http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.928863
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Empoasca vitis (Hemiptera: Cicadellidae) Ningning Zhou1, Mengxin Wang1, Lin Cui1, Xuexin Chen2, and Baoyu Han1
Mitochondrial DNA Downloaded from informahealthcare.com by JHU John Hopkins University on 01/11/15 For personal use only.
1
Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, P.R. China and 2Institute of Insect Sciences, Zhejiang University, Hangzhou, P.R. China Abstract
Keywords
The complete mitochondrial genome of Empoasca vitis was sequenced. The length of the mitogenome is 15,154 bp with 78.35% AT content (GenBank accession No. KJ815009). The genome encode 37 typical mitochondrial genes including 22 transfer RNA genes, 13 proteincoding genes, 2 ribosomal RNA genes and an A+T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. Except for cox2 using GTG as start codon, other protein-coding genes (PCGs) share the start codons ATN. Usual termination codon TAA and incomplete stop codon T are using by 13 protein-coding genes. The A+T-rich region has a length of 977 bp with the AT content high to 88.95%.
Cicadellidae, complete mitochondrial genome, Empoasca vitis
Empoasca vitis (Hemiptera: Cicadellidae) is one of the most tea-damage pests in main tea production areas of China. The specimen of E. vitis used in this study was sampled from Hangzhou City, Zhejiang, China (N30.1889, E120.0868). The complete mitochondrial genome of E. vitis was determined using the traditional PCR amplification method (Wei et al., 2009). The primers were designed from conserved regions of sequenced mitochondrial genes in Cicadellidae. Both strands were determined by primer walking. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene order (Clary et al., 1982). This mitogenome was 15,154 bp long. The AT content of this mitogenome was 78.35%, A for 38.16% and T for 40.19%. The AT-skew and GC-skew was 0.0259 and 0.0332 respectively, indicating that more T than A and more C than G in the genome. The annotation of E. vitis mitogenome is shown in Table 1, which contains 37 typical animal mitochondrial genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and an A+T-rich region. There are 19 overlap regions in the mitogenome with a total length of 79 bp and ranging from 1 bp to 15 bp. The longest overlap region occurs between tRNAL1 and lrRNA. The mitogenome has 5 intergenic spacers in a total length of 13 bp with length varying from 1 bp to 4 bp. The longest intergenic spacer occurs between tRNAQ and tRNAM. The length of the 22 tRNA genes ranges from 60 bp to 72 bp with typical cloverleaf structures. The length of the lrRNA was 1149 bp with AT content of 81.90%. The length of the srRNA was 725 bp with AT content of 81.24%.
Correspondence: Baoyu Han, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, P.R. China. Tel: +86 57186835706. Fax: +86 571 86914449. E-mail: han-insect@ 263.net
History Received 11 May 2014 Accepted 25 May 2014 Published online 25 June 2014
Table 1. Annotation of the E. vitis mitochondrial genome.
Gene tRNAI tRNAQ tRNAM nad2 tRNAW tRNAC tRNAY cox1 TrnaL2 cox2 tRNAK tRNAD atp8 atp6 cox3 tRNAG nad3 tRNAA tRNAR tRNAN TrnaS1 tRNAE tRNAF nad5 tRNAH nad4 nad4l tRNAT tRNAP nad6 Cytb TrnaS2
Strand
Gene position
+ – + + + – – + + + + + + + + + + – + + + + – – – – – + – + + +
1–65 63–130 135–202 203–1177 1176–1238 1231–1293 1294–1357 1359–2892 2893–2957 2958–3636 3637–3708 3709–3770 3771–3923 3917–4570 4571–5350 5349–5410 5411–5764 5767–5827 5832–5892 5891–5956 5956–6022 6022–6082 6082–6147 6148–7822 7820–7881 7881–9188 9182–9460 9459–9524 9525–9588 9591–10,079 10,072–11,208 11,208–11,271
Anti/ Stop Intergenic Length start codon codon nucleotides (bp) 65 68 68 975 63 63 64 1534 65 679 72 62 153 654 780 62 354 61 61 66 67 61 66 1675 60 1308 279 66 62 489 1137 64
GAT TTG CAT ATT TCA GCA GTA ATG TAA GTG CTT GTC ATA ATG ATG TCC ATT TGC TCG GTT GCT TTC GAA ATT GTG ATG ATG TGT TGG ATT ATG TGA
TAA
T T TAA TAA TAA TAA
T TAA TAA TAA TAA
3 4 0 2 8 0 1 0 0 0 0 0 7 0 2 0 2 4 2 1 1 1 0 3 1 7 2 0 2 8 1 (continued )
2
N. Zhou et al.
Mitochondrial DNA, Early Online: 1–2
important role in DNA transcription and replication (Zhang & Hewitt, 1997).
Table 1. Continued
Gene nad1 TrnalL1 lrRNA tRNAV srRNA CR
Gene position
Strand – – – – –
11,271–12,200 12,201–12,266 12,252–13,400 13,388–13,453 13,453–14,177 14,178–15,154
Mitochondrial DNA Downloaded from informahealthcare.com by JHU John Hopkins University on 01/11/15 For personal use only.
+, Majority strand;
Anti/ Stop Intergenic Length start codon codon nucleotides (bp) 930 66 1149 66 725 977
ATT TAG
TAA
TAC
1 0 15 13 1 0
, Minority strand; CR, A+T rich region.
The length of the protein-coding genes are totally 10,942 bp. The size of each protein-coding gene was similar to Homalodisca vitripennis. The AT content of the protein-coding genes is 76.79%. Twelve PCGs using ATN as start codon, including 5 ATT, 6 ATG and 1 ATA. But cox2 used GTG as start codon. In the presently sequenced insect mitochondrial genomes, GTG start codon of the cox1 and nad2 gene was previously found in Bemisia afer (Wang et al., 2014). Ten PCGs use TAA as stop codon, while the other three use incomplete stop codon ‘‘T’’. The incomplete stop codon T is commonly reported in other invertebrates (Crozier & Crozier, 1993; Masta & Boore, 2004). Incomplete stop codons can be completed via polyadenylation (Wolstenholme, 1992). The A+T-rich region is between srRNA and tRNAI with a length of 977 bp. The AT content of the A+T-rich region is high to 88.95%, A for 43.91% and T for 45.04%. This region plays an
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was jointly supported by National Program on Key Basic Research Project (973 Program) (2013CB127600) and a program of the National Natural Science Foundation of China (31071744) and a grant of the Educational Department of Zhejiang Province (Y201329611).
References Clary DO, Goddard JM, Martin SC, Fauron CM, Wolstenholme DR. (1982). Drosophila mitochondrial DNA: A novel gene order. Nucleic Acids Res 10:6619–37. Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133:97–117. Masta SE, Boore JL. (2004). The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol Biol Evol 21:893–902. Wei SJ, Shi M, He JH, Sharkey M, Chen XX. (2009). The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome 52:308–19. Wang HL, Xiao N, Yang J, Wang XW, Colvin J, Liu SS. (2014). The complete mitochondrial genome of Bemisia afer (Hemiptera: Aleyrodidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.873921. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141: 173–216. Zhang DX, Hewitt GM. (1997). Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25:99–120.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Empoasca vitis (Hemiptera: Cicadellidae) Ningning Zhou1, Mengxin Wang1, Lin Cui1, Xuexin Chen2, and Baoyu Han1
Mitochondrial DNA Downloaded from informahealthcare.com by JHU John Hopkins University on 01/11/15 For personal use only.
1
Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, P.R. China and 2Institute of Insect Sciences, Zhejiang University, Hangzhou, P.R. China Abstract
Keywords
The complete mitochondrial genome of Empoasca vitis was sequenced. The length of the mitogenome is 15,154 bp with 78.35% AT content (GenBank accession No. KJ815009). The genome encode 37 typical mitochondrial genes including 22 transfer RNA genes, 13 proteincoding genes, 2 ribosomal RNA genes and an A+T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. Except for cox2 using GTG as start codon, other protein-coding genes (PCGs) share the start codons ATN. Usual termination codon TAA and incomplete stop codon T are using by 13 protein-coding genes. The A+T-rich region has a length of 977 bp with the AT content high to 88.95%.
Cicadellidae, complete mitochondrial genome, Empoasca vitis
Empoasca vitis (Hemiptera: Cicadellidae) is one of the most tea-damage pests in main tea production areas of China. The specimen of E. vitis used in this study was sampled from Hangzhou City, Zhejiang, China (N30.1889, E120.0868). The complete mitochondrial genome of E. vitis was determined using the traditional PCR amplification method (Wei et al., 2009). The primers were designed from conserved regions of sequenced mitochondrial genes in Cicadellidae. Both strands were determined by primer walking. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene order (Clary et al., 1982). This mitogenome was 15,154 bp long. The AT content of this mitogenome was 78.35%, A for 38.16% and T for 40.19%. The AT-skew and GC-skew was 0.0259 and 0.0332 respectively, indicating that more T than A and more C than G in the genome. The annotation of E. vitis mitogenome is shown in Table 1, which contains 37 typical animal mitochondrial genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and an A+T-rich region. There are 19 overlap regions in the mitogenome with a total length of 79 bp and ranging from 1 bp to 15 bp. The longest overlap region occurs between tRNAL1 and lrRNA. The mitogenome has 5 intergenic spacers in a total length of 13 bp with length varying from 1 bp to 4 bp. The longest intergenic spacer occurs between tRNAQ and tRNAM. The length of the 22 tRNA genes ranges from 60 bp to 72 bp with typical cloverleaf structures. The length of the lrRNA was 1149 bp with AT content of 81.90%. The length of the srRNA was 725 bp with AT content of 81.24%.
Correspondence: Baoyu Han, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, P.R. China. Tel: +86 57186835706. Fax: +86 571 86914449. E-mail: han-insect@ 263.net
History Received 11 May 2014 Accepted 25 May 2014 Published online 25 June 2014
Table 1. Annotation of the E. vitis mitochondrial genome.
Gene tRNAI tRNAQ tRNAM nad2 tRNAW tRNAC tRNAY cox1 TrnaL2 cox2 tRNAK tRNAD atp8 atp6 cox3 tRNAG nad3 tRNAA tRNAR tRNAN TrnaS1 tRNAE tRNAF nad5 tRNAH nad4 nad4l tRNAT tRNAP nad6 Cytb TrnaS2
Strand
Gene position
+ – + + + – – + + + + + + + + + + – + + + + – – – – – + – + + +
1–65 63–130 135–202 203–1177 1176–1238 1231–1293 1294–1357 1359–2892 2893–2957 2958–3636 3637–3708 3709–3770 3771–3923 3917–4570 4571–5350 5349–5410 5411–5764 5767–5827 5832–5892 5891–5956 5956–6022 6022–6082 6082–6147 6148–7822 7820–7881 7881–9188 9182–9460 9459–9524 9525–9588 9591–10,079 10,072–11,208 11,208–11,271
Anti/ Stop Intergenic Length start codon codon nucleotides (bp) 65 68 68 975 63 63 64 1534 65 679 72 62 153 654 780 62 354 61 61 66 67 61 66 1675 60 1308 279 66 62 489 1137 64
GAT TTG CAT ATT TCA GCA GTA ATG TAA GTG CTT GTC ATA ATG ATG TCC ATT TGC TCG GTT GCT TTC GAA ATT GTG ATG ATG TGT TGG ATT ATG TGA
TAA
T T TAA TAA TAA TAA
T TAA TAA TAA TAA
3 4 0 2 8 0 1 0 0 0 0 0 7 0 2 0 2 4 2 1 1 1 0 3 1 7 2 0 2 8 1 (continued )
2
N. Zhou et al.
Mitochondrial DNA, Early Online: 1–2
important role in DNA transcription and replication (Zhang & Hewitt, 1997).
Table 1. Continued
Gene nad1 TrnalL1 lrRNA tRNAV srRNA CR
Gene position
Strand – – – – –
11,271–12,200 12,201–12,266 12,252–13,400 13,388–13,453 13,453–14,177 14,178–15,154
Mitochondrial DNA Downloaded from informahealthcare.com by JHU John Hopkins University on 01/11/15 For personal use only.
+, Majority strand;
Anti/ Stop Intergenic Length start codon codon nucleotides (bp) 930 66 1149 66 725 977
ATT TAG
TAA
TAC
1 0 15 13 1 0
, Minority strand; CR, A+T rich region.
The length of the protein-coding genes are totally 10,942 bp. The size of each protein-coding gene was similar to Homalodisca vitripennis. The AT content of the protein-coding genes is 76.79%. Twelve PCGs using ATN as start codon, including 5 ATT, 6 ATG and 1 ATA. But cox2 used GTG as start codon. In the presently sequenced insect mitochondrial genomes, GTG start codon of the cox1 and nad2 gene was previously found in Bemisia afer (Wang et al., 2014). Ten PCGs use TAA as stop codon, while the other three use incomplete stop codon ‘‘T’’. The incomplete stop codon T is commonly reported in other invertebrates (Crozier & Crozier, 1993; Masta & Boore, 2004). Incomplete stop codons can be completed via polyadenylation (Wolstenholme, 1992). The A+T-rich region is between srRNA and tRNAI with a length of 977 bp. The AT content of the A+T-rich region is high to 88.95%, A for 43.91% and T for 45.04%. This region plays an
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was jointly supported by National Program on Key Basic Research Project (973 Program) (2013CB127600) and a program of the National Natural Science Foundation of China (31071744) and a grant of the Educational Department of Zhejiang Province (Y201329611).
References Clary DO, Goddard JM, Martin SC, Fauron CM, Wolstenholme DR. (1982). Drosophila mitochondrial DNA: A novel gene order. Nucleic Acids Res 10:6619–37. Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133:97–117. Masta SE, Boore JL. (2004). The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol Biol Evol 21:893–902. Wei SJ, Shi M, He JH, Sharkey M, Chen XX. (2009). The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome 52:308–19. Wang HL, Xiao N, Yang J, Wang XW, Colvin J, Liu SS. (2014). The complete mitochondrial genome of Bemisia afer (Hemiptera: Aleyrodidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.873921. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141: 173–216. Zhang DX, Hewitt GM. (1997). Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25:99–120.
