Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae) Zhao-Hui Huang, Pan-Feng Dai & Gui-Fang Zhao To cite this article: Zhao-Hui Huang, Pan-Feng Dai & Gui-Fang Zhao (2014): The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945542
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 9
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 05 November 2015, At: 17:36
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945542
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae) Zhao-Hui Huang1,2, Pan-Feng Dai3, and Gui-Fang Zhao1 1
Downloaded by [Deakin University Library] at 17:36 05 November 2015
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, People’s Republic of China, 2Longnan Teachers College, Chengxian, China, and 3College of Agriculture, Henan University of Science and Technology, Luoyang, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome of Heliconius pachinus has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 15,369 bp in length, and comprises the typical components: 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. PCGs are mostly initiated with either the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8) or the TTG codon (ND1); the COI gene may use the unusual CGA as its initiation codon, as suggested for other lepidopteran species. Some PCGs harbor TAG (ND3) or incomplete termination codon T (COI, COII & ND4), while the others use TAA as their termination codons. The nucleotide composition is highly asymmetric (39.2% A, 42.0% T, 7.7% G, 11.1% C) with an overall GC content of 18.8%.
Butterfly, cytochrome c oxidase subunit I (COI), initiation codon, mitogenome, next-generation sequencing
Lepidoptera is a large order of insects, and is estimated to comprise over 3,50,000 species (Powell, 2003). To date, only about 120 mitochondrial genomes have been reported for lepidopteran species (as of 19/06/2014). Here, we present the complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae), which has been reconstructed from the previously published whole-genome Illumina sequencing data (Marcus et al., 2013). In all, 60.94 million 90-bp raw reads were downloaded from the Sequence Read Archive (SRA) of GenBank (Accession number: SRR1057613), and quality-trimmed with default parameters using CLC Genomics Workbench v7.0.4 (CLC Bio, Aarhus, Denmark). The resultant 60.53 million trimmed reads were then used for reconstructing the mitochondrial genome with MITObim v1.7 (Hahn et al., 2013); the mitochondrial genome of Heliconius melpomene melpomene (GenBank: HE579083; The Heliconius Genome Consortium, 2012) was used as the initial reference. A total of 3,12,298 individual mitochondrial reads yielded an average coverage of 1830. The annotation was performed in GENEIOUS R7 (Biomatters Ltd., Auckland, New Zealand) by using the MITOS Web Server (Bernt et al., 2013) and the tRNAscan-SE Search Server (Lowe & Eddy, 1997; Schattner et al., 2005), and by comparing with other lepidopteran mitochondrial genomes. The organization of the H. pachinus mitochondrial genome is shown in Table 1. The circular genome was 15,369 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. The nucleotide composition is highly asymmetric (39.2% A, 42.0% T, Correspondence: Gui-Fang Zhao, College of Life Sciences, Northwest University, 229 Northern Taibai Road, Xi’an, Shaanxi Province 710069, People’s Republic of China. Tel: +86 29 8830 5264. Fax: +86 29 8830 3572. E-mail: [email protected]
History Received 20 June 2014 Accepted 27 June 2014 Published online 4 August 2014
Table 1. Annotation of the complete mitochondrial genome of H. pachinus. Position Gene
Size (bp)
tRNA-Met tRNA-Ile tRNA-Gln ND2 tRNA-Trp tRNA-Cys tRNA-Tyr COI tRNA-Leu(UUR) COII tRNA-Lys tRNA-Asp ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Ala tRNA-Arg tRNA-Asn tRNA-Ser(AGN) tRNA-Glu tRNA-Phe ND5 tRNA-His ND4 ND4L tRNA-Thr tRNA-Pro ND6 Cytb
68 1 68 64 69 132 69 130 198 1011 257 1267 65 1271 1335 65 1348 1412 66 1413 1478 1531 1481 3011 67 3012 3078 676 3079 3754 71 3755 3825 67 3827 3893 165 3894 4058 678 4052 4729 786 4729 5514 65 5517 5581 354 5582 5935 67 5934 6000 62 6000 6061 65 6062 6126 62 6125 6186 65 6197 6261 66 6268 6333 1734 6333 8066 69 8067 8135 1336 8139 9474 282 9474 9755 64 9758 9821 66 9822 9887 531 9890 10,420 1149 10,433 11,581
Start
Stop
Codons IGS (bp) Anticodon Start Stop Direction 0 0 3 58 3 12 0 2 0 0 0 1 0 5 1 2 0 2 1 0 2 10 6 1 0 3 1 2 0 2 12
CAT GAT TTG ATT TAA TCA GCA GTA CGA T(aa) TAA ATG T(aa) CTT GTC ATT TAA ATG TAA ATG TAA TCC ATT TAG TGC TCG GTT GCT TTC GAA ATT TAA GTG ATG T(aa) ATG TAA TGT TGG ATT TAA ATG TAA
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
(continued )
2
Z.-H. Huang et al.
Mitochondrial DNA, Early Online: 1–2
been deposited into GenBank under the accession number KM014809.
Table 1. Continued Position Gene
Size (bp)
Start
Stop
tRNA-Ser(UCN) 65 11,580 11,644 ND1 939 11,662 12,600 (CUN) 68 12,601 12,668 tRNA-Leu 16S rRNA 1380 12,669 14,048 tRNA-Val 67 14,049 14,115 12S rRNA 775 14,116 14,890 D-loop 479 14,891 15,369
Codons IGS (bp) Anticodon Start Stop Direction 2 17 0 0 0 0 0
TGA TTG TAA TAG TAC
F R R R R R NC
Downloaded by [Deakin University Library] at 17:36 05 November 2015
IGS denotes the length of the intergenic spacer region, for which negative numbers indicate nucleotide overlapping between adjacent genes. T(aa) denotes that the TAA stop codon is presumed to be completed by the addition of 3’ A residues to the mRNA. F, R and NC denote Forward, Reverse and Non-Coding, respectively.
7.7% G, and 11.1% C) with an overall GC content of 18.8%. The PCGs, tRNAs, rRNAs and the non-coding DNA account for 72.69% (11,172 bp), 9.46% (1453 bp), 14.02% (2155 bp) and 3.83% (589 bp) of the whole genome, respectively. PCGs are mostly initiated with either the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8) or the TTG codon (ND1). The COI gene may use the unusual CGA as its initiation codon, as suggested for many other lepidopteran species, e.g. Cupido argiades (Zhang et al., 2013), Danaus plexippus (Servı´n-Garciduen˜as & Martı´nez-Romero, 2014) and Grapholita molesta (Gong et al., 2012). Nine PCGs (ND1, ND2, ND4L, ND5, ND6, COIII, Cytb, ATP6 & ATP8) harbor the typical termination codon TAA, one PCG (ND3) terminated with TAG, while the other three PCGs (COI, COII & ND4) have an incomplete termination codon T. The 22 tRNAs ranged in size from 62 to 71 bp, with 14 of them coded on the majority strand. The 2 rRNAs were 775 bp (12S rRNA) and 1380 bp (16S rRNA) in length, with an AT content of 84.1% and 85.6%, respectively. The D-loop or control region was 479 bp long with an AT content of 91.7%, and was located between 12S rRNA and tRNA-Met. There were nine instances of intergenic overlapping regions ranging from 1 to 5 bp, and 13 instances of intergenic spacer regions ranging from 1 to 58 bp in length. The annotated mitochondrial genome sequence of H. pachinus has
Acknowledgements The authors thank Dr. Z.-Q. Qian for his assistance in manuscript preparation.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Gong Y-J, Shi B-C, Kang Z-J, Zhang F, Wei S-J. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucl Acids Res 41:e129. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–64. Marcus KR, Matthew HEB, Nicholas CG, Jason GR, Zhang W, Rob KJ, Durrell KD, Sean MP. (2013). Hybridization reveals the evolving genomic architecture of speciation. Cell Rep 5:666–77. Powell JA. (2003). Lepidoptera (moth and butterflies). In: Resh VH, Carde´ RT, editors. Encyclopedia of Insects. San Diego: Academic Press. p 631–64. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. Servı´n-Garciduen˜as LE, Martı´nez-Romero E. (2014). Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae). Mitochondr DNA, doi: 10.3109/ 19401736.2013.809441. The Heliconius Genome Consortium. (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94–8. Zhang L, Huang D, Sun X, Hao J, Hao J, Peng C, Yang Q. (2013). The complete mitochondrial genome of Cupido argiades (Lepidoptera: Lycaenidae). Mitochondrial DNA 24:475–7.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae) Zhao-Hui Huang, Pan-Feng Dai & Gui-Fang Zhao To cite this article: Zhao-Hui Huang, Pan-Feng Dai & Gui-Fang Zhao (2014): The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945542
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 9
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 05 November 2015, At: 17:36
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945542
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae) Zhao-Hui Huang1,2, Pan-Feng Dai3, and Gui-Fang Zhao1 1
Downloaded by [Deakin University Library] at 17:36 05 November 2015
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, People’s Republic of China, 2Longnan Teachers College, Chengxian, China, and 3College of Agriculture, Henan University of Science and Technology, Luoyang, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome of Heliconius pachinus has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 15,369 bp in length, and comprises the typical components: 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. PCGs are mostly initiated with either the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8) or the TTG codon (ND1); the COI gene may use the unusual CGA as its initiation codon, as suggested for other lepidopteran species. Some PCGs harbor TAG (ND3) or incomplete termination codon T (COI, COII & ND4), while the others use TAA as their termination codons. The nucleotide composition is highly asymmetric (39.2% A, 42.0% T, 7.7% G, 11.1% C) with an overall GC content of 18.8%.
Butterfly, cytochrome c oxidase subunit I (COI), initiation codon, mitogenome, next-generation sequencing
Lepidoptera is a large order of insects, and is estimated to comprise over 3,50,000 species (Powell, 2003). To date, only about 120 mitochondrial genomes have been reported for lepidopteran species (as of 19/06/2014). Here, we present the complete mitochondrial genome of Heliconius pachinus (Insecta: Lepidoptera: Nymphalidae), which has been reconstructed from the previously published whole-genome Illumina sequencing data (Marcus et al., 2013). In all, 60.94 million 90-bp raw reads were downloaded from the Sequence Read Archive (SRA) of GenBank (Accession number: SRR1057613), and quality-trimmed with default parameters using CLC Genomics Workbench v7.0.4 (CLC Bio, Aarhus, Denmark). The resultant 60.53 million trimmed reads were then used for reconstructing the mitochondrial genome with MITObim v1.7 (Hahn et al., 2013); the mitochondrial genome of Heliconius melpomene melpomene (GenBank: HE579083; The Heliconius Genome Consortium, 2012) was used as the initial reference. A total of 3,12,298 individual mitochondrial reads yielded an average coverage of 1830. The annotation was performed in GENEIOUS R7 (Biomatters Ltd., Auckland, New Zealand) by using the MITOS Web Server (Bernt et al., 2013) and the tRNAscan-SE Search Server (Lowe & Eddy, 1997; Schattner et al., 2005), and by comparing with other lepidopteran mitochondrial genomes. The organization of the H. pachinus mitochondrial genome is shown in Table 1. The circular genome was 15,369 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. The nucleotide composition is highly asymmetric (39.2% A, 42.0% T, Correspondence: Gui-Fang Zhao, College of Life Sciences, Northwest University, 229 Northern Taibai Road, Xi’an, Shaanxi Province 710069, People’s Republic of China. Tel: +86 29 8830 5264. Fax: +86 29 8830 3572. E-mail: [email protected]
History Received 20 June 2014 Accepted 27 June 2014 Published online 4 August 2014
Table 1. Annotation of the complete mitochondrial genome of H. pachinus. Position Gene
Size (bp)
tRNA-Met tRNA-Ile tRNA-Gln ND2 tRNA-Trp tRNA-Cys tRNA-Tyr COI tRNA-Leu(UUR) COII tRNA-Lys tRNA-Asp ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Ala tRNA-Arg tRNA-Asn tRNA-Ser(AGN) tRNA-Glu tRNA-Phe ND5 tRNA-His ND4 ND4L tRNA-Thr tRNA-Pro ND6 Cytb
68 1 68 64 69 132 69 130 198 1011 257 1267 65 1271 1335 65 1348 1412 66 1413 1478 1531 1481 3011 67 3012 3078 676 3079 3754 71 3755 3825 67 3827 3893 165 3894 4058 678 4052 4729 786 4729 5514 65 5517 5581 354 5582 5935 67 5934 6000 62 6000 6061 65 6062 6126 62 6125 6186 65 6197 6261 66 6268 6333 1734 6333 8066 69 8067 8135 1336 8139 9474 282 9474 9755 64 9758 9821 66 9822 9887 531 9890 10,420 1149 10,433 11,581
Start
Stop
Codons IGS (bp) Anticodon Start Stop Direction 0 0 3 58 3 12 0 2 0 0 0 1 0 5 1 2 0 2 1 0 2 10 6 1 0 3 1 2 0 2 12
CAT GAT TTG ATT TAA TCA GCA GTA CGA T(aa) TAA ATG T(aa) CTT GTC ATT TAA ATG TAA ATG TAA TCC ATT TAG TGC TCG GTT GCT TTC GAA ATT TAA GTG ATG T(aa) ATG TAA TGT TGG ATT TAA ATG TAA
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
(continued )
2
Z.-H. Huang et al.
Mitochondrial DNA, Early Online: 1–2
been deposited into GenBank under the accession number KM014809.
Table 1. Continued Position Gene
Size (bp)
Start
Stop
tRNA-Ser(UCN) 65 11,580 11,644 ND1 939 11,662 12,600 (CUN) 68 12,601 12,668 tRNA-Leu 16S rRNA 1380 12,669 14,048 tRNA-Val 67 14,049 14,115 12S rRNA 775 14,116 14,890 D-loop 479 14,891 15,369
Codons IGS (bp) Anticodon Start Stop Direction 2 17 0 0 0 0 0
TGA TTG TAA TAG TAC
F R R R R R NC
Downloaded by [Deakin University Library] at 17:36 05 November 2015
IGS denotes the length of the intergenic spacer region, for which negative numbers indicate nucleotide overlapping between adjacent genes. T(aa) denotes that the TAA stop codon is presumed to be completed by the addition of 3’ A residues to the mRNA. F, R and NC denote Forward, Reverse and Non-Coding, respectively.
7.7% G, and 11.1% C) with an overall GC content of 18.8%. The PCGs, tRNAs, rRNAs and the non-coding DNA account for 72.69% (11,172 bp), 9.46% (1453 bp), 14.02% (2155 bp) and 3.83% (589 bp) of the whole genome, respectively. PCGs are mostly initiated with either the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8) or the TTG codon (ND1). The COI gene may use the unusual CGA as its initiation codon, as suggested for many other lepidopteran species, e.g. Cupido argiades (Zhang et al., 2013), Danaus plexippus (Servı´n-Garciduen˜as & Martı´nez-Romero, 2014) and Grapholita molesta (Gong et al., 2012). Nine PCGs (ND1, ND2, ND4L, ND5, ND6, COIII, Cytb, ATP6 & ATP8) harbor the typical termination codon TAA, one PCG (ND3) terminated with TAG, while the other three PCGs (COI, COII & ND4) have an incomplete termination codon T. The 22 tRNAs ranged in size from 62 to 71 bp, with 14 of them coded on the majority strand. The 2 rRNAs were 775 bp (12S rRNA) and 1380 bp (16S rRNA) in length, with an AT content of 84.1% and 85.6%, respectively. The D-loop or control region was 479 bp long with an AT content of 91.7%, and was located between 12S rRNA and tRNA-Met. There were nine instances of intergenic overlapping regions ranging from 1 to 5 bp, and 13 instances of intergenic spacer regions ranging from 1 to 58 bp in length. The annotated mitochondrial genome sequence of H. pachinus has
Acknowledgements The authors thank Dr. Z.-Q. Qian for his assistance in manuscript preparation.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Gong Y-J, Shi B-C, Kang Z-J, Zhang F, Wei S-J. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucl Acids Res 41:e129. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–64. Marcus KR, Matthew HEB, Nicholas CG, Jason GR, Zhang W, Rob KJ, Durrell KD, Sean MP. (2013). Hybridization reveals the evolving genomic architecture of speciation. Cell Rep 5:666–77. Powell JA. (2003). Lepidoptera (moth and butterflies). In: Resh VH, Carde´ RT, editors. Encyclopedia of Insects. San Diego: Academic Press. p 631–64. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. Servı´n-Garciduen˜as LE, Martı´nez-Romero E. (2014). Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae). Mitochondr DNA, doi: 10.3109/ 19401736.2013.809441. The Heliconius Genome Consortium. (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94–8. Zhang L, Huang D, Sun X, Hao J, Hao J, Peng C, Yang Q. (2013). The complete mitochondrial genome of Cupido argiades (Lepidoptera: Lycaenidae). Mitochondrial DNA 24:475–7.
