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Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae) a
a
Lili Shao , QianQian Sun & JiaSheng Hao
a
a
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China Published online: 27 Jan 2014.
Click for updates To cite this article: Lili Shao, QianQian Sun & JiaSheng Hao (2014): The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae), Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis To link to this article: http://dx.doi.org/10.3109/19401736.2013.845759
PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http:// www.tandfonline.com/page/terms-and-conditions
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.845759
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae) Lili Shao, QianQian Sun, and JiaSheng Hao
Downloaded by [University of Manitoba Libraries] at 05:28 05 September 2015
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China
Abstract
Keywords
The mitochondrial genome (mitogenome) of Parara guttata (Hesperiidae: Hesperiinae) is a circular molecule of 15,441 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CGA and GTG as their start codons, respectively. Some PCGs harbor TAG (ND1) or incomplete termination codon T (COI, COII, ND5, ND4), while others use standard TAA as their termination codons. The 411-bp long AT-rich region contains a conserved motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)5 element preceded by the ATTTA motif.
Hesperiidae, Hesperiinae, mitochondrial genome, Parara guttata
Hesperiidae is one of the major groups in lepidopterans, encompassing about 3600 described species (Gorbunov, 2001). Due to its special morphological and behavioral characteristics, the skippers are commonly proposed to represent a separate group that is distinct from butterflies/moths in lepidopterans (Chiba & Eliot, 1991; Chou, 1998). In recent decades, mitochondrial DNA has been widely used as an informative molecular marker for diverse evolutionary studies (Boore, 1999; Krzywinski et al., 2006). However, within Hesperiidae, only three complete mitogenomes have been reported so far (Hao et al., 2012; Wang et al., 2013). Here, we present the complete mitogenome of another hesperid species, namely Parara guttata, aiming to provide more molecular data for the studies of Hesperiidae phylogeny. Whole mitogenome of P. guttata was amplified with 10 pairs of primers and completely sequenced by procedures of Sangon (China). The P. guttata mitogenoeme is 15,441 bp in length, which is the shortest in Hesperiidae determined so far. The whole genome contained 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 putative tRNA genes and 1 non-coding AT-rich region (Table 1). Like those of the overwhelming majority of other lepidopterans, the nucleotide composition of the mitogenome is also remarkably AT biased (80.6%). Total 27 overlapping nucleotides are dispersed in 9 regions throughout the whole genome, with each region ranging from 1 to 8 bp; besides, 15 inter-genic spacer sequences totaling 269 bp are ranged from 1 to 99 bp and spread over the whole genome, with the longest one located between tRNAGln and ND2. All PCGs utilize the standard mitochondrial start codon ATN, except for COI and ND1 which use CGA and GTG as their start
Correspondence: Professor Jiasheng Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, China. Tel: +86 553 3818721. Fax: +86 553 3869571. E-mail: [email protected]
History Received 3 September 2013 Revised 9 September 2013 Accepted 14 September 2013 Published online 24 January 2014
Table 1. Organization of the Parnara guttata mitogenome.
Gene tRNAMet tRNAlle 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 Cyt b tRNASer ND1
Direction
Position
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
1–67 68–132 134–202 302–1303 1302–1369 1362–1426 1434–1497 1514–3044 3045–3111 3112–3790 3791–3861 3886–3952 3953–4120 4114–4791 4791–5579 5582–5647 5649–6002 6005–6072 6072–6139 6137–6204 6234–6294 6346–6410 6409–6473 6474–8211 8212–8279 8280–9621 9622–9897 9900–9965 9966–10,032 10,035–10,568 10,568–11,719 11,718–11,785 11,804–12,745
30 Start Size spacer codon 67 65 69 1002 68 67 64 1532 67 679 71 67 168 678 789 66 354 68 68 68 61 65 65 1738 68 1337 276 66 67 534 1152 68 942
0 1 10 99 2 8 7 15 0 0 0 26 0 7 1 2 1 2 1 3 29 51 2 0 0 0 0 2 0 2 1 2 18
ATA
Stop codon
TAA
CGA T-tRNA ATA T-tRNA
ATC ATG ATG
TAA TAA TAA
ATT
TAA
ATT T-tRNA ATG T-tRNA ATG TAA
ATA ATG
TAA TAA
GTG
TAG
(continued )
2
L. Shao et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene tRNALeu(CUN) RrnL tRNAVal rrnS A þ T-rich region
Direction R R R R
Position
Start 30 Size spacer codon
12,750–12,816 67 12,817–14,184 1368 14,185–14,252 68 14,253–15,030 778 15,031–15,441 411
Stop codon
4 0 0 0 0
Downloaded by [University of Manitoba Libraries] at 05:28 05 September 2015
Direction of the genes is presented as F for forward and R for reverse direction.
codons, respectively. The start codon CGA of COI gene is well conserved, representing a synapomorphy characteristic of Lepidoptera (Gong et al., 2012; Kim et al., 2011), though the unconventional start codon GTG is also found in other lepidopteran mitogenomes, for example ND1 of Ochrogaster lunifer (Salvato et al., 2008) and COII of Sasakia charonda (Hakozaki, unpublished). Nine of the PCGs stop with codon TAN, while the COI, COII, ND5 and ND4 genes stop with the single nucleotide T (Table 1). All of the 22 tRNA genes, ranging from 61 to 71 bp, have a typical cloverleaf structure except for tRNASer(AGN), which loses its D-stem pairings in the DHU arm, and this case is the same with other determined lepidopterans (Kim et al., 2011; Park et al., 2012). The lrRNA and srRNA genes are 1368 bp and 778 bp, with the AT contents of 84.5% and 85.1%, respectively. The 411-bp long AT-rich region exhibits the highest AT content (90.8%) of the whole genome. Some structures characteristic of Lepidoptera (Kim et al., 2010), such as the repeated single nucleotides (T)2–9, (A)2–10 and the motif ATAGA followed by 19 bp poly-T stretches are presented in the region. Besides, a microsatellite-like (TA)5 element preceded by the ATTTA motif is also detected in the region. Nucleotide sequence accession number. The complete genome sequence of Parara guttata has been assigned GenBank accession number JX101619.
Declaration of interest The authors report no conflicts of interests. The authors alone are responsible for the content and writing of this article. This work was supported by the National Science Foundation of China (Grant No.
41172004), the Opening Funds from the State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (Grant No. 104143), and the Program for Innovative Research Team in Anhui Normal University.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Chiba H, Eliot JN. (1991). A review of the genus Parnara Moore (Lepidoptera: Hesperiidae), with special reference to the Asian species. Tyo to Ga 42:179–94. Chou I. (1998). Classification and identification of Chinese butterflies. Zhengzhou, China: Henan Scientific and Technological Publishing House. Gong YJ, Shi BC, Kang ZJ, Zhang F, Wei SJ. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Gorbunov PY. (2001). The butterflies of Russia: Classification, genitalia, keys for identification (Lepidoptera: Hesperioidea and Papilionoidea), Ph.D. thesis, Tezis Izdatel Stvo, Ekaterinburg, Russia. Hao JS, Sun QQ, Zhao HB, Sun XY, Gai YH, Yang Q. (2012). The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genom 2012:328049. doi: http://dx.doi.org/10.1155/2012/328049. Kim MJ, Kang AR, Jeong HC, Kim KG, 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 MJ, Wan X, Kim KG, Hwang JS, Kim I. (2010). Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol 9:735–54. Krzywinski J, Grushko OG, Besansky NJ. (2006). Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39:417–23. Park JS, Cho Y, Kim MJ, Nam SH, Kim I. (2012). Description of complete mitochondrial genome of the black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species. J Asia Pac Entomol 15:331–41. Salvato P, Simonato M, Battisti A, Negrisolo E. (2008). The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Gen 9:331. Wang AR, Jeong HC, Han YS, Kim I. (2013). The complete mitochondrial genome of the mountainous duskywing, Erynnis montanus (Lepidoptera: Hesperiidae): A new gene arrangement in Lepidoptera. Mitochondrial DNA. Available at: http://informahealthcare.com/doi/ abs/10.3109/19401736.2013.784752 (Accessed 16 April 2013).
Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae) a
a
Lili Shao , QianQian Sun & JiaSheng Hao
a
a
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China Published online: 27 Jan 2014.
Click for updates To cite this article: Lili Shao, QianQian Sun & JiaSheng Hao (2014): The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae), Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis To link to this article: http://dx.doi.org/10.3109/19401736.2013.845759
PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http:// www.tandfonline.com/page/terms-and-conditions
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.845759
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae) Lili Shao, QianQian Sun, and JiaSheng Hao
Downloaded by [University of Manitoba Libraries] at 05:28 05 September 2015
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China
Abstract
Keywords
The mitochondrial genome (mitogenome) of Parara guttata (Hesperiidae: Hesperiinae) is a circular molecule of 15,441 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CGA and GTG as their start codons, respectively. Some PCGs harbor TAG (ND1) or incomplete termination codon T (COI, COII, ND5, ND4), while others use standard TAA as their termination codons. The 411-bp long AT-rich region contains a conserved motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)5 element preceded by the ATTTA motif.
Hesperiidae, Hesperiinae, mitochondrial genome, Parara guttata
Hesperiidae is one of the major groups in lepidopterans, encompassing about 3600 described species (Gorbunov, 2001). Due to its special morphological and behavioral characteristics, the skippers are commonly proposed to represent a separate group that is distinct from butterflies/moths in lepidopterans (Chiba & Eliot, 1991; Chou, 1998). In recent decades, mitochondrial DNA has been widely used as an informative molecular marker for diverse evolutionary studies (Boore, 1999; Krzywinski et al., 2006). However, within Hesperiidae, only three complete mitogenomes have been reported so far (Hao et al., 2012; Wang et al., 2013). Here, we present the complete mitogenome of another hesperid species, namely Parara guttata, aiming to provide more molecular data for the studies of Hesperiidae phylogeny. Whole mitogenome of P. guttata was amplified with 10 pairs of primers and completely sequenced by procedures of Sangon (China). The P. guttata mitogenoeme is 15,441 bp in length, which is the shortest in Hesperiidae determined so far. The whole genome contained 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 putative tRNA genes and 1 non-coding AT-rich region (Table 1). Like those of the overwhelming majority of other lepidopterans, the nucleotide composition of the mitogenome is also remarkably AT biased (80.6%). Total 27 overlapping nucleotides are dispersed in 9 regions throughout the whole genome, with each region ranging from 1 to 8 bp; besides, 15 inter-genic spacer sequences totaling 269 bp are ranged from 1 to 99 bp and spread over the whole genome, with the longest one located between tRNAGln and ND2. All PCGs utilize the standard mitochondrial start codon ATN, except for COI and ND1 which use CGA and GTG as their start
Correspondence: Professor Jiasheng Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, China. Tel: +86 553 3818721. Fax: +86 553 3869571. E-mail: [email protected]
History Received 3 September 2013 Revised 9 September 2013 Accepted 14 September 2013 Published online 24 January 2014
Table 1. Organization of the Parnara guttata mitogenome.
Gene tRNAMet tRNAlle 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 Cyt b tRNASer ND1
Direction
Position
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
1–67 68–132 134–202 302–1303 1302–1369 1362–1426 1434–1497 1514–3044 3045–3111 3112–3790 3791–3861 3886–3952 3953–4120 4114–4791 4791–5579 5582–5647 5649–6002 6005–6072 6072–6139 6137–6204 6234–6294 6346–6410 6409–6473 6474–8211 8212–8279 8280–9621 9622–9897 9900–9965 9966–10,032 10,035–10,568 10,568–11,719 11,718–11,785 11,804–12,745
30 Start Size spacer codon 67 65 69 1002 68 67 64 1532 67 679 71 67 168 678 789 66 354 68 68 68 61 65 65 1738 68 1337 276 66 67 534 1152 68 942
0 1 10 99 2 8 7 15 0 0 0 26 0 7 1 2 1 2 1 3 29 51 2 0 0 0 0 2 0 2 1 2 18
ATA
Stop codon
TAA
CGA T-tRNA ATA T-tRNA
ATC ATG ATG
TAA TAA TAA
ATT
TAA
ATT T-tRNA ATG T-tRNA ATG TAA
ATA ATG
TAA TAA
GTG
TAG
(continued )
2
L. Shao et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene tRNALeu(CUN) RrnL tRNAVal rrnS A þ T-rich region
Direction R R R R
Position
Start 30 Size spacer codon
12,750–12,816 67 12,817–14,184 1368 14,185–14,252 68 14,253–15,030 778 15,031–15,441 411
Stop codon
4 0 0 0 0
Downloaded by [University of Manitoba Libraries] at 05:28 05 September 2015
Direction of the genes is presented as F for forward and R for reverse direction.
codons, respectively. The start codon CGA of COI gene is well conserved, representing a synapomorphy characteristic of Lepidoptera (Gong et al., 2012; Kim et al., 2011), though the unconventional start codon GTG is also found in other lepidopteran mitogenomes, for example ND1 of Ochrogaster lunifer (Salvato et al., 2008) and COII of Sasakia charonda (Hakozaki, unpublished). Nine of the PCGs stop with codon TAN, while the COI, COII, ND5 and ND4 genes stop with the single nucleotide T (Table 1). All of the 22 tRNA genes, ranging from 61 to 71 bp, have a typical cloverleaf structure except for tRNASer(AGN), which loses its D-stem pairings in the DHU arm, and this case is the same with other determined lepidopterans (Kim et al., 2011; Park et al., 2012). The lrRNA and srRNA genes are 1368 bp and 778 bp, with the AT contents of 84.5% and 85.1%, respectively. The 411-bp long AT-rich region exhibits the highest AT content (90.8%) of the whole genome. Some structures characteristic of Lepidoptera (Kim et al., 2010), such as the repeated single nucleotides (T)2–9, (A)2–10 and the motif ATAGA followed by 19 bp poly-T stretches are presented in the region. Besides, a microsatellite-like (TA)5 element preceded by the ATTTA motif is also detected in the region. Nucleotide sequence accession number. The complete genome sequence of Parara guttata has been assigned GenBank accession number JX101619.
Declaration of interest The authors report no conflicts of interests. The authors alone are responsible for the content and writing of this article. This work was supported by the National Science Foundation of China (Grant No.
41172004), the Opening Funds from the State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (Grant No. 104143), and the Program for Innovative Research Team in Anhui Normal University.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Chiba H, Eliot JN. (1991). A review of the genus Parnara Moore (Lepidoptera: Hesperiidae), with special reference to the Asian species. Tyo to Ga 42:179–94. Chou I. (1998). Classification and identification of Chinese butterflies. Zhengzhou, China: Henan Scientific and Technological Publishing House. Gong YJ, Shi BC, Kang ZJ, Zhang F, Wei SJ. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Gorbunov PY. (2001). The butterflies of Russia: Classification, genitalia, keys for identification (Lepidoptera: Hesperioidea and Papilionoidea), Ph.D. thesis, Tezis Izdatel Stvo, Ekaterinburg, Russia. Hao JS, Sun QQ, Zhao HB, Sun XY, Gai YH, Yang Q. (2012). The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genom 2012:328049. doi: http://dx.doi.org/10.1155/2012/328049. Kim MJ, Kang AR, Jeong HC, Kim KG, 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 MJ, Wan X, Kim KG, Hwang JS, Kim I. (2010). Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol 9:735–54. Krzywinski J, Grushko OG, Besansky NJ. (2006). Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39:417–23. Park JS, Cho Y, Kim MJ, Nam SH, Kim I. (2012). Description of complete mitochondrial genome of the black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species. J Asia Pac Entomol 15:331–41. Salvato P, Simonato M, Battisti A, Negrisolo E. (2008). The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Gen 9:331. Wang AR, Jeong HC, Han YS, Kim I. (2013). The complete mitochondrial genome of the mountainous duskywing, Erynnis montanus (Lepidoptera: Hesperiidae): A new gene arrangement in Lepidoptera. Mitochondrial DNA. Available at: http://informahealthcare.com/doi/ abs/10.3109/19401736.2013.784752 (Accessed 16 April 2013).
