http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873934
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the common cutworm, Spodoptera litura (Lepidoptera: Noctuidade) Qiu-Ning Liu*, Bao-Jian Zhu*, Li-Shang Dai, Lei Wang, Cen Qian, Guo-Qing Wei, and Chao-Liang Liu
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 08/09/15 For personal use only.
College of Life Science, Anhui Agricultural University, Hefei, People’s Republic of China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374 bp (GenBank accession No. KF543065), including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A + T nucleotides (81.03%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Four of the 13 PCGs harbor the incomplete termination codon by T. All the tRNA genes displayed a typical cloverleaf structure of mitochondrial tRNA, with the exception of trnS1 (AGN). The A + T-rich region of the mitogenome was 326 bp in length.
Gene rearrangement, mitochondrial genome, Noctuoidea, Spodoptera litura
The common cutworm, Spodoptera litura (Lepidoptera: Noctuidae) is an important polyphagous agricultural pest. However, only few mitogenomes of Noctuoidea were sequenced (Chai & Du, 2012; Gong et al., 2013; Wu et al., 2013; Yin et al., 2010; Yuan & Zhang, 2013). The mitogenome of S. litura is a closed circular molecule of 15,374 bp length. The gene content is typical of other insect mitochondrial genomes (Table 1).
History Received 7 December 2013 Accepted 7 December 2013 Published online 3 February 2014
Compared with the ancestral insect gene order, the placement of the trnM tRNA gene in the S. litura mitogenome differs from the ancestral insects. In S. litura, the order is as follows: trnM–trnI–trnQ, whereas the ancestral order is: trnI–trnQ–trnM (Boore et al., 1998) The nucleotide composition of the mitogenome of S. litura is as follows: A ¼ 6308 (41.03%), T ¼ 6150 (40.00%), G ¼ 1169
Table 1. Summary of the mitogenome of S. litura. Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F F R F F R R F F F F F F F F F F F F F
1–68 69–134 132–200 249–1262 1261–1328 1321–1387 1389–1455 1463–2993 2994–3060 3061–3742 3743–3813 3814–3881 3882–4043 4037–4714 4714–5502 5505–5569 5570–5921 5922–5988 5988–6052 6056–6120
68 66 69 1014 68 67 67 1531 67 682 71 68 162 678 789 65 352 67 65 65
CAT GAT TTG – TCA GCA GTA – TAA – CTT GTC – – – TCC – TGC TCG GTT
– – – ATT – – – CGA – ATG – – ATA ATG ATG – ATT – – –
– – – TAA – – – T – T – – TAA TAA TAA – T – – –
0 3 48 2 8 1 7 0 0 0 0 0 7 1 2 0 0 1 3 12 (continued )
*These authors contributed equally to this work. Correspondence: Chao-Liang Liu, College of Life Science, Anhui Agricultural University, Hefei, 130 Changjiang West Road, Hefei 230036, People’s Republic of China. Tel/Fax: +86 551 5786201. E-mail: [email protected]
2
Q.-N. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 08/09/15 For personal use only.
Gene 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 R R R R R F R F F F R R R R R
6133–6200 6201–6265 6289–6355 6356–8104 8102–8167 8168–9506 9554–9844 9851–9915 9916–9980 9989–10,519 10,525–11,673 11,673–11,740 11,759–12,697 12,698–12,765 12,767–14,164 14,165–14,232 14,229–15,048 15,049–15,374
68 65 67 1755 66 1339 291 65 65 531 1149 68 939 68 1398 68 820 326
GCT TTC GAA – GTG – – TGT TGG – – TGA – TAG – TAC – –
– – – ATT – ATG ATG – – ATA ATG – ATT – – – – –
– – – TAA – T TAG – – TAA TAA – TAA – – – – –
0 23 0 3 0 47 6 0 8 5 1 18 0 1 0 4 0 0
(7.60%) and C ¼ 1747 (11.36%). The AT skew for the S. litura mitogenome was slightly positive (0.013), and the GC skew of S. litura mitogenome was slightly negative (0.198). The mitogenome of S. litura has a total of 30 bp overlap between genes in nine locations, with the longest 8 bp overlap located in two locations: trnW and trnC. The mitogenome of S. litura contains 181 bp of intergenic spacer sequence spread over 13 regions, ranging in size from 1 to 48 bp. The longest spacer sequence is 48 bp, located between the trnQ and nad2 genes, is extremely A + T rich (91.67%). All protein-coding sequences in the S. litura mitogenome were initiated by typical ATN codons, with the exception of the cox1. Sequence alignment revealed that the open reading frame of cox1 in S. litura also starts with a CGA codon for encoding arginine. Different from the other protein-coding genes (PCGs), cox1 is initiated by CGA codon and this non-canonical putative start codon is also found in some insects (Liu et al., 2013; Zhu et al., 2013). The canonical termination codon (TAA) occurs in 8 PCGs in the S. litura mitogenome. The remaining four PCGs, including cox1, cox2 nad3 and nad4, were terminated with a single T. All tRNAs displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes, except for trnS1 (AGN) lacking a stable dihydrouridine arm, which has been observed in several insects, including the lepidopteran species and metazoan mitogenomes (Dai et al., 2013; Liu et al., 2012). The lengths of the rrnL and rrnS were 1398 and 820 bp, respectively. The A + T content of the two rRNA genes are 84.99%. The A + T-rich region of S. litura extends over 326 bp and is located between the rrnS and trnM genes. The A + T content of this region is 93.87%. Several conserved structures of other lepidopteran mitogenomes, including the motif ‘‘ATAGA’’, a 18-bp poly-T stretch, macrosatellite (AT)7 and (AT)9 element, a 10-bp poly-A were observed in the A + T-rich region of S. litura mitogenome. Two tandem repeats were found in the A + T-rich region of the S. litura mitogenome containing a duplicate 34 bp repeat element.
Declaration of interest This work was supported by the earmarked fund for Modern Agroindustry Technology Research System (CARS-22-SYZ10), Youth Foundation of Anhui Agricultural University (2010zd10) and Natural Science Foundation of Anhui Province of China (11040606M98). The authors declare no competing interests. The authors alone are responsible for the content and writing of the paper.
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667–8. Chai HN, Du YZ. (2012). The complete mitochondrial genome of the pink stem borer, Sesamia inferens, in comparison with four other Noctuid moths. Int J Mol Sci 13:10236–56. 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. Gong YJ, Wu QL, Wei SJ. (2013). Complete mitogenome of the Argyrogramma agnate (Lepidoptera: Noctuidae). Mitochondrial DNA 24:391–3. 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. 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. Wu QL, Gong YJ, Gu Y, Wei SJ. (2013). The complete mitochondrial genome of the beet armyworm Spodoptera exigua (Hu¨bner) (Lepodiptera: Noctuidae). Mitochondrial DNA 24:31–3. Yin J, Hong GY, Wang AM, Cao YZ, Wei ZJ. (2010). Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans. Mitochondrial DNA 21:160–9. Yuan ML, Zhang QL. (2013). The complete mitochondrial genome of Gynaephora menyuanensis (Lepidoptera: Lymantriidae) from the Qinghai-Tibetan Plateau. Mitochondrial DNA 24:328–30. 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 common cutworm, Spodoptera litura (Lepidoptera: Noctuidade) Qiu-Ning Liu*, Bao-Jian Zhu*, Li-Shang Dai, Lei Wang, Cen Qian, Guo-Qing Wei, and Chao-Liang Liu
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 08/09/15 For personal use only.
College of Life Science, Anhui Agricultural University, Hefei, People’s Republic of China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374 bp (GenBank accession No. KF543065), including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A + T nucleotides (81.03%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Four of the 13 PCGs harbor the incomplete termination codon by T. All the tRNA genes displayed a typical cloverleaf structure of mitochondrial tRNA, with the exception of trnS1 (AGN). The A + T-rich region of the mitogenome was 326 bp in length.
Gene rearrangement, mitochondrial genome, Noctuoidea, Spodoptera litura
The common cutworm, Spodoptera litura (Lepidoptera: Noctuidae) is an important polyphagous agricultural pest. However, only few mitogenomes of Noctuoidea were sequenced (Chai & Du, 2012; Gong et al., 2013; Wu et al., 2013; Yin et al., 2010; Yuan & Zhang, 2013). The mitogenome of S. litura is a closed circular molecule of 15,374 bp length. The gene content is typical of other insect mitochondrial genomes (Table 1).
History Received 7 December 2013 Accepted 7 December 2013 Published online 3 February 2014
Compared with the ancestral insect gene order, the placement of the trnM tRNA gene in the S. litura mitogenome differs from the ancestral insects. In S. litura, the order is as follows: trnM–trnI–trnQ, whereas the ancestral order is: trnI–trnQ–trnM (Boore et al., 1998) The nucleotide composition of the mitogenome of S. litura is as follows: A ¼ 6308 (41.03%), T ¼ 6150 (40.00%), G ¼ 1169
Table 1. Summary of the mitogenome of S. litura. Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN
Direction
Location
Size
Anticodon
Start codon
Stop codon
Intergenic nucleotides
F F R F F R R F F F F F F F F F F F F F
1–68 69–134 132–200 249–1262 1261–1328 1321–1387 1389–1455 1463–2993 2994–3060 3061–3742 3743–3813 3814–3881 3882–4043 4037–4714 4714–5502 5505–5569 5570–5921 5922–5988 5988–6052 6056–6120
68 66 69 1014 68 67 67 1531 67 682 71 68 162 678 789 65 352 67 65 65
CAT GAT TTG – TCA GCA GTA – TAA – CTT GTC – – – TCC – TGC TCG GTT
– – – ATT – – – CGA – ATG – – ATA ATG ATG – ATT – – –
– – – TAA – – – T – T – – TAA TAA TAA – T – – –
0 3 48 2 8 1 7 0 0 0 0 0 7 1 2 0 0 1 3 12 (continued )
*These authors contributed equally to this work. Correspondence: Chao-Liang Liu, College of Life Science, Anhui Agricultural University, Hefei, 130 Changjiang West Road, Hefei 230036, People’s Republic of China. Tel/Fax: +86 551 5786201. E-mail: [email protected]
2
Q.-N. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 08/09/15 For personal use only.
Gene 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 R R R R R F R F F F R R R R R
6133–6200 6201–6265 6289–6355 6356–8104 8102–8167 8168–9506 9554–9844 9851–9915 9916–9980 9989–10,519 10,525–11,673 11,673–11,740 11,759–12,697 12,698–12,765 12,767–14,164 14,165–14,232 14,229–15,048 15,049–15,374
68 65 67 1755 66 1339 291 65 65 531 1149 68 939 68 1398 68 820 326
GCT TTC GAA – GTG – – TGT TGG – – TGA – TAG – TAC – –
– – – ATT – ATG ATG – – ATA ATG – ATT – – – – –
– – – TAA – T TAG – – TAA TAA – TAA – – – – –
0 23 0 3 0 47 6 0 8 5 1 18 0 1 0 4 0 0
(7.60%) and C ¼ 1747 (11.36%). The AT skew for the S. litura mitogenome was slightly positive (0.013), and the GC skew of S. litura mitogenome was slightly negative (0.198). The mitogenome of S. litura has a total of 30 bp overlap between genes in nine locations, with the longest 8 bp overlap located in two locations: trnW and trnC. The mitogenome of S. litura contains 181 bp of intergenic spacer sequence spread over 13 regions, ranging in size from 1 to 48 bp. The longest spacer sequence is 48 bp, located between the trnQ and nad2 genes, is extremely A + T rich (91.67%). All protein-coding sequences in the S. litura mitogenome were initiated by typical ATN codons, with the exception of the cox1. Sequence alignment revealed that the open reading frame of cox1 in S. litura also starts with a CGA codon for encoding arginine. Different from the other protein-coding genes (PCGs), cox1 is initiated by CGA codon and this non-canonical putative start codon is also found in some insects (Liu et al., 2013; Zhu et al., 2013). The canonical termination codon (TAA) occurs in 8 PCGs in the S. litura mitogenome. The remaining four PCGs, including cox1, cox2 nad3 and nad4, were terminated with a single T. All tRNAs displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes, except for trnS1 (AGN) lacking a stable dihydrouridine arm, which has been observed in several insects, including the lepidopteran species and metazoan mitogenomes (Dai et al., 2013; Liu et al., 2012). The lengths of the rrnL and rrnS were 1398 and 820 bp, respectively. The A + T content of the two rRNA genes are 84.99%. The A + T-rich region of S. litura extends over 326 bp and is located between the rrnS and trnM genes. The A + T content of this region is 93.87%. Several conserved structures of other lepidopteran mitogenomes, including the motif ‘‘ATAGA’’, a 18-bp poly-T stretch, macrosatellite (AT)7 and (AT)9 element, a 10-bp poly-A were observed in the A + T-rich region of S. litura mitogenome. Two tandem repeats were found in the A + T-rich region of the S. litura mitogenome containing a duplicate 34 bp repeat element.
Declaration of interest This work was supported by the earmarked fund for Modern Agroindustry Technology Research System (CARS-22-SYZ10), Youth Foundation of Anhui Agricultural University (2010zd10) and Natural Science Foundation of Anhui Province of China (11040606M98). The authors declare no competing interests. The authors alone are responsible for the content and writing of the paper.
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667–8. Chai HN, Du YZ. (2012). The complete mitochondrial genome of the pink stem borer, Sesamia inferens, in comparison with four other Noctuid moths. Int J Mol Sci 13:10236–56. 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. Gong YJ, Wu QL, Wei SJ. (2013). Complete mitogenome of the Argyrogramma agnate (Lepidoptera: Noctuidae). Mitochondrial DNA 24:391–3. 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. 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. Wu QL, Gong YJ, Gu Y, Wei SJ. (2013). The complete mitochondrial genome of the beet armyworm Spodoptera exigua (Hu¨bner) (Lepodiptera: Noctuidae). Mitochondrial DNA 24:31–3. Yin J, Hong GY, Wang AM, Cao YZ, Wei ZJ. (2010). Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other Lepidopterans. Mitochondrial DNA 21:160–9. Yuan ML, Zhang QL. (2013). The complete mitochondrial genome of Gynaephora menyuanensis (Lepidoptera: Lymantriidae) from the Qinghai-Tibetan Plateau. Mitochondrial DNA 24:328–30. 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.
