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
Mitochondrial genome of the African lion Panthera leo leo Yue-ping Ma & Shuo Wang To cite this article: Yue-ping Ma & Shuo Wang (2015) Mitochondrial genome of the African lion Panthera leo leo, Mitochondrial DNA, 26:6, 951-952, DOI: 10.3109/19401736.2013.865171 To link to this article: http://dx.doi.org/10.3109/19401736.2013.865171
Published online: 10 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: [University of Lethbridge]
Date: 05 October 2015, At: 03:14
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 951–952 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.865171
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the African lion Panthera leo leo Yue-ping Ma1 and Shuo Wang2 College of Life and Health Sciences, Northeastern University, Shenyang, China and 2Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
Downloaded by [University of Lethbridge] at 03:14 05 October 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome sequence of the African lion P. leo leo was reported. The total length of the mitogenome was 17,054 bp. It contained the typical mitochondrial structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region; 21 of the tRNA genes folded into typical cloverleaf secondary structure except for tRNASe. The overall composition of the mitogenome was A (32.0%), G (14.5%), C (26.5%) and T (27.0%). The new sequence will provide molecular genetic information for conservation genetics study of this important large carnivore.
African lion (Panthera leo leo), genome, mitochondrion
Lion (Panthera leo) was once one of the most broadly distributed terrestrial large carnivores which had a wide species distribution range that included most of the non-Saharan Africa, the Middle East and southwest Asia into the eastern Balkans in Europe and western India from the history of human being (Coheleach, 1982; Guggisberg, 1961). Twenty-four different names have been used to distinguish each geographic distributed populations of African P. leo (Allen, 1939; Meester & Setzer, 1971 (as revised 1977)), but only two extant subspecies of lions, P. leo leo and P. leo persicus, respectively, representing African and Asian populations, were acknowledged by most taxonomic authorities. While recent surveys of wild lion populations have estimated that only about 18–47 thousands of wild lions are currently living in Africa, compared to the already critically shrinking populations of Asiatic lion (consisting only 411 wild individuals (Singh &
History Received 30 October 2013 Revised 5 November 2013 Accepted 10 November 2013 Published online 10 January 2014
Gibson, 2011)), researchers suggested that the African lion might soon become endangered too (Bauer & Van Der Merwe, 2002; Chardonnet, 2002). Bagatharia et al. (2013) reported the mitochondrial genome of Asiatic lion P. leo persicus (GenBank accession number: KC834784). Here, we assembled the complete mitogenome of African lion P. leo leo with Illumina sequence data produced by Cho et al. (2013) and the CLC Genomic Workbench v3.6 (2010). The sequence was deposited in GenBank with the accession number KF776494. The complete mtDNA of P. leo leo (17,054 bp in length) had 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 1 non-coding control region (D-loop). Most of the genes were encoded on the H-strand except the ND6 subunit gene and 8 tRNA genes (Table 1), which were similar to the typical mitochondrial genomes
Table 1. List of genes encoded by P. leo leo mitochondrial genome. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
From 1 866 938 1900 1969 3543 3620 4576 4642 4717 4786 5828 5912
Base composition (%) To 865 937 1895 1968 3539 3617 4576 4644 4715 4785 5829 5896 5980
Size (bp)
A
C
G
T
865 72 958 69 1571 75 957 69 74 69 1044 69 69
32.0 38.9 35.8 33.3 36.6 28.0 30.4 37.7 27.0 30.4 36.3 36.2 30.4
27.5 20.8 24.1 21.7 21.6 25.3 31.4 14.5 9.5 26.1 29.3 20.3 11.6
15.5 18.1 17.8 17.4 18.5 20.0 12.1 17.4 24.3 17.4 9.7 17.4 20.3
25.0 22.2 22.3 27.6 23.3 26.7 26.1 30.4 39.2 26.1 24.7 26.1 37.7
Start codon
Stop codon
Strand
ATG
TAA
ATC
TAG
H H H H H H H H L H H H L (continued )
Correspondence: Shuo Wang, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China. E-mail: [email protected]
952
Y.-P. Ma & S. Wang
Mitochondrial DNA, 2015; 26(6): 951–952
Table 1. Continued
Position Gene
Downloaded by [University of Lethbridge] at 03:14 05 October 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
Base composition (%)
From
To
Size (bp)
A
C
G
T
5982 6055 6088 6153 6211 7762 7837 7906 8593 8662 8823 9503 10,287 10,356 10,703 10,772 11,062 12,440 12,509 12,568 12,638 14,442 14,970 15,042 16,182 16,252 16,318
6054 6087 6152 6218 7764 7830 7905 8589 8660 8865 9503 10,286 10,355 10,701 10,771 11,068 12,430 12,508 12,567 12,637 14,458 14,969 15,038 16,181 16,251 16,318 17,054
73 33 65 66 1554 69 69 684 68 204 681 784 69 346 69 297 1369 69 59 70 1821 528 69 1140 70 67 737
26.0 30.3 27.7 33.3 26.6 27.6 34.8 31.3 36.8 38.7 28.9 27.2 34.8 29.8 37.7 28.3 31.8 40.6 35.6 40.0 31.3 21.0 27.5 28.0 32.8 23.9 30.7
16.4 27.3 21.5 16.7 23.8 15.9 14.5 26.6 19.1 26.5 28.2 28.4 18.8 29.2 14.5 26.6 29.9 13.0 22.0 15.7 28.6 10.8 11.6 29.7 22.9 13.4 22.5
28.8 27.3 26.2 21.2 18.4 23.2 15.9 15.2 14.7 7.8 13.1 16.5 16.0 12.7 11.6 14.5 12.3 13.0 17.0 18.6 11.9 29.0 20.3 13.9 18.6 28.4 15.1
28.8 15.1 24.6 28.8 31.2 33.3 34.8 26.9 29.4 27.0 29.8 27.9 30.4 28.3 36.2 30.6 26.0 33.4 25.4 25.7 28.2 39.2 40.6 28.4 25.7 34.3 37.7
of vertebrate. The base composition was A (32.0%)4T (27.0%)4C (26.5%)4G (14.5%), and the A–T bias (59.0%) was detected. Each of the 13 protein-coding genes was identified by comparing with published sequences of other Panthera species. Their total length was 11,409 bp and they encoded 3792 amino acids. Nine of the 13 protein-coding genes initiated with ATG, while ND3 and ND5 shared ATA as the start codon, COX1 utilized ATT and ND2 used ATC. Eight protein-coding genes ended with TAA, whereas Cyt b terminated with AGA. Incomplete stop codons (T-) were found in COX3, ND3 and ND4, which was presumably completed as TAA via posttranscriptional polyadenylation (Boore, 1999). The 22 tRNA genes of P. leo ranged in size from 59 bp (tRNASer) to 75 bp (tRNALeu). The small non-coding region, a putative origin of the light-strand replication, was in the length of 33 bp and located between the tRNAAsn and tRNACys genes. The 12S and 16S rRNA genes were 958 bp and 1571 bp in length, respectively. The ribosomal subunit genes were located between the tRNAPhe and tRNALeu genes and further separated by the tRNAVal gene. The control region of the P. leo leo mtDNA was 1602 bp long and located between tRNAPro and tRNAPhe. This sequenced mitogenome of P. leo leo is quite similar to other sequenced Panthera genomes in genome size, gene numbers and content. The new sequence will provide molecular genetic information for conservation genetics study of this important large carnivore (Dubach et al., 2005).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This project was
Start codon
Stop codon
ATT
TAA
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATA
T– –
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L L H L H H H H H H H H H H H H H H H L L H H L H
funded by the National Natural Science Foundation of China (No. 30800885).
References Allen GM. (1939). A checklist of African mammals. Bull Mus Compar Zool 83:1–763. Bagatharia SB, Joshi MN, Pandya RV, Pandit AS, Patel RP, Desai SM, Sharma A, et al. (2013). Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera. BMC Genomics 14:572. Bauer H, Van Der Merwe S. (2002). The African lion database. Cat News 36:41–53. Boore JL. (1999). Animal mitochondrial genomes. Nucl Acids Res 27: 1767–80. Chardonnet P. (2002). Conservation of the African lion: Contribution to a Status Survey. Paris, France: International Foundation for the Conservation of Wildlife. USA: Conservation Force, USA. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, et al. (2013). The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Commun 4:2433. doi: 10.1038/ncomms3433. CLC Genomics Workbench v3.6. (2010). Now new version can be available at: http://www.clcbio.com/products/clcgenomics-workbench/ (Accessed 5 December 2013) Coheleach G. (1982). The big cats: The paintings of Guy Coheleach. New York: Harry N. Abrams, Inc. Dubach J, Patterson BD, Briggs MB, Venzke K, Flamand J, Stander P, Scheepers L, Kays RW. (2005). Molecular genetic variation across the southern and eastern geographic ranges of the African lion, Panthera leo. Conserv Genet 6:15–24. Guggisberg CAW. (1961). Simba, the life of the lion. Capetown, South Africa: Howard Timmins. Meester JAJ, Setzer HW. 1971 (revised 1977). The mammals of Africa. An identification manual. Washington, DC: Smithsonian Institution. Singh HS, Gibson L. (2011). A conservation success story in the otherwise dire megafauna extinction crisis: The Asiatic lion (Panthera leo persica) of Gir forest. Biol Conserv 144:1753–7.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Mitochondrial genome of the African lion Panthera leo leo Yue-ping Ma & Shuo Wang To cite this article: Yue-ping Ma & Shuo Wang (2015) Mitochondrial genome of the African lion Panthera leo leo, Mitochondrial DNA, 26:6, 951-952, DOI: 10.3109/19401736.2013.865171 To link to this article: http://dx.doi.org/10.3109/19401736.2013.865171
Published online: 10 Jan 2014.
Submit your article to this journal
Article views: 25
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Lethbridge]
Date: 05 October 2015, At: 03:14
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 951–952 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.865171
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the African lion Panthera leo leo Yue-ping Ma1 and Shuo Wang2 College of Life and Health Sciences, Northeastern University, Shenyang, China and 2Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
Downloaded by [University of Lethbridge] at 03:14 05 October 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome sequence of the African lion P. leo leo was reported. The total length of the mitogenome was 17,054 bp. It contained the typical mitochondrial structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region; 21 of the tRNA genes folded into typical cloverleaf secondary structure except for tRNASe. The overall composition of the mitogenome was A (32.0%), G (14.5%), C (26.5%) and T (27.0%). The new sequence will provide molecular genetic information for conservation genetics study of this important large carnivore.
African lion (Panthera leo leo), genome, mitochondrion
Lion (Panthera leo) was once one of the most broadly distributed terrestrial large carnivores which had a wide species distribution range that included most of the non-Saharan Africa, the Middle East and southwest Asia into the eastern Balkans in Europe and western India from the history of human being (Coheleach, 1982; Guggisberg, 1961). Twenty-four different names have been used to distinguish each geographic distributed populations of African P. leo (Allen, 1939; Meester & Setzer, 1971 (as revised 1977)), but only two extant subspecies of lions, P. leo leo and P. leo persicus, respectively, representing African and Asian populations, were acknowledged by most taxonomic authorities. While recent surveys of wild lion populations have estimated that only about 18–47 thousands of wild lions are currently living in Africa, compared to the already critically shrinking populations of Asiatic lion (consisting only 411 wild individuals (Singh &
History Received 30 October 2013 Revised 5 November 2013 Accepted 10 November 2013 Published online 10 January 2014
Gibson, 2011)), researchers suggested that the African lion might soon become endangered too (Bauer & Van Der Merwe, 2002; Chardonnet, 2002). Bagatharia et al. (2013) reported the mitochondrial genome of Asiatic lion P. leo persicus (GenBank accession number: KC834784). Here, we assembled the complete mitogenome of African lion P. leo leo with Illumina sequence data produced by Cho et al. (2013) and the CLC Genomic Workbench v3.6 (2010). The sequence was deposited in GenBank with the accession number KF776494. The complete mtDNA of P. leo leo (17,054 bp in length) had 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 1 non-coding control region (D-loop). Most of the genes were encoded on the H-strand except the ND6 subunit gene and 8 tRNA genes (Table 1), which were similar to the typical mitochondrial genomes
Table 1. List of genes encoded by P. leo leo mitochondrial genome. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
From 1 866 938 1900 1969 3543 3620 4576 4642 4717 4786 5828 5912
Base composition (%) To 865 937 1895 1968 3539 3617 4576 4644 4715 4785 5829 5896 5980
Size (bp)
A
C
G
T
865 72 958 69 1571 75 957 69 74 69 1044 69 69
32.0 38.9 35.8 33.3 36.6 28.0 30.4 37.7 27.0 30.4 36.3 36.2 30.4
27.5 20.8 24.1 21.7 21.6 25.3 31.4 14.5 9.5 26.1 29.3 20.3 11.6
15.5 18.1 17.8 17.4 18.5 20.0 12.1 17.4 24.3 17.4 9.7 17.4 20.3
25.0 22.2 22.3 27.6 23.3 26.7 26.1 30.4 39.2 26.1 24.7 26.1 37.7
Start codon
Stop codon
Strand
ATG
TAA
ATC
TAG
H H H H H H H H L H H H L (continued )
Correspondence: Shuo Wang, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China. E-mail: [email protected]
952
Y.-P. Ma & S. Wang
Mitochondrial DNA, 2015; 26(6): 951–952
Table 1. Continued
Position Gene
Downloaded by [University of Lethbridge] at 03:14 05 October 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
Base composition (%)
From
To
Size (bp)
A
C
G
T
5982 6055 6088 6153 6211 7762 7837 7906 8593 8662 8823 9503 10,287 10,356 10,703 10,772 11,062 12,440 12,509 12,568 12,638 14,442 14,970 15,042 16,182 16,252 16,318
6054 6087 6152 6218 7764 7830 7905 8589 8660 8865 9503 10,286 10,355 10,701 10,771 11,068 12,430 12,508 12,567 12,637 14,458 14,969 15,038 16,181 16,251 16,318 17,054
73 33 65 66 1554 69 69 684 68 204 681 784 69 346 69 297 1369 69 59 70 1821 528 69 1140 70 67 737
26.0 30.3 27.7 33.3 26.6 27.6 34.8 31.3 36.8 38.7 28.9 27.2 34.8 29.8 37.7 28.3 31.8 40.6 35.6 40.0 31.3 21.0 27.5 28.0 32.8 23.9 30.7
16.4 27.3 21.5 16.7 23.8 15.9 14.5 26.6 19.1 26.5 28.2 28.4 18.8 29.2 14.5 26.6 29.9 13.0 22.0 15.7 28.6 10.8 11.6 29.7 22.9 13.4 22.5
28.8 27.3 26.2 21.2 18.4 23.2 15.9 15.2 14.7 7.8 13.1 16.5 16.0 12.7 11.6 14.5 12.3 13.0 17.0 18.6 11.9 29.0 20.3 13.9 18.6 28.4 15.1
28.8 15.1 24.6 28.8 31.2 33.3 34.8 26.9 29.4 27.0 29.8 27.9 30.4 28.3 36.2 30.6 26.0 33.4 25.4 25.7 28.2 39.2 40.6 28.4 25.7 34.3 37.7
of vertebrate. The base composition was A (32.0%)4T (27.0%)4C (26.5%)4G (14.5%), and the A–T bias (59.0%) was detected. Each of the 13 protein-coding genes was identified by comparing with published sequences of other Panthera species. Their total length was 11,409 bp and they encoded 3792 amino acids. Nine of the 13 protein-coding genes initiated with ATG, while ND3 and ND5 shared ATA as the start codon, COX1 utilized ATT and ND2 used ATC. Eight protein-coding genes ended with TAA, whereas Cyt b terminated with AGA. Incomplete stop codons (T-) were found in COX3, ND3 and ND4, which was presumably completed as TAA via posttranscriptional polyadenylation (Boore, 1999). The 22 tRNA genes of P. leo ranged in size from 59 bp (tRNASer) to 75 bp (tRNALeu). The small non-coding region, a putative origin of the light-strand replication, was in the length of 33 bp and located between the tRNAAsn and tRNACys genes. The 12S and 16S rRNA genes were 958 bp and 1571 bp in length, respectively. The ribosomal subunit genes were located between the tRNAPhe and tRNALeu genes and further separated by the tRNAVal gene. The control region of the P. leo leo mtDNA was 1602 bp long and located between tRNAPro and tRNAPhe. This sequenced mitogenome of P. leo leo is quite similar to other sequenced Panthera genomes in genome size, gene numbers and content. The new sequence will provide molecular genetic information for conservation genetics study of this important large carnivore (Dubach et al., 2005).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This project was
Start codon
Stop codon
ATT
TAA
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATA
T– –
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L L H L H H H H H H H H H H H H H H H L L H H L H
funded by the National Natural Science Foundation of China (No. 30800885).
References Allen GM. (1939). A checklist of African mammals. Bull Mus Compar Zool 83:1–763. Bagatharia SB, Joshi MN, Pandya RV, Pandit AS, Patel RP, Desai SM, Sharma A, et al. (2013). Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera. BMC Genomics 14:572. Bauer H, Van Der Merwe S. (2002). The African lion database. Cat News 36:41–53. Boore JL. (1999). Animal mitochondrial genomes. Nucl Acids Res 27: 1767–80. Chardonnet P. (2002). Conservation of the African lion: Contribution to a Status Survey. Paris, France: International Foundation for the Conservation of Wildlife. USA: Conservation Force, USA. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, et al. (2013). The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Commun 4:2433. doi: 10.1038/ncomms3433. CLC Genomics Workbench v3.6. (2010). Now new version can be available at: http://www.clcbio.com/products/clcgenomics-workbench/ (Accessed 5 December 2013) Coheleach G. (1982). The big cats: The paintings of Guy Coheleach. New York: Harry N. Abrams, Inc. Dubach J, Patterson BD, Briggs MB, Venzke K, Flamand J, Stander P, Scheepers L, Kays RW. (2005). Molecular genetic variation across the southern and eastern geographic ranges of the African lion, Panthera leo. Conserv Genet 6:15–24. Guggisberg CAW. (1961). Simba, the life of the lion. Capetown, South Africa: Howard Timmins. Meester JAJ, Setzer HW. 1971 (revised 1977). The mammals of Africa. An identification manual. Washington, DC: Smithsonian Institution. Singh HS, Gibson L. (2011). A conservation success story in the otherwise dire megafauna extinction crisis: The Asiatic lion (Panthera leo persica) of Gir forest. Biol Conserv 144:1753–7.
