitten crab E. sinensis. In the present study, the complete mitochondrial genome of an ovulated individual of Chinese mitten crab E. sinensis was sequenced, it was determined to be 16,353 bp in length (GenBank accession no. KP126617). This ovulated crab was sampled from a commercial farm (Dalian city, Liaoning province, China). The genomic DNA was extracted from leg muscle of Chinese mitten
Table 1. Organization of the mitochondrial genome of Eriocheir sinensis. Position Locus Gln
tRNA tRNACys tRNATyr tRNALys tRNAAsp tRNAGlu tRNAPhe ND4 ND4L ND6 Cyt b tRNASer(UCN) tRNAIle tRNAMet ND2 tRNATrp COX I
Abbreviations Q C Y K D E F nd4 nd4L nd6 cytb S I M nd2 W cox1
From 1 80 143 226 295 376 452 541 1872 2256 2780 3915 4060 4141 4209 5218 5300
To 69 142 206 296 360 441 516 1878 2174 2780 3914 3980 4126 4208 5219 5286 6833
Codon SizeNucleotide (bp) 69 63 64 71 66 66 65 1338 303 525 1135 66 67 68 1011 69 1534
Start
ATG ATG ATT ATG
Stop
TAA TAA TAG T– –
Aminoacid
Anti-codon
Intergenicnucleotide
Strand
TTG GCA GTA TTT GTC TTC GAA
10 0 19 2 15 10 24 7 81 1 0 80 14 0 2 13 0
L H L H H H L L L H H H H H H H H
460 98 173 380 TGA GAT CAT
ATC
TAG
348
ATG
T– –
516
TCA
(continued )
Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, PRChina. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
G. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/19/15 For personal use only.
Leu(UUR)
tRNA COX II ATP8 ATP6 COX III tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer(AGY) tRNAThr tRNAPro ND1 tRNALeu(CUN) 16S rRNA 12S rRNA tRNAHis ND5 tRNAVal Control region
Codon
Abbreviations
From
To
SizeNucleotide (bp)
L cox2 atp8 atp6 cox3 G nd3 A R N S T P nd1 L 16S 12S H nd5 V CR
6834 6907 7661 7816 8490 9281 9344 9696 9761 9823 9890 10,007 10,077 10,160 11,130 11,198 12,564 13,456 13,563 15,386 15,459
6900 7602 7822 8490 9281 9343 9694 9758 9823 9887 9957 10,075 10,141 11,095 11,196 12,508 13,455 13,524 15,293 15,458 16,353
67 696 162 675 792 63 351 63 63 65 68 69 65 936 67 1311 892 69 1731 73 895
crab E. sinensis using a DNA extraction kit (Simgen, China) according to the manufacturer’s instructions. 11 primer pairs were designed and used, the total volume of PCR amplification is 30 ml including: 0.2 ml Ex-Taq DNA polymerase (5U/ml), 2.0 mM MgCl2, 2 mM dNTP, 50 ng genomic DNA, and 10 pM of each primers. The characteristics of the mitogenome are presented in Table 1. The mitogenome content (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes), gene arrangement and gene coding strand of E. sinensis mitogenome is similar to the crustacean consensus. The overall base composition is 36.37% T; 17.63% C; 35.3% A; and 10.7% G. The AT content (71.67%) is higher than GC content (28.33%), which is similar to other crustacean. Of the 37 genes, 4 PCGs (ND1, ND4, ND4L, and ND5) and 7 tRNA genes (tRNAGln, tRNATyr, tRNAPhe, tRNAPro, tRNALeu (CUN) , tRNAHis, and tRNAVal) are on the light strand (L-strand), and 26 genes are on the heavy strand (H-strand). The proteincoding genes were determined to be 11,189 bp in length. Eight PCGs begin with an ATG start codon (ND4, ND4L, ND5, Cyt b, COX I, COX II, COX III, and ATP8), ND6 and ATP6 begin with ATT, ND2 and ND3 begin with ATC, and ND1 begins with ATA (Table 1). Eight PCGs (ND1, ND4, ND4L, ND5, COX II, COX III, ATP6, and ATP8) stop with TAA; 3 PCGs (ND2, ND3, and ND6) use TAG as a stop codon, while the Cytb and COX I genes use an incomplete stop codon of T (Table 1). The tRNA genes was 1466 bp in length varying from 63 bp (tRNACys, tRNAGly, tRNAAla, and tRNAArg) to 73 bp (tRNAVal). Two rRNA genes,
Start
Stop
Aminoacid
ATG ATG ATT ATG
TAA TAA TAA TAA
230 54 227 261
ATC
TAG
116
Anti-codon
Intergenicnucleotide
Strand
TAA
6 58 7 1 1 0 1 2 1 2 59 1 18 34 1 55 0 48 92 0
H H H H H H H H H H H H L L L H H L L L –
TCC TGC TCG GTT TGT TGG ATA
TAA
324 TAG GTG
ATG
TAA
611 TAC
12S rRNA gene (rrnS) and 16S rRNA gene (rrnL), had 2203 bp length, both of which are encoded on the H-strand, and there is no intervention between them. The control region was determined to be 895 bp in length. This study will provide useful data for species identification, and analysis of the mechanisms of aging and death in Chinese mitten crab E. sinensis.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We thank the Young & Middle-aged Academic Backbone Project of Shaoxing University (2014) for financial support.
References Nan TZ, Chen YX, Wu XY. (2006). Comparison of Eriocheir sinensis embryos and larvae of Z1 quality of the first and two incubation. J Shanghai Fish Univ 15:41–6. Xu XC. (1991). Discussion on the problems of Chinese Mitten Crab quality retention. Fish Sci Technol Inform 18:17–19. Ying XP, Luo YY, Zhang YP. (2004). A comparative study on the composition of faminoacid and fatty acid in the fertilized eggs and lost eggs of Eriocheir sinensis. Acta Hydrobiol Sin 28:802–8. Zhang LS, Xu QY. (200l). Natural and aquaculture water crab sex maturation and precocious puberty study. Sci Technol Inform 28: 106–11. Zhao NG, Du NS, Bao XS. (1988). Artificial propagation and aquaculture of Chinese Mitten Crab. Hefei: Anhui Science and Technology Press.
