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
Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae) Jiequn Yi, Shengquan Que, Tianrong Xin, Bin Xia & Zhiwen Zou To cite this article: Jiequn Yi, Shengquan Que, Tianrong Xin, Bin Xia & Zhiwen Zou (2014): Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.873926
Published online: 17 Jan 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Australian National University]
Date: 07 November 2015, At: 04:02
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873926
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae) Jiequn Yi1,2, Shengquan Que1,2, Tianrong Xin1,2, Bin Xia1,2, and Zhiwen Zou1 School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China and 2Institute of Life Science, Nanchang University, Nanchang, People’s Republic of China
Downloaded by [Australian National University] at 04:02 07 November 2015
1
Abstract
Keywords
To know the genetic structure and phylogeny status, the complete mitochondrial genome of Thitarodes pui was the first time to be sequenced. The genome was 15,064 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, as well as an AT rich region. The base composition of the genome was A (40.93%), T (39.80%), C (11.72%) and G (7.55%), with an AT content of 80.73%. It is interesting to that the COI would start with CGA. The tRNA order between ND2 and AT rich region was tRNAIle–tRNAGln–tRNAMet, which confirms the thesis that Thitarodes has the ancestral gene arrangement. It is surprised that AT-rich region was 287 bp in length and became the shortest in contrast to other insects of Hepialidae.
Control region, mitogenome, start codon, Thitarodes pui, tRNA order
In China, Ophiocordyceps sinensis (Berkeley) Saccardo is a special natural invigorant as well as a traditional medicine for thousands of years (Chu & Wang, 1985). As the host of Hirsutella sinensis, Thitarodes pui is precious to form the O. sinensis (Berkeley) Saccardo. It has a limited geographical distribution along the Nyainqentanglha Range and Hengduan Mountains of the Tibetan Plateau (Zou, 2009). At present, we know little about it, including its genetic structure and phylogeny status. In addition, climate change and habitat degradation caused the continuous reduction of T. pui over the past years. It is necessary to reserve its mitochondrial genome data as the natural resources.
History Received 5 December 2013 Accepted 7 December 2013 Published online 17 January 2014
The specimen of T. pui was collected from Mt. Segrila of Tibet, China. Total genomic DNA was extracted by the phenol– chloroform method. Eleven pairs of primers were designed to amplify the mitochondrial DNA. Major PCR products were directly sequenced. The remaining products were first cloned into a vector. The complete mitochondrial DNA of T. pui was 15,064 bp (KF908880), which was smaller than other insects of Hepialidae (Cao et al., 2012). It was composed of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 non-coding AT-rich region (Table 1).
Table 1. Characteristics of the mitochondrial genome of Thitarodes pui. Position Gene
Strandy Ile
tRNA tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr COI tRNALeu COII tRNALys tRNAAsp ATP8 ATP6
H L H H H L L H H H H H H H
From 1 86 164 234 1252 1310 1382 1451 2982 3052 3734 3804 3870 4025
Codon To 65 154 233 1253 1317 1376 1448 2981 3050 3733 3804 3869 4031 4702
Size (bp) 65 69 70 1020 66 67 67 1531 69 682 71 66 162 678
Start
Stop
ATT
TAA
CGA
T
ATG
T
ATC ATG
TAA TAA
Intergenic nucleotides* 20 9 0 2 8 5 2 0 1 0 1 0 7 1 (continued )
Correspondence: Zhiwen Zou, School of Life Sciences and Food Engineering, Nanchang University, Nanchang 330031, People’s Republic of China. Tel: +86 791 83969530. E-mail: [email protected]
2
J.-Q. Yi et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position
Downloaded by [Australian National University] at 04:02 07 November 2015
Gene COIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer ND1 tRNALeu 16S rRNA tRNAVal 12S rRNA AT-rich region
Codon
Strandy
From
To
Size (bp)
Start
Stop
Intergenic nucleotides*
H H H H H H H H L L L L L H L H H H L L L L L
4702 5493 5558 5910 5982 6055 6121 6184 6251 6318 8056 8124 9464 9760 9826 9893 10,417 11,569 11,653 12,586 12,660 13,941 14,001 14,778
5490 5556 5911 5978 6047 6120 6182 6248 6317 8055 8122 9464 9757 9825 9890 10,417 11,562 11,637 12,585 12,659 13,940 14,005 14,777 15,064
789 64 354 69 66 66 62 65 67 1738 67 1341 294 66 65 525 1146 69 933 74 1281 65 777 287
ATG
TAA
ATT
TAG
ATT
T
ATG ATG
TAA TAA
ATA ATG
TAA TAA
ATG
TAA
2 1 2 3 7 0 1 2 0 0 1 1 2 0 2 1 6 15 0 0 0 5 0
*Positive numbers indicate separation between neighboring genes and negative numbers indicate overlapping between different genes. yH and L represent heavy and light strands, respectively.
The overall base composition of the heavy strand was 40.93% A, 39.80% T, 11.72% C and 7.55% G, with an AT content of 80.73%. It is generally present in other Lepidoptera mitochondrial genomes (Jiang et al., 2009; Salvato et al., 2008). Relative position and transcription direction of all the mitochondrial genes were consistent with Drosophila yakuba (Clary & Wolstenholme, 1985). The 13 protein-coding genes were located on H-strand with the exception of ND5, ND4, ND4L and ND1. Major coding genes were encoded with the normal start codons (ATN). It is proved that COI could start with CGA and some mitochondrial genes end up with an incomplete stop codon. Twenty-two tRNA (8 on the L-strand) ranged in size from 62 to 74 bp and dispersed in mitogenome. The tRNA order between the AT-rich region and ND2 was tRNAIle–tRNAGln–tRNAMet, which is considered to be the ancestral type (Cha et al., 2007; Krzywinski et al., 2006). The 12S and 16SrRNAs were 777 and 1281 bp, respectively. They existed between tRNALeu and AT-rich region, separated by tRNAVal. Overlapped nucleotides were observed to range from 1 to 8 bp in nine locations while the total length of intergenic nucleotides is 79 bp. The AT-rich region is surprised, 287 bp in length, to be the shortest in Lepidoptera. This region is believed to be involved in the regulation of transcription and control of DNA replication (Zhang & Hewitt, 1997).
Declaration of interest The work was financially supported by the Natural Science Foundation of China Science (31160081), the National Key Technology R&D Program (2011BAI13B06) and Department of Education Fund (GJJ13104) of Jiangxi Province. The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Cao YQ, Ma C, Chen JY, Yang DR. (2012). The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: The ancestral gene arrangement in Lepidoptera. BMC genomics 13:276. Cha SY, Yoon HJ, Lee EM, Yoon MH, Hwang JS, Jin BR, Han YS, Kim I. (2007). The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene 392: 206–20. Chu HF, Wang LY. (1985). ‘‘Insect-Herb’’ versus Hepialids with descriptions of new genera and new species of Chinese Hepialidae. Sinozoology 3:121–34. Clary DO, Wolstenholme DR. (1985). The mitochondrial DNA molecule of Drosophila yakuba: Nucleotide sequence, gene organization, and genetic code. J Mol Evol 22:252–71. Jiang ST, Hong GY, Yu M, Li N, Yang Y, Liu YQ, Wei ZJ. (2009). Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). Int J Biol Sci 5:351–65. 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. Salvato P, Simonato M, Battisti A, Negrisolo E. (2008). The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics 9:331. Zhang DX, Hewitt GM. (1997). Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25:99–120. Zou ZW. (2009). On the insects of the genus Thitarodes in Mt. Sejila of Tibet. Guangzhou: Sun Yat-sen University. p 47–66.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae) Jiequn Yi, Shengquan Que, Tianrong Xin, Bin Xia & Zhiwen Zou To cite this article: Jiequn Yi, Shengquan Que, Tianrong Xin, Bin Xia & Zhiwen Zou (2014): Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.873926
Published online: 17 Jan 2014.
Submit your article to this journal
Article views: 21
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: [Australian National University]
Date: 07 November 2015, At: 04:02
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873926
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Thitarodes pui (Lepidoptera: Hepialidae) Jiequn Yi1,2, Shengquan Que1,2, Tianrong Xin1,2, Bin Xia1,2, and Zhiwen Zou1 School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China and 2Institute of Life Science, Nanchang University, Nanchang, People’s Republic of China
Downloaded by [Australian National University] at 04:02 07 November 2015
1
Abstract
Keywords
To know the genetic structure and phylogeny status, the complete mitochondrial genome of Thitarodes pui was the first time to be sequenced. The genome was 15,064 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, as well as an AT rich region. The base composition of the genome was A (40.93%), T (39.80%), C (11.72%) and G (7.55%), with an AT content of 80.73%. It is interesting to that the COI would start with CGA. The tRNA order between ND2 and AT rich region was tRNAIle–tRNAGln–tRNAMet, which confirms the thesis that Thitarodes has the ancestral gene arrangement. It is surprised that AT-rich region was 287 bp in length and became the shortest in contrast to other insects of Hepialidae.
Control region, mitogenome, start codon, Thitarodes pui, tRNA order
In China, Ophiocordyceps sinensis (Berkeley) Saccardo is a special natural invigorant as well as a traditional medicine for thousands of years (Chu & Wang, 1985). As the host of Hirsutella sinensis, Thitarodes pui is precious to form the O. sinensis (Berkeley) Saccardo. It has a limited geographical distribution along the Nyainqentanglha Range and Hengduan Mountains of the Tibetan Plateau (Zou, 2009). At present, we know little about it, including its genetic structure and phylogeny status. In addition, climate change and habitat degradation caused the continuous reduction of T. pui over the past years. It is necessary to reserve its mitochondrial genome data as the natural resources.
History Received 5 December 2013 Accepted 7 December 2013 Published online 17 January 2014
The specimen of T. pui was collected from Mt. Segrila of Tibet, China. Total genomic DNA was extracted by the phenol– chloroform method. Eleven pairs of primers were designed to amplify the mitochondrial DNA. Major PCR products were directly sequenced. The remaining products were first cloned into a vector. The complete mitochondrial DNA of T. pui was 15,064 bp (KF908880), which was smaller than other insects of Hepialidae (Cao et al., 2012). It was composed of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 non-coding AT-rich region (Table 1).
Table 1. Characteristics of the mitochondrial genome of Thitarodes pui. Position Gene
Strandy Ile
tRNA tRNAGln tRNAMet ND2 tRNATrp tRNACys tRNATyr COI tRNALeu COII tRNALys tRNAAsp ATP8 ATP6
H L H H H L L H H H H H H H
From 1 86 164 234 1252 1310 1382 1451 2982 3052 3734 3804 3870 4025
Codon To 65 154 233 1253 1317 1376 1448 2981 3050 3733 3804 3869 4031 4702
Size (bp) 65 69 70 1020 66 67 67 1531 69 682 71 66 162 678
Start
Stop
ATT
TAA
CGA
T
ATG
T
ATC ATG
TAA TAA
Intergenic nucleotides* 20 9 0 2 8 5 2 0 1 0 1 0 7 1 (continued )
Correspondence: Zhiwen Zou, School of Life Sciences and Food Engineering, Nanchang University, Nanchang 330031, People’s Republic of China. Tel: +86 791 83969530. E-mail: [email protected]
2
J.-Q. Yi et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position
Downloaded by [Australian National University] at 04:02 07 November 2015
Gene COIII tRNAGly ND3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer ND1 tRNALeu 16S rRNA tRNAVal 12S rRNA AT-rich region
Codon
Strandy
From
To
Size (bp)
Start
Stop
Intergenic nucleotides*
H H H H H H H H L L L L L H L H H H L L L L L
4702 5493 5558 5910 5982 6055 6121 6184 6251 6318 8056 8124 9464 9760 9826 9893 10,417 11,569 11,653 12,586 12,660 13,941 14,001 14,778
5490 5556 5911 5978 6047 6120 6182 6248 6317 8055 8122 9464 9757 9825 9890 10,417 11,562 11,637 12,585 12,659 13,940 14,005 14,777 15,064
789 64 354 69 66 66 62 65 67 1738 67 1341 294 66 65 525 1146 69 933 74 1281 65 777 287
ATG
TAA
ATT
TAG
ATT
T
ATG ATG
TAA TAA
ATA ATG
TAA TAA
ATG
TAA
2 1 2 3 7 0 1 2 0 0 1 1 2 0 2 1 6 15 0 0 0 5 0
*Positive numbers indicate separation between neighboring genes and negative numbers indicate overlapping between different genes. yH and L represent heavy and light strands, respectively.
The overall base composition of the heavy strand was 40.93% A, 39.80% T, 11.72% C and 7.55% G, with an AT content of 80.73%. It is generally present in other Lepidoptera mitochondrial genomes (Jiang et al., 2009; Salvato et al., 2008). Relative position and transcription direction of all the mitochondrial genes were consistent with Drosophila yakuba (Clary & Wolstenholme, 1985). The 13 protein-coding genes were located on H-strand with the exception of ND5, ND4, ND4L and ND1. Major coding genes were encoded with the normal start codons (ATN). It is proved that COI could start with CGA and some mitochondrial genes end up with an incomplete stop codon. Twenty-two tRNA (8 on the L-strand) ranged in size from 62 to 74 bp and dispersed in mitogenome. The tRNA order between the AT-rich region and ND2 was tRNAIle–tRNAGln–tRNAMet, which is considered to be the ancestral type (Cha et al., 2007; Krzywinski et al., 2006). The 12S and 16SrRNAs were 777 and 1281 bp, respectively. They existed between tRNALeu and AT-rich region, separated by tRNAVal. Overlapped nucleotides were observed to range from 1 to 8 bp in nine locations while the total length of intergenic nucleotides is 79 bp. The AT-rich region is surprised, 287 bp in length, to be the shortest in Lepidoptera. This region is believed to be involved in the regulation of transcription and control of DNA replication (Zhang & Hewitt, 1997).
Declaration of interest The work was financially supported by the Natural Science Foundation of China Science (31160081), the National Key Technology R&D Program (2011BAI13B06) and Department of Education Fund (GJJ13104) of Jiangxi Province. The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Cao YQ, Ma C, Chen JY, Yang DR. (2012). The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: The ancestral gene arrangement in Lepidoptera. BMC genomics 13:276. Cha SY, Yoon HJ, Lee EM, Yoon MH, Hwang JS, Jin BR, Han YS, Kim I. (2007). The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene 392: 206–20. Chu HF, Wang LY. (1985). ‘‘Insect-Herb’’ versus Hepialids with descriptions of new genera and new species of Chinese Hepialidae. Sinozoology 3:121–34. Clary DO, Wolstenholme DR. (1985). The mitochondrial DNA molecule of Drosophila yakuba: Nucleotide sequence, gene organization, and genetic code. J Mol Evol 22:252–71. Jiang ST, Hong GY, Yu M, Li N, Yang Y, Liu YQ, Wei ZJ. (2009). Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). Int J Biol Sci 5:351–65. 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. Salvato P, Simonato M, Battisti A, Negrisolo E. (2008). The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics 9:331. Zhang DX, Hewitt GM. (1997). Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25:99–120. Zou ZW. (2009). On the insects of the genus Thitarodes in Mt. Sejila of Tibet. Guangzhou: Sun Yat-sen University. p 47–66.
