http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971241
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tyspanodes hypsalis (Lepidoptera: Crambidae) Jia Wang, Pengfei Li, and Ping You
Mitochondrial DNA Downloaded from informahealthcare.com by University of Connecticut on 01/10/15 For personal use only.
Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, P.R. China
Abstract
Keywords
The size of Tyspanodes hypsalis (Warren, 1891) mitogenome was 15,329 bp in which the base composition of mitogenome was 40.0% A, 41.4% T, 11.9% G and 7.7% C. All protein-coding genes (PCGs) utilized the standard ATN, while COI used CGA as the initial codon. In addition, all PCGs had the common stop codon (TAN), except COI and ND5 respectively used incomplete termination codon T and TA. All tRNAs had the typical cloverleaf structure of mitochondrial tRNAs, with the exception of tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The A + T-rich region of 350 bp contains several features common to the Lepidoptera insects. Including the motif ‘‘ATAGA’’ followed by a 17-bp poly-T stretch, a microsatellite-like (AT)8 element preceded by the ATTTA motif, and a 12 bp polyA-like stretch (AAATAAAAAAAAA) present immediately upstream tRNAMet.
Crambidae, lepidoptera, mitochodrial genome, Tyspanodes hypsalis
The complete mitogenome sequences from 15 species of Pyraloidea have been published in GenBank, by far. In this research, we described the complete mitochondrial genome sequence of Tyspanodes hypsalis (Warren, 1891) (Pyraloidea: Crambidae: Spilomelinae) which spread over mainly in China, Korea, Japan and Sikkim. The mitogenome sequence of T. hypsalis could provide further research for the phylogenetic relationships among Pyraloidea and Lepidoptera. Specimens of T. hypsalis were collected from Xunyangba (33.33 N; 108.33 E), Ningshan County, Shaanxi Province, China. The total DNA extraction was performed by saturated NaCl extraction (Zhang et al., 2005). The complete mitochondrial genome was determined by amplifying of PCR, sequencing and annotations. The mitochondrial genome of T. hypsalis was a circular molecule of 15,329 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and an A + T-rich region (Table 1). The T. hypsalis mitogenome had the typical lepidopteran gene order that differs from the ancestral gene order of insects for the placement of tRNAMet (Hong et al., 2009). Among 37 genes, 23 genes were encoded on majority strand, including 9 PCGs and 14 tRNA genes, and other 14 genes were founded in the minority strand.
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]
History Received 2 September 2014 Revised 8 September 2014 Accepted 19 September 2014 Published online 15 October 2014
The nucleotide composition of T. hypsalis mitogenome was significantly biased toward A + T. The A + T content of mtDNA, PCGs, tRNAs, rRNAs and A + T-rich region were 81.42%, 79.98%, 82.02%, 85.11% and 95.43%, respectively. The mitochondrial genome of the T. hypsalis included 14 intergenic regions ranging from 1 to 47 bp and 9 overlapping regions spanning 1 to 8 bp. All PCGs started with ATN codons (ND2, ND3, ND5 and ND6 with ATT; COII, ATP6, COIII, ND4, ND4L and Cytb with ATG; ATP8 with ATC, and ND1 with ATA), while the COI gene began with CGA. In addition, all PCGs had the common stop codon (TAN), except COI and ND5 respectively used incomplete termination codon T and TA. The 22 traditional tRNA genes were interspersed throughout the T. hypsalis mitogenome, ranging in length from 63 bp (tRNAAsn) to 71 bp (tRNALys). All tRNAs had the typical cloverleaf structure of mitochondrial RNAs, with the exception of tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The incomplete tRNASer(AGN) (67 bp) structure has been detected in many lepidopteran insects (Kim et al., 2006; Yang et al., 2009) The T. hypsalis A + T-rich region of 350 bp was composed of non-repetitive sequences, but harbors several features common to the Lepidoptera insects. The motif ATAGA followed by a 17 bp poly-T stretch. A microsatellite-like (AT)8 element preceded by the ATTTA motif was present in the 30 -end of the A + T-rich region. The presence of a microsatellite preceded by the ATTTA motif was common in the control regions of insect mitogenomes, and has been found in the majority of other sequenced lepidopteran A + T-rich regions (Cameron & Whiting, 2008). Finally, a 12 bp polyA-like stretch (AAATAAAAAAAAA) present immediately upstream of tRNAMet.
Nucleotide sequence accession number The complete mitochondrial genome sequence of T. hypsalis has been assigned with GenBank accession number was KM453724.
2
J. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of mitochondrial genome of T. hypsalis.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Connecticut on 01/10/15 For personal use only.
Gene
Direction
Location
Size
Intergenic nucleotides
F F R F F R R F F F F F F F F F F F F F F F R R R R R F R F F F R R R R R
1–66 67–130 128–196 244–1257 1282–1349 1342–1409 1415–1480 1494–3026 3029–3095 3096–3777 3778–3848 3857–3924 3925–4087 4080–4751 4751–5539 5543–5607 5608–5961 6001–6064 6064–6126 6127–6193 6194–6260 6261–6326 6334–6402 6402–8140 8141–8207 8207–9547 9547–9837 9838–9903 9904–9969 9972–10,505 10,509–11,660 11,659–11,725 11,743–12,678 12,683–12,750 12,758–14,122 14,123–14,188 14,189–14,979 14,980–15,329
66 64 69 1014 68 68 66 1533 67 682 71 68 163 672 789 65 354 64 63 67 67 66 69 1739 67 1341 291 66 66 534 1152 67 936 68 1365 66 791 350
– 0 3 47 24 8 5 13 2 0 0 8 0 8 1 3 0 39 1 0 0 0 7 1 0 1 1 0 0 2 3 2 17 4 7 0 0 0
tRNAMet tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly 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
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.
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATG
T– –
ATC ATG ATG
TAA TAA TAA
ATT
TAA
ATT
TA–
ATG ATG
TAA TAA
ATT ATG
TAA TAA
ATA
TAG
Hong GY, Jiang ST, Yu M, Yang Y, Li F, Xue FS, Wei ZJ. (2009). The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly, Artogeia melete (Lepidoptera: Pieridae). Acta Biochim Biophys Sinica 6:446–55. Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR. (2006). The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol 15: 217–25. Warren W. (1891). Descriptions of new genera and species of Pyralidae contained in the British-Museum collection. Ann Mag Nat Hist 7: 423–38. Yang L, Wei ZJ, Hong GY, Jiang ST, Wen LP, Wen LP. (2009). The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep 36:1441–9. Zhang M, Zhang JZ, Guo YP, Cao TW, Ma EB. (2005). DNA extraction of dry samples and RAPD-PCR reaction of butterflies. Acta Zool Sinica 51:253–7.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tyspanodes hypsalis (Lepidoptera: Crambidae) Jia Wang, Pengfei Li, and Ping You
Mitochondrial DNA Downloaded from informahealthcare.com by University of Connecticut on 01/10/15 For personal use only.
Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, P.R. China
Abstract
Keywords
The size of Tyspanodes hypsalis (Warren, 1891) mitogenome was 15,329 bp in which the base composition of mitogenome was 40.0% A, 41.4% T, 11.9% G and 7.7% C. All protein-coding genes (PCGs) utilized the standard ATN, while COI used CGA as the initial codon. In addition, all PCGs had the common stop codon (TAN), except COI and ND5 respectively used incomplete termination codon T and TA. All tRNAs had the typical cloverleaf structure of mitochondrial tRNAs, with the exception of tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The A + T-rich region of 350 bp contains several features common to the Lepidoptera insects. Including the motif ‘‘ATAGA’’ followed by a 17-bp poly-T stretch, a microsatellite-like (AT)8 element preceded by the ATTTA motif, and a 12 bp polyA-like stretch (AAATAAAAAAAAA) present immediately upstream tRNAMet.
Crambidae, lepidoptera, mitochodrial genome, Tyspanodes hypsalis
The complete mitogenome sequences from 15 species of Pyraloidea have been published in GenBank, by far. In this research, we described the complete mitochondrial genome sequence of Tyspanodes hypsalis (Warren, 1891) (Pyraloidea: Crambidae: Spilomelinae) which spread over mainly in China, Korea, Japan and Sikkim. The mitogenome sequence of T. hypsalis could provide further research for the phylogenetic relationships among Pyraloidea and Lepidoptera. Specimens of T. hypsalis were collected from Xunyangba (33.33 N; 108.33 E), Ningshan County, Shaanxi Province, China. The total DNA extraction was performed by saturated NaCl extraction (Zhang et al., 2005). The complete mitochondrial genome was determined by amplifying of PCR, sequencing and annotations. The mitochondrial genome of T. hypsalis was a circular molecule of 15,329 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and an A + T-rich region (Table 1). The T. hypsalis mitogenome had the typical lepidopteran gene order that differs from the ancestral gene order of insects for the placement of tRNAMet (Hong et al., 2009). Among 37 genes, 23 genes were encoded on majority strand, including 9 PCGs and 14 tRNA genes, and other 14 genes were founded in the minority strand.
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]
History Received 2 September 2014 Revised 8 September 2014 Accepted 19 September 2014 Published online 15 October 2014
The nucleotide composition of T. hypsalis mitogenome was significantly biased toward A + T. The A + T content of mtDNA, PCGs, tRNAs, rRNAs and A + T-rich region were 81.42%, 79.98%, 82.02%, 85.11% and 95.43%, respectively. The mitochondrial genome of the T. hypsalis included 14 intergenic regions ranging from 1 to 47 bp and 9 overlapping regions spanning 1 to 8 bp. All PCGs started with ATN codons (ND2, ND3, ND5 and ND6 with ATT; COII, ATP6, COIII, ND4, ND4L and Cytb with ATG; ATP8 with ATC, and ND1 with ATA), while the COI gene began with CGA. In addition, all PCGs had the common stop codon (TAN), except COI and ND5 respectively used incomplete termination codon T and TA. The 22 traditional tRNA genes were interspersed throughout the T. hypsalis mitogenome, ranging in length from 63 bp (tRNAAsn) to 71 bp (tRNALys). All tRNAs had the typical cloverleaf structure of mitochondrial RNAs, with the exception of tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The incomplete tRNASer(AGN) (67 bp) structure has been detected in many lepidopteran insects (Kim et al., 2006; Yang et al., 2009) The T. hypsalis A + T-rich region of 350 bp was composed of non-repetitive sequences, but harbors several features common to the Lepidoptera insects. The motif ATAGA followed by a 17 bp poly-T stretch. A microsatellite-like (AT)8 element preceded by the ATTTA motif was present in the 30 -end of the A + T-rich region. The presence of a microsatellite preceded by the ATTTA motif was common in the control regions of insect mitogenomes, and has been found in the majority of other sequenced lepidopteran A + T-rich regions (Cameron & Whiting, 2008). Finally, a 12 bp polyA-like stretch (AAATAAAAAAAAA) present immediately upstream of tRNAMet.
Nucleotide sequence accession number The complete mitochondrial genome sequence of T. hypsalis has been assigned with GenBank accession number was KM453724.
2
J. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of mitochondrial genome of T. hypsalis.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Connecticut on 01/10/15 For personal use only.
Gene
Direction
Location
Size
Intergenic nucleotides
F F R F F R R F F F F F F F F F F F F F F F R R R R R F R F F F R R R R R
1–66 67–130 128–196 244–1257 1282–1349 1342–1409 1415–1480 1494–3026 3029–3095 3096–3777 3778–3848 3857–3924 3925–4087 4080–4751 4751–5539 5543–5607 5608–5961 6001–6064 6064–6126 6127–6193 6194–6260 6261–6326 6334–6402 6402–8140 8141–8207 8207–9547 9547–9837 9838–9903 9904–9969 9972–10,505 10,509–11,660 11,659–11,725 11,743–12,678 12,683–12,750 12,758–14,122 14,123–14,188 14,189–14,979 14,980–15,329
66 64 69 1014 68 68 66 1533 67 682 71 68 163 672 789 65 354 64 63 67 67 66 69 1739 67 1341 291 66 66 534 1152 67 936 68 1365 66 791 350
– 0 3 47 24 8 5 13 2 0 0 8 0 8 1 3 0 39 1 0 0 0 7 1 0 1 1 0 0 2 3 2 17 4 7 0 0 0
tRNAMet tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly 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
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.
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATG
T– –
ATC ATG ATG
TAA TAA TAA
ATT
TAA
ATT
TA–
ATG ATG
TAA TAA
ATT ATG
TAA TAA
ATA
TAG
Hong GY, Jiang ST, Yu M, Yang Y, Li F, Xue FS, Wei ZJ. (2009). The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly, Artogeia melete (Lepidoptera: Pieridae). Acta Biochim Biophys Sinica 6:446–55. Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR. (2006). The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol 15: 217–25. Warren W. (1891). Descriptions of new genera and species of Pyralidae contained in the British-Museum collection. Ann Mag Nat Hist 7: 423–38. Yang L, Wei ZJ, Hong GY, Jiang ST, Wen LP, Wen LP. (2009). The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep 36:1441–9. Zhang M, Zhang JZ, Guo YP, Cao TW, Ma EB. (2005). DNA extraction of dry samples and RAPD-PCR reaction of butterflies. Acta Zool Sinica 51:253–7.
