http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919484
MITOGENOME ANNOUNCEMENT
The mitochondrial genome of the Vespa bicolor Fabricius (Hymenoptera: Vespidae: Vespinae) Shu-Jun Wei1, Fang-Fang Niu1,2, and Jiang-Li Tan3 Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China, 2College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, and 3College of Life Sciences, Northwest University, Xi’an, China
Mitochondrial DNA Downloaded from informahealthcare.com by Universitat de Girona on 03/26/15 For personal use only.
1
Abstract
Keywords
Here, we report the first representative mitochondrial genome of the subfamily Vespinae (Hymenopterea: Vespidae) from the Vespa bicolor Fabricius (GenBank accession No. KJ735511). Nearly complete mitochondrial genome was sequenced with a length of 16,937 bp, including 13 protein-coding genes, 2 rRNA and 20 tRNA genes, as well as a portion of A+T-rich region. Two tRNA genes, i.e. trnI and trnY, were failed to sequence, which were presumed to be located within a region between A+T-rich region and trnM-trnQ-nad2. In the V. bicolor mitochondrial genome, at least three tRNA genes were rearranged. trnY was rearranged to the unsequenced region between A+T-rich region and trnM-trnQ-nad2. trnL1 was rearranged from a location between nad1 and rrnL to the upstream of nad1 gene. trnS1 and trnE were shuffled in the tRNA cluster of trnA-trnR-trnN-trnS1-trnE-trnF. Our study showed that the mitochondrial genomes between Vespinae and Polistinae shared more arrangement pattern than that between Vespinae and Eumeninae.
Hornet, gene rearrangement, mitochondrial genome, Vespa bicolor
Mitochondrial genomes from Hymenoptera are usually characterized by high A + T content (Dowton & Austin, 1997; Gotzek et al., 2010), frequent gene rearrangement (Dowton et al., 2009), rapid evolutionary rate (Oliveira et al., 2008) and presence of minicircular (Mao et al., 2013). Sequencing of the mitochondrial genomes from unsampled groups will contribute to our understanding of their evolutionary patterns and utility in phylogenetic studies (Wei et al., 2010). The Vespidae is a large family of Hymenoptera, exhibiting diverse behaviours of sociality, nesting and predation. Presently, two mitochondrial genomes were reported from the family Vespidae, representing the subfamily Eumeninae and Polistinae (Cameron et al., 2008). Here, we sequenced the nearly complete mitochondrial genome of Vespa bicolor Fabricius (1787) from the subfamily Vespinae of Vespidae (GenBank accession No. KJ735511). The length of the sequenced region was 16,937 bp long with an A + T content of 81.72%, including 13 protein-coding, 2 rRNA and 20 tRNA genes, and a portion of A + T-rich region (Table 1). A region between A + T-rich region and trnM-trnQ-nad2, which was presumed to include two tRNA genes of trnI and trnY, was failed to sequence. There are totally 21 overlapped nucleotides between neighboring genes in five locations and the length of overlapped sequence is 1–7 bp, while there are
Correspondence: Shu-Jun Wei, Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing 100097, China. Tel: +86 01051503439. Fax: +86 01051503899. E-mail: [email protected]
History Received 23 April 2014 Accepted 26 April 2014 Published online 24 June 2014
totally 1164 bp intergenic nucleotides in 22 locations and the length of intergenic spacer is 1–252 bp. Eight pairs of genes are directly adjacent without intergenetic or overlapping nucleotides. In the V. bicolor mitochondrial genome, at least three tRNA genes were rearranged. First, trnY was rearranged to the unsequenced region between A + T-rich region and trnMtrnQ-nad2. The absent of trnY in its ancestral location was found in Polistes (Vespidae: Polistinae), but not in Abispa (Vespidae: Eumeninae) (Cameron et al., 2008). Second, trnL1 was rearranged from a location between nad1 and rrnL to the upstream of nad1 gene, which was also found in the mitochondrial genome of Polistes, but not in Abispa. Third, a novel gene arrangement in Vespidae was present caused by gene shuffling of trnS1 and trnE in the tRNA cluster of trnA-trnR-trnN-trnS1-trnE-trnF. This derived arrangement pattern was reported in Philanthus (Hymenoptera: Crabronidae) (Kaltenpoth et al., 2012). It is obivious that the mitochondrial genomes between Vespinae and Polistinae shared more gene arrangement patterns than that between Vespinae and Eumeninae. In the protein-coding genes, the lowest A + T content was 71.4% in the cox1, while the highest was 87.1% in nad2. All protein-coding genes started with ATN codons (4 with ATA, 4 with ATG, 2 with ATT and 3 ATC ). Twelve protein-coding genes stoped with termination codon TAA. One protein-coding gene used T as the incomplete stop codon which is commonly reported in other invertebrates (Masta & Boore, 2004). The rrnL was 1451 bp long with an A + T content of 84.8% while the rrnS was 837 bp long with an A + T content of 85.2%. The sequenced portion of A + T-region was 898 bp long with an A + T content of 88.2%.
2
S.- J. Wei et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Universitat de Girona on 03/26/15 For personal use only.
Table 1. Annotation of the mitochondrial genome of Vespa bicolor. Gene
Strand
Position
Length (bp)
Anti/Start codon
trnM trnQ nad2 trnW trnC cox1 trnL2 cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnE trnS1 trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 trnL1 nad1 rrnL trnV rrnS AT
+ – + + – + + + + + + + + + + + + + + + – – – – – + – + + + – – – – –
1–69 71–137 140–1237 1275–1342 1336–1404 1657–3195 3201–3271 3272–3952 4000–4069 4277–4343 4344–4505 4506–5174 5175–5959 5959–6026 6027–6383 6387–6466 6464–6531 6596–6664 6768–6832 6855–6915 6991–7058 7067–8743 8741–8807 8823–10,139 10,133–10,429 10,485–10,551 10,557–10,623 10,626–11,177 11,182–12,321 12,342–12,410 12,419–12,487 12,659–13,618 13,619–15,069 15,128–15,202 15,203–16,039 16,040–16,937
69 67 1098 68 69 1539 71 681 70 67 162 669 785 68 357 80 68 69 65 61 68 1677 67 1317 297 67 67 552 1140 69 69 960 1451 75 837 898
CAT TTG ATA TCA GCA ATG TAA ATT CTT GTC ATC ATA ATG TCC ATC TGC TCG GTT TTC TCT GAA ATT GTG ATG ATT TGT TGG ATC ATG TGA TAG ATT TAC
Stop codon
TAA TAA TAA TAA TAA TA TAA
TAA TAA TAA TAA TAA TAA
Intergenic nucleotides (bp) 1 2 37 –7 252 5 0 47 207 0 0 0 –1 0 3 –3 64 103 22 75 8 –3 15 –7 55 5 2 4 20 8 171 0 58 0 0
+ Indicates that the gene is coded on the majority strand, while – indicates that the gene is coded on the minority strand; AT indicates the A+T-rich region.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funding for this study was provided jointly by the National Science Foundation of China (31101661, 31201732) and the State Key Program of National Natural Science Foundation of China (31230068).
References Cameron SL, Dowton M, Castro LR, Ruberu K, Whiting MF, Austin AD, Diement K, Stevens J. (2008). Mitochondrial genome organization and phylogeny of two vespid wasps. Genome 51:800–8. Dowton M, Austin AD. (1997). The evolution of strandspecific compositional bias. A case study in the hymenopteran mitochondrial 16S rRNA gene. Mol Biol Evol 14:109–12. Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting MF. (2009). Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. Mol Biol Evol 26:1607–17. Gotzek D, Clarke J, Shoemaker D. (2010). Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol Biol 10: 300.
Kaltenpoth M, Showers Corneli P, Dunn DM, Weiss RB, Strohm E, Seger J. (2012). Accelerated evolution of mitochondrial but not nuclear genomes of hymenoptera: New evidence from crabronid wasps. PLoS One 7:e32826. Mao M, Austin AD, Johnson NF, Dowton M. (2013). Coexistence of minicircular and a highly rearranged mtDNA molecule suggests that recombination shapes mitochondrial genome organization. Mol Biol Evol. doi: 10.1093/molbev/mst255. 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. Oliveira DCSG, Raychoudhury R, Lavrov DV, Werren JH. (2008). Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae). Mol Biol Evol 25:2167–80. Wei SJ, Shi M, Sharkey MJ, Van Achterberg C, Chen XX. (2010). Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to holometabolous insects. BMC Genomics 11:371.
MITOGENOME ANNOUNCEMENT
The mitochondrial genome of the Vespa bicolor Fabricius (Hymenoptera: Vespidae: Vespinae) Shu-Jun Wei1, Fang-Fang Niu1,2, and Jiang-Li Tan3 Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China, 2College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, and 3College of Life Sciences, Northwest University, Xi’an, China
Mitochondrial DNA Downloaded from informahealthcare.com by Universitat de Girona on 03/26/15 For personal use only.
1
Abstract
Keywords
Here, we report the first representative mitochondrial genome of the subfamily Vespinae (Hymenopterea: Vespidae) from the Vespa bicolor Fabricius (GenBank accession No. KJ735511). Nearly complete mitochondrial genome was sequenced with a length of 16,937 bp, including 13 protein-coding genes, 2 rRNA and 20 tRNA genes, as well as a portion of A+T-rich region. Two tRNA genes, i.e. trnI and trnY, were failed to sequence, which were presumed to be located within a region between A+T-rich region and trnM-trnQ-nad2. In the V. bicolor mitochondrial genome, at least three tRNA genes were rearranged. trnY was rearranged to the unsequenced region between A+T-rich region and trnM-trnQ-nad2. trnL1 was rearranged from a location between nad1 and rrnL to the upstream of nad1 gene. trnS1 and trnE were shuffled in the tRNA cluster of trnA-trnR-trnN-trnS1-trnE-trnF. Our study showed that the mitochondrial genomes between Vespinae and Polistinae shared more arrangement pattern than that between Vespinae and Eumeninae.
Hornet, gene rearrangement, mitochondrial genome, Vespa bicolor
Mitochondrial genomes from Hymenoptera are usually characterized by high A + T content (Dowton & Austin, 1997; Gotzek et al., 2010), frequent gene rearrangement (Dowton et al., 2009), rapid evolutionary rate (Oliveira et al., 2008) and presence of minicircular (Mao et al., 2013). Sequencing of the mitochondrial genomes from unsampled groups will contribute to our understanding of their evolutionary patterns and utility in phylogenetic studies (Wei et al., 2010). The Vespidae is a large family of Hymenoptera, exhibiting diverse behaviours of sociality, nesting and predation. Presently, two mitochondrial genomes were reported from the family Vespidae, representing the subfamily Eumeninae and Polistinae (Cameron et al., 2008). Here, we sequenced the nearly complete mitochondrial genome of Vespa bicolor Fabricius (1787) from the subfamily Vespinae of Vespidae (GenBank accession No. KJ735511). The length of the sequenced region was 16,937 bp long with an A + T content of 81.72%, including 13 protein-coding, 2 rRNA and 20 tRNA genes, and a portion of A + T-rich region (Table 1). A region between A + T-rich region and trnM-trnQ-nad2, which was presumed to include two tRNA genes of trnI and trnY, was failed to sequence. There are totally 21 overlapped nucleotides between neighboring genes in five locations and the length of overlapped sequence is 1–7 bp, while there are
Correspondence: Shu-Jun Wei, Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing 100097, China. Tel: +86 01051503439. Fax: +86 01051503899. E-mail: [email protected]
History Received 23 April 2014 Accepted 26 April 2014 Published online 24 June 2014
totally 1164 bp intergenic nucleotides in 22 locations and the length of intergenic spacer is 1–252 bp. Eight pairs of genes are directly adjacent without intergenetic or overlapping nucleotides. In the V. bicolor mitochondrial genome, at least three tRNA genes were rearranged. First, trnY was rearranged to the unsequenced region between A + T-rich region and trnMtrnQ-nad2. The absent of trnY in its ancestral location was found in Polistes (Vespidae: Polistinae), but not in Abispa (Vespidae: Eumeninae) (Cameron et al., 2008). Second, trnL1 was rearranged from a location between nad1 and rrnL to the upstream of nad1 gene, which was also found in the mitochondrial genome of Polistes, but not in Abispa. Third, a novel gene arrangement in Vespidae was present caused by gene shuffling of trnS1 and trnE in the tRNA cluster of trnA-trnR-trnN-trnS1-trnE-trnF. This derived arrangement pattern was reported in Philanthus (Hymenoptera: Crabronidae) (Kaltenpoth et al., 2012). It is obivious that the mitochondrial genomes between Vespinae and Polistinae shared more gene arrangement patterns than that between Vespinae and Eumeninae. In the protein-coding genes, the lowest A + T content was 71.4% in the cox1, while the highest was 87.1% in nad2. All protein-coding genes started with ATN codons (4 with ATA, 4 with ATG, 2 with ATT and 3 ATC ). Twelve protein-coding genes stoped with termination codon TAA. One protein-coding gene used T as the incomplete stop codon which is commonly reported in other invertebrates (Masta & Boore, 2004). The rrnL was 1451 bp long with an A + T content of 84.8% while the rrnS was 837 bp long with an A + T content of 85.2%. The sequenced portion of A + T-region was 898 bp long with an A + T content of 88.2%.
2
S.- J. Wei et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Universitat de Girona on 03/26/15 For personal use only.
Table 1. Annotation of the mitochondrial genome of Vespa bicolor. Gene
Strand
Position
Length (bp)
Anti/Start codon
trnM trnQ nad2 trnW trnC cox1 trnL2 cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnE trnS1 trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 trnL1 nad1 rrnL trnV rrnS AT
+ – + + – + + + + + + + + + + + + + + + – – – – – + – + + + – – – – –
1–69 71–137 140–1237 1275–1342 1336–1404 1657–3195 3201–3271 3272–3952 4000–4069 4277–4343 4344–4505 4506–5174 5175–5959 5959–6026 6027–6383 6387–6466 6464–6531 6596–6664 6768–6832 6855–6915 6991–7058 7067–8743 8741–8807 8823–10,139 10,133–10,429 10,485–10,551 10,557–10,623 10,626–11,177 11,182–12,321 12,342–12,410 12,419–12,487 12,659–13,618 13,619–15,069 15,128–15,202 15,203–16,039 16,040–16,937
69 67 1098 68 69 1539 71 681 70 67 162 669 785 68 357 80 68 69 65 61 68 1677 67 1317 297 67 67 552 1140 69 69 960 1451 75 837 898
CAT TTG ATA TCA GCA ATG TAA ATT CTT GTC ATC ATA ATG TCC ATC TGC TCG GTT TTC TCT GAA ATT GTG ATG ATT TGT TGG ATC ATG TGA TAG ATT TAC
Stop codon
TAA TAA TAA TAA TAA TA TAA
TAA TAA TAA TAA TAA TAA
Intergenic nucleotides (bp) 1 2 37 –7 252 5 0 47 207 0 0 0 –1 0 3 –3 64 103 22 75 8 –3 15 –7 55 5 2 4 20 8 171 0 58 0 0
+ Indicates that the gene is coded on the majority strand, while – indicates that the gene is coded on the minority strand; AT indicates the A+T-rich region.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funding for this study was provided jointly by the National Science Foundation of China (31101661, 31201732) and the State Key Program of National Natural Science Foundation of China (31230068).
References Cameron SL, Dowton M, Castro LR, Ruberu K, Whiting MF, Austin AD, Diement K, Stevens J. (2008). Mitochondrial genome organization and phylogeny of two vespid wasps. Genome 51:800–8. Dowton M, Austin AD. (1997). The evolution of strandspecific compositional bias. A case study in the hymenopteran mitochondrial 16S rRNA gene. Mol Biol Evol 14:109–12. Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting MF. (2009). Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. Mol Biol Evol 26:1607–17. Gotzek D, Clarke J, Shoemaker D. (2010). Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol Biol 10: 300.
Kaltenpoth M, Showers Corneli P, Dunn DM, Weiss RB, Strohm E, Seger J. (2012). Accelerated evolution of mitochondrial but not nuclear genomes of hymenoptera: New evidence from crabronid wasps. PLoS One 7:e32826. Mao M, Austin AD, Johnson NF, Dowton M. (2013). Coexistence of minicircular and a highly rearranged mtDNA molecule suggests that recombination shapes mitochondrial genome organization. Mol Biol Evol. doi: 10.1093/molbev/mst255. 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. Oliveira DCSG, Raychoudhury R, Lavrov DV, Werren JH. (2008). Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae). Mol Biol Evol 25:2167–80. Wei SJ, Shi M, Sharkey MJ, Van Achterberg C, Chen XX. (2010). Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to holometabolous insects. BMC Genomics 11:371.
