http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987255
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Pseudargyria interruptella (Lepidoptera: Crambidae) Jingrui Song, Pengfei Li, and Ping You
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 02/09/15 For personal use only.
Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, China
Abstract
Keywords
The complete mitochondrial genome of the Pseudargyria interruptella (Lepidoptera, Crambidae) has been determined in this study. The mitochondrial genome of the moth was a circular molecule of 15,231 bp. The gene content and organization were the same as those of other lepidopteran species. The 13 protein-coding genes (PCGs) started with the typical ATN codon, except the COI that used CGA as its initiation codon. Two of 13 PCGs harbored the incomplete termination codon, T or TA. All tRNAs had a typical clover-leaf structure of mitochondrial tRNAs, except for tRNASer (AGN). The A + T-rich region was also highly A + T biased, accounting for 90.9%. Several conserved motifs like ATAGA, ATTTA, poly-T stretch were founded in this region.
Lepidoptera, mitochondrial genome, Pseudargyria interruptella
At present, only four complete mitochondrial genome sequences have been published from Crambinae in GenBank database. The complete mitochondrial genome sequence of Pseudargyria interruptella has been determined in this study. Pseudargyria interruptella is spread mainly in China, Korea and Japan. The new date of the sequence could provide useful information for the systematics and evolution research for pyraloidea at the genomic level. The moth P. interruptella (Crambidae: Crambinae) was collected in Xunyangba (33 330 N; 108 330 E), Ningshan country, Shaanxi province in the Qinling Mountain region of
History Received 5 November 2014 Accepted 10 November 2014 Published online 4 December 2014
central China. The total DNA was extracted from the adult P. interruptella by saturated NaCl extraction (Ye et al., 2014a; Zhang et al., 2005). The complete mitochondrial genome was determined by amplifying PCR, sequencing and annotating. The mitogenome of P. interruptella was a circular molecule 15,231 bp long and consisted of 13 PCGs (ND1-6, ND4L, COI-III, Cytb, ATP6, ATP8), 2 ribosomal RNAs (12S and 16S), 22 putative tRNAs and an A + T-rich region (Table 1). Similar to many insect mitochondrial genomes, the heavy strand encoded more genes (9 PCGs and 14 tRNAs), whereas the light stand encoded less genes (4 PCGs, 8 tRNAs and 2 rRNA).
Table 1. Annotation of mitochondrial genome of P. interruptella. Gene Met
tRNA tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly
Direction
Location
Size
Intergenic nucleotides
F F R F F R R F F F F F F F F F
1–68 71–134 137–205 257–1270 1277–1345 1338–1402 1403–1468 1472–3007 3003–3069 3070–3751 3752–3822 3827–3893 3894–4061 4055–4735 4735–5523 5526–5592
68 64 69 1014 69 65 66 1536 67 682 71 67 168 681 789 67
/ 2 2 51 6 8 0 3 5 0 0 4 0 7 1 2
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATT
T
ATC ATG ATG
TAA TAA TAA (continued )
Correspondence: Ping You, Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, No. 199, South Changan Rd., Xi’an, Shaanxi Province 710062, P. R. China. Tel: + 86-29-85303361. Fax: + 86-29-85310623. E-mail: [email protected]
2
J. Song et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 02/09/15 For personal use only.
Gene ND3 tRNAAla tRNAArg tRNAAsn tRNASer (AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer (UCN) ND1 tRNALeu (CUN) lrRNA tRNAVal srRNA A + T-rich region
Direction
Location
Size
Intergenic nucleotides
Start codon
Stop codon
F F F F F F R R R R R F R F F F R R R R R
5593–5946 5950–6014 6014–6077 6078–6142 6140–6211 6213–6280 6279–6344 6345–8079 8080–8147 8147–9487 9487–9780 9783–9846 9847–9911 9914–10,444 10,444–11,589 11,588–11,652 11,662–12,609 12,611–12,677 12,678–14,010 14,011–14,077 14,078–14,858 14,859–15,231
354 65 64 65 72 68 66 1735 68 1341 294 64 65 531 1146 66 948 67 1333 67 781 373
0 3 1 0 3 1 2 0 0 1 1 2 0 2 1 2 9 1 0 0 0 0
ATC
TAG
ATT
TA
ATG ATG
TAA TAA
ATA ATG
TAA TAA
ATG
TAA
The base composition of P. interruptella mitochondrial genome was: A (39.3%), T (40.1%), C (12.5%), G (8.1%) on the majority chain. The overall A + T content of the moth was 79.4% higher than the C + G content. Large ribosomal subunit (lrRNA) and small ribosomal subunit (srRNA) genes of P. interruptella were 1333 bp and 781 bp in size, and the average A + T content of rRNAs was 84.7%. All PCGs in the P. interruptella mitogenome were initiated by typical ATN codons (6 with ATG, 3 with ATT, 2 with ATC, 1 with ATA), except the COI gene which was designated by the CGA codon. For terminate codon usage, ND5 and COII terminated with the incomplete codon TA and T; the ND3 stopped with TAG; the remaining 10 PCGs with the typical stop codon TAA. There were intergenic spacers and overlapping regions scattered throughout the whole mitochondrial genome of P. interruptella, which included a total of 88 bp in 13 intergenic spacers, ranging in size from 1 to 51 bp, as well as interleaved 11 overlaps range in size from 1 to 8 bp, giving a total 32 bp. All tRNAs had a typical clover-leaf structure of mitochondrial tRNAs. However, the tRNASer (AGN) presented an unusual secondary structure lacking a stable stem-loop structure in the DHU arm, which had been observed in most insects (Hong et al., 2008; Wang et al., 2014; Wolstenholme., 1992; Ye & You, 2014). In P. interruptella, A + T-rich region of 373 bp was located between the srRNA and tRNAMet, and the A + T content was the highest (90.9%). This region had some common or similar structural features for lepidopteran insects (Cameron & Whiting, 2008; Ye et al., 2014b). It harbored 19 bp ploy-T stretch located 18 bp upstream from srRNA and preceded by a motif ATAGA. Additionally, there was a microsatellite-like repeats of (TA)10, which was preceded by a motif ATTTA.
Nucleotide sequence accession number The complete mitochondrial genome sequence of P. interruptella has been assigned with GenBank accession number was KP071469.
Acknowledgements The authors would like to thank M.S. Fei Ye (College of Life Sciences, Shaanxi Normal University) for assistance with sequencing and annotations.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported in part by the National Natural Science Foundation of China (31372158).
References Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–13. Hong MY, Lee EM, Jo YH, Park HC, Kim SR, Hwang JS, Jin BR, et al. (2008). Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene 413:49–57. Wang J, Li PF, You P. (2014). The complete mitochondrial genome of Tyspanodes hypsalis (Lepidoptera: Crambidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2014.971241. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Ye F, Shi YR, Xing LX, Yu HL, You P. (2014a). The complete mitochondrial genome of Paracymoriza prodigalis (Leech, 1889) (Lepidoptera), with a preliminary phylogenetic analysis of Pyraloidea. Aquat Insects, in Press. doi: 10.1080/01650424.2014.948454. Ye F, You P. (2014). The complete mitochondrial genome of Paracymoriza distinctalis (Lepidoptera: Crambidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2013.869678. Ye F, Yu HL, Li PF, You P. (2014b). The complete mitochondrial genome of Lista haraldusalis (Lepidoptera:Pyralidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2013.861427. Zhang M, Zhang JZ, Guo YP, Cao TW, Ma EB. (2005). DNA extraction of dry samples and RAPD-PCR reaction of butterflies. Acta Zool Sin 51:253–7.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Pseudargyria interruptella (Lepidoptera: Crambidae) Jingrui Song, Pengfei Li, and Ping You
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 02/09/15 For personal use only.
Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, China
Abstract
Keywords
The complete mitochondrial genome of the Pseudargyria interruptella (Lepidoptera, Crambidae) has been determined in this study. The mitochondrial genome of the moth was a circular molecule of 15,231 bp. The gene content and organization were the same as those of other lepidopteran species. The 13 protein-coding genes (PCGs) started with the typical ATN codon, except the COI that used CGA as its initiation codon. Two of 13 PCGs harbored the incomplete termination codon, T or TA. All tRNAs had a typical clover-leaf structure of mitochondrial tRNAs, except for tRNASer (AGN). The A + T-rich region was also highly A + T biased, accounting for 90.9%. Several conserved motifs like ATAGA, ATTTA, poly-T stretch were founded in this region.
Lepidoptera, mitochondrial genome, Pseudargyria interruptella
At present, only four complete mitochondrial genome sequences have been published from Crambinae in GenBank database. The complete mitochondrial genome sequence of Pseudargyria interruptella has been determined in this study. Pseudargyria interruptella is spread mainly in China, Korea and Japan. The new date of the sequence could provide useful information for the systematics and evolution research for pyraloidea at the genomic level. The moth P. interruptella (Crambidae: Crambinae) was collected in Xunyangba (33 330 N; 108 330 E), Ningshan country, Shaanxi province in the Qinling Mountain region of
History Received 5 November 2014 Accepted 10 November 2014 Published online 4 December 2014
central China. The total DNA was extracted from the adult P. interruptella by saturated NaCl extraction (Ye et al., 2014a; Zhang et al., 2005). The complete mitochondrial genome was determined by amplifying PCR, sequencing and annotating. The mitogenome of P. interruptella was a circular molecule 15,231 bp long and consisted of 13 PCGs (ND1-6, ND4L, COI-III, Cytb, ATP6, ATP8), 2 ribosomal RNAs (12S and 16S), 22 putative tRNAs and an A + T-rich region (Table 1). Similar to many insect mitochondrial genomes, the heavy strand encoded more genes (9 PCGs and 14 tRNAs), whereas the light stand encoded less genes (4 PCGs, 8 tRNAs and 2 rRNA).
Table 1. Annotation of mitochondrial genome of P. interruptella. Gene Met
tRNA tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly
Direction
Location
Size
Intergenic nucleotides
F F R F F R R F F F F F F F F F
1–68 71–134 137–205 257–1270 1277–1345 1338–1402 1403–1468 1472–3007 3003–3069 3070–3751 3752–3822 3827–3893 3894–4061 4055–4735 4735–5523 5526–5592
68 64 69 1014 69 65 66 1536 67 682 71 67 168 681 789 67
/ 2 2 51 6 8 0 3 5 0 0 4 0 7 1 2
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATT
T
ATC ATG ATG
TAA TAA TAA (continued )
Correspondence: Ping You, Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Sciences, Shaanxi Normal University, No. 199, South Changan Rd., Xi’an, Shaanxi Province 710062, P. R. China. Tel: + 86-29-85303361. Fax: + 86-29-85310623. E-mail: [email protected]
2
J. Song et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 02/09/15 For personal use only.
Gene ND3 tRNAAla tRNAArg tRNAAsn tRNASer (AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer (UCN) ND1 tRNALeu (CUN) lrRNA tRNAVal srRNA A + T-rich region
Direction
Location
Size
Intergenic nucleotides
Start codon
Stop codon
F F F F F F R R R R R F R F F F R R R R R
5593–5946 5950–6014 6014–6077 6078–6142 6140–6211 6213–6280 6279–6344 6345–8079 8080–8147 8147–9487 9487–9780 9783–9846 9847–9911 9914–10,444 10,444–11,589 11,588–11,652 11,662–12,609 12,611–12,677 12,678–14,010 14,011–14,077 14,078–14,858 14,859–15,231
354 65 64 65 72 68 66 1735 68 1341 294 64 65 531 1146 66 948 67 1333 67 781 373
0 3 1 0 3 1 2 0 0 1 1 2 0 2 1 2 9 1 0 0 0 0
ATC
TAG
ATT
TA
ATG ATG
TAA TAA
ATA ATG
TAA TAA
ATG
TAA
The base composition of P. interruptella mitochondrial genome was: A (39.3%), T (40.1%), C (12.5%), G (8.1%) on the majority chain. The overall A + T content of the moth was 79.4% higher than the C + G content. Large ribosomal subunit (lrRNA) and small ribosomal subunit (srRNA) genes of P. interruptella were 1333 bp and 781 bp in size, and the average A + T content of rRNAs was 84.7%. All PCGs in the P. interruptella mitogenome were initiated by typical ATN codons (6 with ATG, 3 with ATT, 2 with ATC, 1 with ATA), except the COI gene which was designated by the CGA codon. For terminate codon usage, ND5 and COII terminated with the incomplete codon TA and T; the ND3 stopped with TAG; the remaining 10 PCGs with the typical stop codon TAA. There were intergenic spacers and overlapping regions scattered throughout the whole mitochondrial genome of P. interruptella, which included a total of 88 bp in 13 intergenic spacers, ranging in size from 1 to 51 bp, as well as interleaved 11 overlaps range in size from 1 to 8 bp, giving a total 32 bp. All tRNAs had a typical clover-leaf structure of mitochondrial tRNAs. However, the tRNASer (AGN) presented an unusual secondary structure lacking a stable stem-loop structure in the DHU arm, which had been observed in most insects (Hong et al., 2008; Wang et al., 2014; Wolstenholme., 1992; Ye & You, 2014). In P. interruptella, A + T-rich region of 373 bp was located between the srRNA and tRNAMet, and the A + T content was the highest (90.9%). This region had some common or similar structural features for lepidopteran insects (Cameron & Whiting, 2008; Ye et al., 2014b). It harbored 19 bp ploy-T stretch located 18 bp upstream from srRNA and preceded by a motif ATAGA. Additionally, there was a microsatellite-like repeats of (TA)10, which was preceded by a motif ATTTA.
Nucleotide sequence accession number The complete mitochondrial genome sequence of P. interruptella has been assigned with GenBank accession number was KP071469.
Acknowledgements The authors would like to thank M.S. Fei Ye (College of Life Sciences, Shaanxi Normal University) for assistance with sequencing and annotations.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported in part by the National Natural Science Foundation of China (31372158).
References Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–13. Hong MY, Lee EM, Jo YH, Park HC, Kim SR, Hwang JS, Jin BR, et al. (2008). Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene 413:49–57. Wang J, Li PF, You P. (2014). The complete mitochondrial genome of Tyspanodes hypsalis (Lepidoptera: Crambidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2014.971241. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Ye F, Shi YR, Xing LX, Yu HL, You P. (2014a). The complete mitochondrial genome of Paracymoriza prodigalis (Leech, 1889) (Lepidoptera), with a preliminary phylogenetic analysis of Pyraloidea. Aquat Insects, in Press. doi: 10.1080/01650424.2014.948454. Ye F, You P. (2014). The complete mitochondrial genome of Paracymoriza distinctalis (Lepidoptera: Crambidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2013.869678. Ye F, Yu HL, Li PF, You P. (2014b). The complete mitochondrial genome of Lista haraldusalis (Lepidoptera:Pyralidae). Mitochondrial DNA, Early Online: 1–2. doi: 10.3109/19401736.2013.861427. Zhang M, Zhang JZ, Guo YP, Cao TW, Ma EB. (2005). DNA extraction of dry samples and RAPD-PCR reaction of butterflies. Acta Zool Sin 51:253–7.
