http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913163
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the mulberry white caterpillar Rondotia menciana (Lepidoptera: Bombycidae) Min Jee Kim1, Jumin Jun2, and Iksoo Kim1 College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea and 2Wildlife Genetic Resources Center, National Institute of Biological Resources, Incheon, Republic of Korea
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
1
Abstract
Keywords
The mulberry white caterpillar, Rondotia menciana, belongs to the lepidopteran family Bombycidae, in which the domestic silkworm, Bombyx mori is included. In this study, we describe the complete mitochondrial genome of R. menciana in terms of general genomic features and characteristic features found in the A+T-rich region. The 15,364 bp long genome consisted of a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and 1 major non-coding A+T-rich region, with the typical arrangement found in Lepidoptera. Twelve of the 13 PCGs started with typical ATN codons, except for the COI, which began with CGA and twelve of 13 PCGs had complete stop codons, except for the COII, which ended with a single T. The 360 bp long A+T-rich region harbored the conserved sequence blocks typically found in lepidopteran insects. Additionally, the A+T-rich region of R. menciana contained one tRNAMet-like structure, which had a proper anticodon and secondary structure.
A+T-rich region, mitochondrial genome, Rondotia menciana
The mulberry white caterpillar, Rondotia menciana, belongs to Bombycidae, which includes the domestic silkworm, Bombyx mori in the lepidopteran superfamily Bombycoidea. The species has a wing expanse of 35 mm, with a characteristic dark stripe at the median cell in the forewing (Park et al., 1999). This species is distributed in Korea, China, Japan, and India and occurs from early October to early November in Korea (Park et al., 1999). Partially due to a close relationship to B. mori as the withinsubfamilial species, R. menciana has often been the subject of metabolic studies, as it commonly feeds on mulberry leaves (e.g. Hirayama et al., 2013). The complete mitochondrial genome (mitogenome) sequences of Bombycidae are available only for two species (B. mori and B. mandarina) with a few additional geographic strains (Sima et al., 2013). Thus, more mitogenome sequences of Bombycidae are essential to conduct mitogenome-based phylogeny and to understand the genomic evolution of the family. Thus, in this study, we sequenced the complete mitogenome of R. menciana collected in Korea. Three overlapping long fragments (COI – ND4 for LF1, ND5 – lrRNA for LF2, and lrRNA – COI for LF3) were amplified (Figure 1A) using three sets of Lepidoptera-specific primers (Kim et al., 2012) to sequence R. menciana mitogenome. These long fragments were used as templates for 26 short fragments
Correspondence: I. Kim, Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 500757, Republic of Korea. Tel: +82 625305117. Fax: +82 62 530 2079. E-mail: [email protected]
History Received 3 April 2014 Accepted 5 April 2014 Published online 29 April 2014
(SF1 – SF26). The other experimental methods used have been described in detail elsewhere (Kim et al., 2011, 2012). The 15,364 bp long complete mitogenome of R. menciana (GenBank accession number KJ647172) consisted of 2 rRNAs, 22 tRNAs, 13 protein-coding genes (PCGs), and 1 major non-coding region, referred to as the A+T-rich region. Arrangement of the R. menciana mitogenome is identical to the typical lepidopteran specific arrangement found in the majority of Lepidoptera including other bombycoid species (Kim et al., 2013; Li et al., 2010; Wan et al., 2013). Twelve of the 13 PCGs started with typical ATN codons (data not shown), but the COI began with CGA (arginine). Twelve of 13 PCGs had a complete stop codon, but COII had T as a stop codon (data not shown). A total of 167 intergenic spacer sequences were found, spreading over 18 regions, with the sizes 1 to 54 bp (Figure 1A). The longest one, located between tRNAGln and ND2, has been suggested to originate by duplication of a partial ND2 due to its high sequence similarity to the neighboring ND2 (Kim et al., 2010). Genes overlapped in a total of 24 bp in six locations, ranging in size from 1-8 bp. The 360 bp long A+T-rich region displayed several Lepidoptera-specific features, such as the ATAGA motif and adjacent poly-T stretch, microsatellite-A/T repeat, A/T-repeat precedent ATTTA, and a poly-A stretch (Figure 1B). In addition, a tRNAMet-like structure was found in the A+T-rich region of the R. menciana mitogenome (Figure 1C). It had a proper anticodon (TAT), mostly matched-stems, and conserved lengths for aminoacyl stem (7 bp), anticodon stem (5 bp), and anticodon loop (7 bp), but the functionality in its respective amino acid transfers remain uncertain.
M. J. Kim et al. O (1)
I (4)
I (2)
G
(6
I (10)
ND5 (1740)
ND (13 4 41)
I (1) I (2) I (1) I (10) I (27)
H (6 6)
(A)
) F (68 4) E (6 69) S( 68) N ( 3)
6)
CO III (79 2) ATP 6 (67 8) ATP8 (16 2)
4L ND
I (3)
T
1
6 ND L F2
O (1)
) 91 (2
Rondotia menciana
D (66) K (71)
) I (2) (65 66) ( P
(53
1)
I (7)
CytB (1155)
Mitochondrial genome 15,364 bp
82) COII (6
S* (68)
I (8) I (17)
ND1 (939 )
67)
L* (
6) 53 1 ( I CO
LF 3
M (68)
I (65)
)
Q (69)
)
)
ND2 (101 4)
)
I (1)
(1 3
(66
W
(67
Y
(6
70)
V
C
L(
97
775
O (8) I (7)
( NA srR
I (9)
lrR
NA
(6 5) 4)
O (5)
I (2)
LF
O (7)
egion ri c h r A+T- 360) (
Figure 1. Circular map of the Rondotia menciana mitochondrial genome, with the sequences of the A+T-rich region and tRNAMet-like structure. (A) Circular map. Abbreviations for the genes are: COI, COII and COIII refer to the cytochrome oxidase subunits, CytB refers to cytochrome b, and ND1–6 refers to NADH dehydrogenase components. tRNAs are denoted as one-letter symbols in accordance with the IUPAC-IUB single-letter amino acid codes. The one-letter symbols L, L*, S and S* denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN), and tRNASer(UCN), respectively. SF and LF refer to short and long fragments, respectively. The R. menciana mitogenome was sequenced by 26 overlapping fragments (SF1SF26) shown as single lines within a circle using three LFs as templates. Gene names that are not underlined indicate a clockwise direction of transcription, whereas those underlined indicate a counter-clockwise direction. I and O, respectively indicate overlapping and intergenic spacer sequence. Values in parenthesis indicate the size of gene, overlapping sequences, and intergenic spacer sequence. (B) Sequences of 360 bp long A+T-rich region. The nucleotides with a shaded box indicate the conserved motif, ATAGA, the poly-T stretch, the conserved ATTTA sequence precedent to microsatellite A/Trepeat, microsatellite A/T-repeat, and poly-A stretch. Microsatellite-A/T repeats are italicized and bold-faced. tRNAMet-like sequence is underlined. (C) Secondary structure of tRNAMet-like structure found in the A+T-rich region. The nucleotide position is indicated at the beginning and end sites of the structure. Bar (-) indicates Watson–Crick and dot () indicates G-U base pairing, respectively.
Mitochondrial DNA, Early Online: 1–3
(6 4) R ) (70 35 A 3( ND
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
2
I (54) O (2)
(B) 15,005-
TTTAATGTAACTTTTTTTGCATAGATCTTTTTTTTTTTTTTTTTATAATAAAATATTTAA TATAAGTTATTAAACTTTTAATATTATCCCTCTCTTATTTTCATAATATTCTAGTTTAAA TAAAAAATCAATATTGAAATTTCAATATTCTTTAAAATTAAAAAATAATAATATAATTAA TCTTAATTTTTTAATAATTTATTGTATATATATATATATTAATATAATAAATAATTTAAT tRNAMet-like structure
TTATATATATATATATTAATTAATTAAAAATTTAATATGTATATATATAAATTGAATAAA AATTATTTAAATATAACCATAAACCGTAGGTAATTTTTTTTCATTAAATAAAAAAAA -15,364 A -3’ 15,290 U U A A U U G A U U A A U AA A A U UU A AU A A UU A U AU U U A A U AA U U AA A U A U AA A U AA U UA U A UA U U U A A U A A A U U U UAU 5’ 15,215- A
(C)
Declaration of interest
References
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the manuscript. This research was supported by a research grant from the National Institute of Biological Resources, ‘‘Origin of Biological Diversity of Korea: Molecular Phylogenetic Analyses of Major Korean Taxa’’ awarded to Iksoo Kim.
Hirayama C, Ono H, Meng Y, Shimada T, Daimon T. (2013). Flavonoids from the cocoon of Rondotia menciana. Phytochemistry 94:108–12. Kim MJ, Choi S-W, Kim I. (2013). Complete mitochondrial genome of the larch hawk moth, Sphinx morio (Lepidoptera: Sphingidae). Mitochondrial DNA 24:622–4.
DOI: 10.3109/19401736.2014.913163
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
Kim MJ, Kang AR, Jeong HC, Kim K-G, Kim I. (2011). Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phylogenet Evol 61:436–45. Kim JS, Park JS, Kim MJ, Kang PD, Kim SG, Jin BR, Han YS, Kim I. (2012). Complete nucleotide sequence and organization of the mitochondrial genome of eri-silkworm, Samia cynthia ricini (Lepidoptera: Saturniidae). J Asia Pac Entomol 15:162–73. Kim MJ, Wan X, Kim KG, Hwang JS, Kim I. (2010). Complete nucleotide sequence and organization of the mitochondrial genome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol 9:735–54.
Mitogenome of R. menciana
3
Li YP, Wu S, Shi SL, Liu YQ, Pan MH, Dai FY, Lu C, Xiang ZH. (2010). Mitochondrial genome nucleotide substitution pattern between domesticated silkmoth, Bombyx mori and its wild ancestors, Chinese Bombyx mandarina and Japanese Bombyx mandarina. Genet Mol Biol 33: 186–9. Park KT, Kim SS, Tshistjakov YA, Kwon YD. (1999). Illustrated catalogue of moths in Korea (I). Seoul: Junghaens-Sa. Sima Y-H, Chen M, Yao R, Li Y-P, Liu T, Jin X, Wang L, et al. (2013). The complete mitochondrial genome of the Ailanthus silkmoth, Samia cynthia cynthia (Lepidoptera: Saturniidae). Gene 339:309–17. Wan X, Kim MJ, Kim I. (2013). Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. Mol Biol Rep 40:6333–49.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the mulberry white caterpillar Rondotia menciana (Lepidoptera: Bombycidae) Min Jee Kim1, Jumin Jun2, and Iksoo Kim1 College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea and 2Wildlife Genetic Resources Center, National Institute of Biological Resources, Incheon, Republic of Korea
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
1
Abstract
Keywords
The mulberry white caterpillar, Rondotia menciana, belongs to the lepidopteran family Bombycidae, in which the domestic silkworm, Bombyx mori is included. In this study, we describe the complete mitochondrial genome of R. menciana in terms of general genomic features and characteristic features found in the A+T-rich region. The 15,364 bp long genome consisted of a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and 1 major non-coding A+T-rich region, with the typical arrangement found in Lepidoptera. Twelve of the 13 PCGs started with typical ATN codons, except for the COI, which began with CGA and twelve of 13 PCGs had complete stop codons, except for the COII, which ended with a single T. The 360 bp long A+T-rich region harbored the conserved sequence blocks typically found in lepidopteran insects. Additionally, the A+T-rich region of R. menciana contained one tRNAMet-like structure, which had a proper anticodon and secondary structure.
A+T-rich region, mitochondrial genome, Rondotia menciana
The mulberry white caterpillar, Rondotia menciana, belongs to Bombycidae, which includes the domestic silkworm, Bombyx mori in the lepidopteran superfamily Bombycoidea. The species has a wing expanse of 35 mm, with a characteristic dark stripe at the median cell in the forewing (Park et al., 1999). This species is distributed in Korea, China, Japan, and India and occurs from early October to early November in Korea (Park et al., 1999). Partially due to a close relationship to B. mori as the withinsubfamilial species, R. menciana has often been the subject of metabolic studies, as it commonly feeds on mulberry leaves (e.g. Hirayama et al., 2013). The complete mitochondrial genome (mitogenome) sequences of Bombycidae are available only for two species (B. mori and B. mandarina) with a few additional geographic strains (Sima et al., 2013). Thus, more mitogenome sequences of Bombycidae are essential to conduct mitogenome-based phylogeny and to understand the genomic evolution of the family. Thus, in this study, we sequenced the complete mitogenome of R. menciana collected in Korea. Three overlapping long fragments (COI – ND4 for LF1, ND5 – lrRNA for LF2, and lrRNA – COI for LF3) were amplified (Figure 1A) using three sets of Lepidoptera-specific primers (Kim et al., 2012) to sequence R. menciana mitogenome. These long fragments were used as templates for 26 short fragments
Correspondence: I. Kim, Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 500757, Republic of Korea. Tel: +82 625305117. Fax: +82 62 530 2079. E-mail: [email protected]
History Received 3 April 2014 Accepted 5 April 2014 Published online 29 April 2014
(SF1 – SF26). The other experimental methods used have been described in detail elsewhere (Kim et al., 2011, 2012). The 15,364 bp long complete mitogenome of R. menciana (GenBank accession number KJ647172) consisted of 2 rRNAs, 22 tRNAs, 13 protein-coding genes (PCGs), and 1 major non-coding region, referred to as the A+T-rich region. Arrangement of the R. menciana mitogenome is identical to the typical lepidopteran specific arrangement found in the majority of Lepidoptera including other bombycoid species (Kim et al., 2013; Li et al., 2010; Wan et al., 2013). Twelve of the 13 PCGs started with typical ATN codons (data not shown), but the COI began with CGA (arginine). Twelve of 13 PCGs had a complete stop codon, but COII had T as a stop codon (data not shown). A total of 167 intergenic spacer sequences were found, spreading over 18 regions, with the sizes 1 to 54 bp (Figure 1A). The longest one, located between tRNAGln and ND2, has been suggested to originate by duplication of a partial ND2 due to its high sequence similarity to the neighboring ND2 (Kim et al., 2010). Genes overlapped in a total of 24 bp in six locations, ranging in size from 1-8 bp. The 360 bp long A+T-rich region displayed several Lepidoptera-specific features, such as the ATAGA motif and adjacent poly-T stretch, microsatellite-A/T repeat, A/T-repeat precedent ATTTA, and a poly-A stretch (Figure 1B). In addition, a tRNAMet-like structure was found in the A+T-rich region of the R. menciana mitogenome (Figure 1C). It had a proper anticodon (TAT), mostly matched-stems, and conserved lengths for aminoacyl stem (7 bp), anticodon stem (5 bp), and anticodon loop (7 bp), but the functionality in its respective amino acid transfers remain uncertain.
M. J. Kim et al. O (1)
I (4)
I (2)
G
(6
I (10)
ND5 (1740)
ND (13 4 41)
I (1) I (2) I (1) I (10) I (27)
H (6 6)
(A)
) F (68 4) E (6 69) S( 68) N ( 3)
6)
CO III (79 2) ATP 6 (67 8) ATP8 (16 2)
4L ND
I (3)
T
1
6 ND L F2
O (1)
) 91 (2
Rondotia menciana
D (66) K (71)
) I (2) (65 66) ( P
(53
1)
I (7)
CytB (1155)
Mitochondrial genome 15,364 bp
82) COII (6
S* (68)
I (8) I (17)
ND1 (939 )
67)
L* (
6) 53 1 ( I CO
LF 3
M (68)
I (65)
)
Q (69)
)
)
ND2 (101 4)
)
I (1)
(1 3
(66
W
(67
Y
(6
70)
V
C
L(
97
775
O (8) I (7)
( NA srR
I (9)
lrR
NA
(6 5) 4)
O (5)
I (2)
LF
O (7)
egion ri c h r A+T- 360) (
Figure 1. Circular map of the Rondotia menciana mitochondrial genome, with the sequences of the A+T-rich region and tRNAMet-like structure. (A) Circular map. Abbreviations for the genes are: COI, COII and COIII refer to the cytochrome oxidase subunits, CytB refers to cytochrome b, and ND1–6 refers to NADH dehydrogenase components. tRNAs are denoted as one-letter symbols in accordance with the IUPAC-IUB single-letter amino acid codes. The one-letter symbols L, L*, S and S* denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN), and tRNASer(UCN), respectively. SF and LF refer to short and long fragments, respectively. The R. menciana mitogenome was sequenced by 26 overlapping fragments (SF1SF26) shown as single lines within a circle using three LFs as templates. Gene names that are not underlined indicate a clockwise direction of transcription, whereas those underlined indicate a counter-clockwise direction. I and O, respectively indicate overlapping and intergenic spacer sequence. Values in parenthesis indicate the size of gene, overlapping sequences, and intergenic spacer sequence. (B) Sequences of 360 bp long A+T-rich region. The nucleotides with a shaded box indicate the conserved motif, ATAGA, the poly-T stretch, the conserved ATTTA sequence precedent to microsatellite A/Trepeat, microsatellite A/T-repeat, and poly-A stretch. Microsatellite-A/T repeats are italicized and bold-faced. tRNAMet-like sequence is underlined. (C) Secondary structure of tRNAMet-like structure found in the A+T-rich region. The nucleotide position is indicated at the beginning and end sites of the structure. Bar (-) indicates Watson–Crick and dot () indicates G-U base pairing, respectively.
Mitochondrial DNA, Early Online: 1–3
(6 4) R ) (70 35 A 3( ND
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
2
I (54) O (2)
(B) 15,005-
TTTAATGTAACTTTTTTTGCATAGATCTTTTTTTTTTTTTTTTTATAATAAAATATTTAA TATAAGTTATTAAACTTTTAATATTATCCCTCTCTTATTTTCATAATATTCTAGTTTAAA TAAAAAATCAATATTGAAATTTCAATATTCTTTAAAATTAAAAAATAATAATATAATTAA TCTTAATTTTTTAATAATTTATTGTATATATATATATATTAATATAATAAATAATTTAAT tRNAMet-like structure
TTATATATATATATATTAATTAATTAAAAATTTAATATGTATATATATAAATTGAATAAA AATTATTTAAATATAACCATAAACCGTAGGTAATTTTTTTTCATTAAATAAAAAAAA -15,364 A -3’ 15,290 U U A A U U G A U U A A U AA A A U UU A AU A A UU A U AU U U A A U AA U U AA A U A U AA A U AA U UA U A UA U U U A A U A A A U U U UAU 5’ 15,215- A
(C)
Declaration of interest
References
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the manuscript. This research was supported by a research grant from the National Institute of Biological Resources, ‘‘Origin of Biological Diversity of Korea: Molecular Phylogenetic Analyses of Major Korean Taxa’’ awarded to Iksoo Kim.
Hirayama C, Ono H, Meng Y, Shimada T, Daimon T. (2013). Flavonoids from the cocoon of Rondotia menciana. Phytochemistry 94:108–12. Kim MJ, Choi S-W, Kim I. (2013). Complete mitochondrial genome of the larch hawk moth, Sphinx morio (Lepidoptera: Sphingidae). Mitochondrial DNA 24:622–4.
DOI: 10.3109/19401736.2014.913163
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 08/06/15 For personal use only.
Kim MJ, Kang AR, Jeong HC, Kim K-G, Kim I. (2011). Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phylogenet Evol 61:436–45. Kim JS, Park JS, Kim MJ, Kang PD, Kim SG, Jin BR, Han YS, Kim I. (2012). Complete nucleotide sequence and organization of the mitochondrial genome of eri-silkworm, Samia cynthia ricini (Lepidoptera: Saturniidae). J Asia Pac Entomol 15:162–73. Kim MJ, Wan X, Kim KG, Hwang JS, Kim I. (2010). Complete nucleotide sequence and organization of the mitochondrial genome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol 9:735–54.
Mitogenome of R. menciana
3
Li YP, Wu S, Shi SL, Liu YQ, Pan MH, Dai FY, Lu C, Xiang ZH. (2010). Mitochondrial genome nucleotide substitution pattern between domesticated silkmoth, Bombyx mori and its wild ancestors, Chinese Bombyx mandarina and Japanese Bombyx mandarina. Genet Mol Biol 33: 186–9. Park KT, Kim SS, Tshistjakov YA, Kwon YD. (1999). Illustrated catalogue of moths in Korea (I). Seoul: Junghaens-Sa. Sima Y-H, Chen M, Yao R, Li Y-P, Liu T, Jin X, Wang L, et al. (2013). The complete mitochondrial genome of the Ailanthus silkmoth, Samia cynthia cynthia (Lepidoptera: Saturniidae). Gene 339:309–17. Wan X, Kim MJ, Kim I. (2013). Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. Mol Biol Rep 40:6333–49.
