http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.953122
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Qiu-Ning Liu*, Dan-Dan Bian*, Sen-Hao Jiang, Zhen-Xing Li, Bao-Ming Ge, Fu-Jun Xuan, Li Yang, Chao-Feng Li, Dai-Zhen Zhang, Chun-Lin Zhou, and Bo-Ping Tang Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, P.R. China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Tribolium castaneum (Coleoptera: Tenebrionidae) was determined to be 15,883 bp (GenBank accession No. KM009121), which contains 22 tRNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and a major non-coding A + T-rich region. It has the typical gene organization and order of mitogenomes from ancestral insects. The nucleotide composition was also biased toward A + T nucleotides (71.72%) and the AT skew of this mitogenome was slightly positive. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by AAT. Eight of the 13 PCGs harbor the incomplete termination codon by T or TA. The A + T-rich region of the mitogenome was 1237 bp in length and the A + T content was 82.30%.
Coleoptera, mitochondrial genome, Tribolium castaneum
Mitochondrial genome (mitogenome) has been widely used as an informative molecular marker for diverse evolutionary studies (Boore et al., 1998). The red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae) is a major pest of stored grain and grain products. In this study, the complete mitogenome of T. castaneum is a circular molecule of 15,883 bp length, containing typical 13 protein-coding genes (PCGs), 22 transfer
History Received 3 August 2014 Accepted 6 August 2014 Published online 27 August 2014
RNA genes (tRNAs), 2 ribosomal RNA genes (rrnL and rrnS) and a major non-coding A + T-rich region. Its gene content and orientation are typical of other coleopteran insect mitochondrial genomes (Table 1). The nucleotide composition of the mitogenome of T. castaneum is as follows: As (39.86%), Ts (31.86%), Cs (18.55%) and Gs (9.72%). The AT skew for the T. castaneum
Table 1. Summary of the mitogenome of T. castaneum. Gene trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F R F F F R R F F F F F F
1–63 61–129 129–196 203–1205 1206–1272 1272–1332 1335–1398 1406–2941 2943–3007 3008–3692 3693–3763 3797–3862 3863–4021
63 69 68 1003 67 61 64 1536 65 685 71 66 159
GAT TTG CAT – TCA GCA GTA – TAA – CTT GTC –
– – – ATA – – – AAT – ATA – – ATT
– – – T – – – TAA – T – – TAG
3 1 6 0 1 2 7 1 0 0 34 0 7 (continued )
*These authors contributed equally to this work. Correspondence: Bo-Ping Tang, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, 50 Kaifang Avenue, Yancheng 224051, P.R. China. Tel/Fax: +86 515 88233991. E-mail: [email protected]
2
Q.-N. Liu et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Gene atp6 cox3 trnG nad3 trnA trnR trnN trnS1(AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2(UCN) nad1 trnL1(CUN) rrnL trnV rrnS A + T-rich region
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F F F F F F F F F R R R R R F R F F F R R R R R
4015–4685 4686–5471 5474–5535 5529–5886 5887–5953 5953–6015 6015–6078 6079–6137 6138–6202 6201–6265 6266–7976 7977–8041 8042–9374 9368–9655 9658–9720 9721–9786 9789–10,282 10,283–11,420 11,421–11,488 11,506–12,453 12,457–12,520 12,521–13,801 13,803–13,871 13,873–14,646 14,647–15,883
671 786 62 358 67 63 64 59 65 65 1711 65 1333 288 63 66 494 1138 68 948 64 1281 69 774 1237
– – TCC – TGC TCG GTT TCT TTC GAA – GTG – – TGT TGG – – TGA – TAG – TAC – –
ATG ATG – ATA – – – – – – ATT – ATG ATG – – ATC ATG – ATT – – – – –
TA TAA – T – – – – – – T – T TAA – – TA T – TAG – – – – –
0 2 7 0 1 1 0 0 2 0 0 0 7 2 0 2 0 0 17 3 0 1 1 0 –
mitogenome was slightly positive (0.112), and the GC skew of T. castaneum mitogenome was slightly negative ( 0.312). The mitogenome of T. castaneum has a total of 30 bp overlap between genes in nine locations, with the longest 7 bp overlap located in two locations: trnG and nad3, nad4 and nad4L. The mitogenome of T. castaneum contains 78 bp of intergenic spacer sequence spread over 12 regions, ranging in size from 1 to 34 bp. The longest spacer sequence is 34 bp, located between the trnK and trnD genes. Ten pairs of genes are directly adjacent without overlapping nucleotide. All of the 13 PCGs in the T. castaneum mitogenome were initiated by typical ATN codons (three with ATA, one with ATC, five with ATG and three with ATT), with the exception of the cox1. Sequence alignment revealed that the open reading frame of cox1 in T. castaneum also started with AAT codon for encoding asparagine. Compared to the other PCGs, cox1 was initiated by different codon and this non-canonical putative start codon is also found in some insects (Kim et al., 2012, 2013; Liu et al., 2012, 2013, 2014; Ou et al., 2014; Sheffield et al., 2008, 2009). The canonical termination codon (TAA or TAG) occurs in 5 PCGs in the T. castaneum mitogenome. The remaining PCGs including nad2, cox2, nad3, nad4, nad5 and cob were terminated with a single T, atp6 and nad6 were terminated with a single TA, which are commonly reported in other invertebrates (Masta & Boore, 2004). All of the 22 tRNAs, ranging from 59 to 71 bp, have a typical clover-leaf secondary structure, except for trnS1 (AGN) lacking a stable dihydrouridine (DHU) arm, which has been observed in several insects (Dai et al., 2013; Shao & Barker, 2003; Zhu et al., 2013). The rrnL was 1281 long with an AT content of 76.19%, while the rrnS is 774 bp long with an AT content of 76.23%. The A + T-rich region was located between the rrnS and trnI genes with a length of 1237 bp. The A + T content of this region was 82.30%. Two tandem repeats were found in the A + T-rich region of the T. castaneum mitogenome containing a duplicate 17 bp repeat element.
Declaration of interest The authors declare no competing interests. The authors alone are responsible for the content and writing of the paper. This work was supported by the Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources (JKLBS2014013), the National Natural Science Foundation of China (31301871), the Natural Science Foundation of Education Department of Jiangsu Province (12KJA180009) and the Natural Science Foundation of Jiangsu Province (BK20130422).
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667–8. Dai LS, Zhu BJ, Liu QN, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae). Gene 519:326–34. Kim MJ, Kim KG, Kim SR, Kim I. (2013). Complete mitochondrial genome of the two-spotted stag beetle, Metopodontus blanchardi (Coleoptera: Lucanidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.825788. Kim MJ, Wan XL, Kim I. (2012). Complete mitochondrial genome of the seven-spotted lady beetle, Coccinella septempunctata (Coleoptera: Coccinellidae). Mitochondrial DNA 23:179–81. Liu QN, Zhu BJ, Dai LS, Liu CL. (2013). The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects. Genomics 101:64–73. Liu QN, Zhu BJ, Dai LS, Wang L, Qian C, Wei GQ, Liu CL. (2014). The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.873934. Liu QN, Zhu BJ, Dai LS, Wei GQ, Liu CL. (2012). The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene 505:291–9. 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. Ou J, Liu JB, Yao FJ, Wang XG, Wei ZM. (2014). The complete mitochondrial genome of the American black flour beetle Tribolium audax (Coleoptera: Tenebrionidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.926504.
DOI: 10.3109/19401736.2014.953122
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Shao R, Barker SC. (2003). The highly rearranged mitochondrial genome of the plague thrips, Thrips imagines (Insecta: Thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 20:362–70. Sheffield NC, Song H, Cameron SL, Whiting MF. (2008). A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol 25: 2499–509.
Mitogenome of Tribolium castaneum
3
Sheffield NC, Song H, Cameron SL, Whiting MF. (2009). Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Systematic Biology 58:381–94. Zhu BJ, Liu QN, Dai LS, Wang L, Sun Y, Lin KZ, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae). Gene 527:283–91.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Qiu-Ning Liu*, Dan-Dan Bian*, Sen-Hao Jiang, Zhen-Xing Li, Bao-Ming Ge, Fu-Jun Xuan, Li Yang, Chao-Feng Li, Dai-Zhen Zhang, Chun-Lin Zhou, and Bo-Ping Tang Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, P.R. China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Tribolium castaneum (Coleoptera: Tenebrionidae) was determined to be 15,883 bp (GenBank accession No. KM009121), which contains 22 tRNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and a major non-coding A + T-rich region. It has the typical gene organization and order of mitogenomes from ancestral insects. The nucleotide composition was also biased toward A + T nucleotides (71.72%) and the AT skew of this mitogenome was slightly positive. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by AAT. Eight of the 13 PCGs harbor the incomplete termination codon by T or TA. The A + T-rich region of the mitogenome was 1237 bp in length and the A + T content was 82.30%.
Coleoptera, mitochondrial genome, Tribolium castaneum
Mitochondrial genome (mitogenome) has been widely used as an informative molecular marker for diverse evolutionary studies (Boore et al., 1998). The red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae) is a major pest of stored grain and grain products. In this study, the complete mitogenome of T. castaneum is a circular molecule of 15,883 bp length, containing typical 13 protein-coding genes (PCGs), 22 transfer
History Received 3 August 2014 Accepted 6 August 2014 Published online 27 August 2014
RNA genes (tRNAs), 2 ribosomal RNA genes (rrnL and rrnS) and a major non-coding A + T-rich region. Its gene content and orientation are typical of other coleopteran insect mitochondrial genomes (Table 1). The nucleotide composition of the mitogenome of T. castaneum is as follows: As (39.86%), Ts (31.86%), Cs (18.55%) and Gs (9.72%). The AT skew for the T. castaneum
Table 1. Summary of the mitogenome of T. castaneum. Gene trnI trnQ trnM nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F R F F F R R F F F F F F
1–63 61–129 129–196 203–1205 1206–1272 1272–1332 1335–1398 1406–2941 2943–3007 3008–3692 3693–3763 3797–3862 3863–4021
63 69 68 1003 67 61 64 1536 65 685 71 66 159
GAT TTG CAT – TCA GCA GTA – TAA – CTT GTC –
– – – ATA – – – AAT – ATA – – ATT
– – – T – – – TAA – T – – TAG
3 1 6 0 1 2 7 1 0 0 34 0 7 (continued )
*These authors contributed equally to this work. Correspondence: Bo-Ping Tang, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, 50 Kaifang Avenue, Yancheng 224051, P.R. China. Tel/Fax: +86 515 88233991. E-mail: [email protected]
2
Q.-N. Liu et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Gene atp6 cox3 trnG nad3 trnA trnR trnN trnS1(AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2(UCN) nad1 trnL1(CUN) rrnL trnV rrnS A + T-rich region
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F F F F F F F F F R R R R R F R F F F R R R R R
4015–4685 4686–5471 5474–5535 5529–5886 5887–5953 5953–6015 6015–6078 6079–6137 6138–6202 6201–6265 6266–7976 7977–8041 8042–9374 9368–9655 9658–9720 9721–9786 9789–10,282 10,283–11,420 11,421–11,488 11,506–12,453 12,457–12,520 12,521–13,801 13,803–13,871 13,873–14,646 14,647–15,883
671 786 62 358 67 63 64 59 65 65 1711 65 1333 288 63 66 494 1138 68 948 64 1281 69 774 1237
– – TCC – TGC TCG GTT TCT TTC GAA – GTG – – TGT TGG – – TGA – TAG – TAC – –
ATG ATG – ATA – – – – – – ATT – ATG ATG – – ATC ATG – ATT – – – – –
TA TAA – T – – – – – – T – T TAA – – TA T – TAG – – – – –
0 2 7 0 1 1 0 0 2 0 0 0 7 2 0 2 0 0 17 3 0 1 1 0 –
mitogenome was slightly positive (0.112), and the GC skew of T. castaneum mitogenome was slightly negative ( 0.312). The mitogenome of T. castaneum has a total of 30 bp overlap between genes in nine locations, with the longest 7 bp overlap located in two locations: trnG and nad3, nad4 and nad4L. The mitogenome of T. castaneum contains 78 bp of intergenic spacer sequence spread over 12 regions, ranging in size from 1 to 34 bp. The longest spacer sequence is 34 bp, located between the trnK and trnD genes. Ten pairs of genes are directly adjacent without overlapping nucleotide. All of the 13 PCGs in the T. castaneum mitogenome were initiated by typical ATN codons (three with ATA, one with ATC, five with ATG and three with ATT), with the exception of the cox1. Sequence alignment revealed that the open reading frame of cox1 in T. castaneum also started with AAT codon for encoding asparagine. Compared to the other PCGs, cox1 was initiated by different codon and this non-canonical putative start codon is also found in some insects (Kim et al., 2012, 2013; Liu et al., 2012, 2013, 2014; Ou et al., 2014; Sheffield et al., 2008, 2009). The canonical termination codon (TAA or TAG) occurs in 5 PCGs in the T. castaneum mitogenome. The remaining PCGs including nad2, cox2, nad3, nad4, nad5 and cob were terminated with a single T, atp6 and nad6 were terminated with a single TA, which are commonly reported in other invertebrates (Masta & Boore, 2004). All of the 22 tRNAs, ranging from 59 to 71 bp, have a typical clover-leaf secondary structure, except for trnS1 (AGN) lacking a stable dihydrouridine (DHU) arm, which has been observed in several insects (Dai et al., 2013; Shao & Barker, 2003; Zhu et al., 2013). The rrnL was 1281 long with an AT content of 76.19%, while the rrnS is 774 bp long with an AT content of 76.23%. The A + T-rich region was located between the rrnS and trnI genes with a length of 1237 bp. The A + T content of this region was 82.30%. Two tandem repeats were found in the A + T-rich region of the T. castaneum mitogenome containing a duplicate 17 bp repeat element.
Declaration of interest The authors declare no competing interests. The authors alone are responsible for the content and writing of the paper. This work was supported by the Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources (JKLBS2014013), the National Natural Science Foundation of China (31301871), the Natural Science Foundation of Education Department of Jiangsu Province (12KJA180009) and the Natural Science Foundation of Jiangsu Province (BK20130422).
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667–8. Dai LS, Zhu BJ, Liu QN, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae). Gene 519:326–34. Kim MJ, Kim KG, Kim SR, Kim I. (2013). Complete mitochondrial genome of the two-spotted stag beetle, Metopodontus blanchardi (Coleoptera: Lucanidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.825788. Kim MJ, Wan XL, Kim I. (2012). Complete mitochondrial genome of the seven-spotted lady beetle, Coccinella septempunctata (Coleoptera: Coccinellidae). Mitochondrial DNA 23:179–81. Liu QN, Zhu BJ, Dai LS, Liu CL. (2013). The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects. Genomics 101:64–73. Liu QN, Zhu BJ, Dai LS, Wang L, Qian C, Wei GQ, Liu CL. (2014). The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.873934. Liu QN, Zhu BJ, Dai LS, Wei GQ, Liu CL. (2012). The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene 505:291–9. 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. Ou J, Liu JB, Yao FJ, Wang XG, Wei ZM. (2014). The complete mitochondrial genome of the American black flour beetle Tribolium audax (Coleoptera: Tenebrionidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.926504.
DOI: 10.3109/19401736.2014.953122
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/05/14 For personal use only.
Shao R, Barker SC. (2003). The highly rearranged mitochondrial genome of the plague thrips, Thrips imagines (Insecta: Thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 20:362–70. Sheffield NC, Song H, Cameron SL, Whiting MF. (2008). A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol 25: 2499–509.
Mitogenome of Tribolium castaneum
3
Sheffield NC, Song H, Cameron SL, Whiting MF. (2009). Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Systematic Biology 58:381–94. Zhu BJ, Liu QN, Dai LS, Wang L, Sun Y, Lin KZ, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae). Gene 527:283–91.
