Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera
© Bagatharia et al.; licensee BioMed Central Ltd. 2013
Received: 25 June 2012
Accepted: 12 August 2013
Published: 23 August 2013
The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology.
The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya.
This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.
KeywordsAsiatic lion Big cats Panthera leo persica Mitogenome Ion torrent Phylogeny Evolution Felidae Divergence time
Five big charismatic cats: Panthera leo (lion), Panthera tigris (tiger), Panthera onca (jaguar), Panthera pardus (leopard) and Uncia uncia (snow leopard) have been placed taxonomically in Pantherinae subfamily. They have been drawing attention of biologists due to important ecological roles . Consequently, extensive information is available on their natural history, morphology, behaviour, reproduction, evolutionary history and population genetic structure, which provides a rich basis for interpreting genetic data . The information is still not adequate to overcome their highly threatened status. Hence, molecular study is vital to further explore the genetic information which can be helpful for conservation.
Panthera leo has two geographically isolated populations; Panthera leo leo (African lion), and Panthera leo persica (Asiatic lion) . The Asiatic lion population is accorded endangered species status under the Indian Wildlife Protection Act, consisting only 411 wild animals . This population exist in and around Gir forest in the southwest part of Saurashtra region in the State of Gujarat, India. Presence of geographically confined single population having its origin from small nucleus group and constituting single gene pool, raises concerns about genetic diversity in Asiatic lion population. Morphological and molecular approaches like allozyme study  microsatellite analysis , protein markers and mitochondrial 12S gene  have been used to unveil the evolutionary history of this species. Earlier efforts have been made to undertake the population study of Panthera leo persica (NCBI Taxonomy ID: 83386) and other allied species  to establish phylogenetic status. However, it has been found to be perplexing .
For the last decade, mitochondrial DNA has been one of the most commonly used molecular marker in vertebrates for studying phylogeny and evolutionary relationships  among closely related species and subspecies . It can reveal evolutionary relatedness and elucidate large numbers of genome-level characteristics, such as relative arrangements of genes . It also has a great importance for the molecular identification of species. Cytochrome b and Cytochrome oxidase subunit I  are mitochondrial genes widely used for molecular identification of animals. Further, key mitochondrial features - a lack of recombination, essentially maternal inheritance, high evolutionary rate, compact size, and conserved gene order , have led to its wide spread use.
Earlier, phylogenetic relationship of the genus Panthera was studied using morphological, biochemical as well as molecular characters but it is still debatable and troublesome because of large disparities between these studies. The difficulty in resolving their phylogenetic relationships is a result of (i) a poor fossil record, (ii) recent and rapid radiation during the Pliocene, (iii) individual speciation events occurring within less than 1 million years (iv) probable introgression between lineages following their divergence . Phylogenetic relationship and position of Panthera leo, amongst the genus Panthera, has some knowledge gaps. The present study aims to provide some insights through the complete mitogenome of the Asiatic lion.
Results and discussion
Mitochondrial genome sequence of any subspecies of Panthera leo, is not reported in literature. Present study describes sequencing of complete mitogenome of Asiatic Lion (P. leo persica) with the use of next generation sequencing technology on Ion TorrentPGM platform. The relationship of lion subspecies with other Felidae species and their evolutionary status has also been described on the basis of comparative analysis of mitogenomes.
Base composition of mitochondrial genome of Panthera leo persica
General mitogenome features of Felidae family
NCBI Taxonomy ID
Prionailurus bengalensis euptilurus
Amur leopard cat
Panthera leo persica
Panthera tigris amoyensis
Structure of mitogenome of Panthera leo persica
Location of features in the mitochondrial DNA of Panthera leo persica
Proteins and codons
The studied mitogenome comprise of 13 protein coding genes (11,364 bp) and share 66.62% of total genome. These genes encode 3788 amino acids (Table 2). The longest gene was ND5 (1815 bp) and the shortest gene was ATP8 (198 bp). The start and termination codons appeared universal among species. ATG was commonly used as start codon for all the genes except ND2, ND5, COX1, ND6 and ND3, which used ATA, ATT and ATC, respectively. TAA was commonly found as stop codon while Cyt b ended with AGA. Termination of Cyt b gene with AGA, is typical for mammalian species [15–17] which is distinct from others such as amphibians , reptiles [19, 20], Aves  and Nematoda . ND3, ND4, ND2 and COX3 have incomplete stop codons. These incomplete termination codons are common in metazoan mitogenome and can be converted into complete ones by poly A after transcription (TAA) .
tRNA and rRNA
Repeat sequence comparison in Felidae family
RS2 (No. of repeats)
RS3 (No. of repeats)
RS3 motif length
Panthera leo persica
Panthera tigris amoyensis
Prionailurus bengalensis euptilurus
Phylogenetic analyses based on gene cluster
Estimates of divergence times
Present study is the first report of complete mitogenome of P. leo persica among all eight subspecies. The evolutionary timeline estimates of big cats based on mitogenome analysis, indicates existence of common ancestor of P. leo and P. pardus 2.96 mya in modern Piacenzian era. The significant degree of genetic differentiation of Asiatic lion from other big cats, suggest independent evolution of subspecies described as P. leo persica. Complete mitogenome sequence provide sufficient information to resolve the events of divergence of Felidae.
Materials and methods
Sample collection and DNA extraction
Tissue sample of a freshly dead lion cub (female, 1.5 yrs) with chip ID 00-06B7-22E3 was collected from Sakkarbag Zoo, Junagadh, Gujarat, India (N 21.540848, E 70.468481). The samples were immediately transferred to laboratory and stored in Allprotect Tissue Reagent (Qiagen) at −80°C. Tissue sample was homogenized in liquid nitrogen and DNA extraction was carried out using BioVison Mitochondrial DNA Isolation Kit (BioVision Research Products, CA, USA) following manufacturer’s protocol.
DNA quality such as ratio of absorbance at 260/280 nm and 260/230 nm was measured using Nanophotometer (Imlpen). Qubit® 2.0 Fluorometer was used to obtain an accurate quantitation of DNA. Library was prepared using Ion Express Plus Fragment library kit (Life Technologies). Mitochondrial DNA was sheared into blunt ended fragments by enzymatic lysis using Ion Shear Plus Reagents (Life Technologies). The fragmented DNA was ligated to Ion-compatible adapters, followed by nick repair to complete the linkage between adapters and DNA inserts. Sequencing was performed using Ion Express Template 300 chemistry (Life Technologies) on 316 chip following manufacturer’s protocol.
Capillary Sequencing of D-loop region was performed to validate Ion Torrent data. PCR of D-loop was performed using forward (5’TCAAGGAAGAAGCAATAGCC 3’) and reverse (5’GGATTGTTGGGCGTGTAAA 3’) primers. Further sequencing was carried out using PCR primers and internal primer (5’TATTCTCTATGCGGGGGTTC 3’) using Big Dye v3.1 Chemistry (Applied Biosystems) on 3500 Genetic Analyzer (Applied Biosystems) following manufacturer’s protocol.
Reads longer than 100 bp were mapped to the P. pardus reference mitogenome [GenBank: NC_010641], using CLC Genomic Workbench 5 . Assembled mitogenome was annotated, using MITOS online mitochondrial genome annotation server . Control region repeats RS-2 and RS-3 were identified using Tandem Repeats Finder .
Molecular phylogenetic analysis
Phylogeny of P. leo was constructed based on partial and full mitochondrial gene cluster (12S rRNA+16S rRNA+ND2+ND4+ND5+ATP8+Cyt b). Partial P. leo genes having accession number A79300, AF006457, AY170043, AY634398, AF006458, S79302 and DQ899945  were retrieved from NCBI. Full sequences of above same genes of P. leo persica were compared with gene sequences of P. uncia [NC_010638], P. pardus [NC_010641], P. tigris [NC_010642], P. tigris amoyensis [NC_014770], N. nebulosa [NC_008450], A. jubatus [NC_005212], P. concolor [NC_016470], L. rufus [NC_014456], F. catus [NC_001700] and P. bengalensis euptilurus [NC_016189] obtained from NCBI organelle genome resource (Table 1). The data was subjected to Maximum likelihood (ML) and Maximum parsimony (MP) methods using MEGA v5.05 software package  to establish phylogenetic relationship.
These seven genes were concatenated and multiple alignment was carried out using ClustalW built-in MEGA. The number of bootstrap replicates was set to 1000 and phylogeny was constructed using Hasegawa-Kishino-Yano model, determined by MEGA 5.05 as the best fitting nucleotide substitution model.
Divergence time estimation
Multiple sequence alignment of genomes was carried out and phylogenetic tree was constructed using HKY+G+T substitution model at 1000 bootstrap replicates. Divergence times were estimated between species using Bayesian evolutionary analysis by sampling trees (BEAST v1.7.1) software . Markov Chain Monte Carlo (MCMC) procedure was used within a Bayesian analysis framework to estimate posterior distributions of evolutionary rates and divergence times. These analyses were performed using DNA sequence alignment of complete mitogenomes, excluding control region. Divergence times were estimated using an uncorrelated lognormal relaxed clock to account for lineage-specific rate heterogeneity as well as using strict molecular clock model (Additional file 1: Figure S1). Bayesian MCMC analyses in BEAST were performed using HKY model of evolution and gamma+ invariant rate heterogeneity models. Divergences were estimated under a Yule speciation process that is generally more appropriate when considering sequences from different species . Monophyletic constraints were imposed for the node to calibrate evolutionary rates. Normal priors were used for the times to the most recent common ancestor (TMRCA) of Pantherinae and Felinae is (mean 10.78 ±1.87 mya), based on the posterior distributions obtained .
Simultaneous Markov chains were run for 10,000,000 generations, sampling every 1000 steps. Thus the “.trees” file will contain 10,000 trees and after removing 10% burnin, tree was annotated using TreeAnnotator. Posterior probability limit was set to zero to annotate all nodes. Maximum clade credibility tree was selected for target tree to find highest product of the posterior probability for all nodes. The phylogenetic tree graphic was generated using FigTree v1.3.1 .
GenBank accession number
The complete mitogenome sequence with gene prediction and functional annotation was submitted to GenBank with accession no. KC834784. The raw sequence data generated from Ion Torrent was submitted to SRA with accession no SRR821548. Mitochondrial D-loop sequence was submitted to GenBank with accession no. KC917264.
- DHU arm:
Million years ago
Next generation sequencing.
This research was majorly supported by Gujarat State Biotechnology Mission, Department of Science & Technology, Government of Gujarat, INDIA under The LeoGen pilot project. Authors are thankful to Shri Ravi Saxena, IAS, Additional Chief Secretary, Department of Science & Technology, Government of Gujarat for providing full support and administrative freedom for Gujarat State Biotechnology Mission for undertaking this project. Authors are also thankful to Gujarat State Forest Department for providing bio-materials and part financial support. Authors are specially thankful to Dr. S. K. Nanda, IAS, Principal Secretary, Forest & Environment, Government of Gujarat, Shri Pradeep Khanna, IFS, Principal Chief Conservator of Forest & Head of Forest Force, Gujarat, Shri S. K. Goyal, IFS, Principal Chief Conservator of Forest, Wildlife & Chief Wildlife Warden, Gujarat who facilitated in getting the necessary permission from Ministry of Forest & Environment, Government of India, Government of Gujarat. Authors are also thankful to Shri M. M. Sharma, IFS, Ex-chief Conservator of Forest, Junagadh Wildlife Circle, Shri R. L. Meena, IFS, Chief Conservator of Forest, Wildlife, Junagadh, Dr. Sandeep Kumar, IFS, Deputy Conservator of Forest, Sasan and Shri V. J. Rana, Director, Shakkarbaug Zoo for providing all help and co-operation in enabling the availability of bio-material from different areas. Authors are thankful to the field staff and veterinarians, involved in collection of samples.
- Warren EJ, Peter AD, Janice SM, Stephen JO: Resolution of recent radiations within three evolutionary lineages of felidae using mitochondrial restriction fragment length polymorphism variation. J Mamm Evol. 1996, 3 (2): 97-120. 10.1007/BF01454358.View Article
- Seung-Jin S, Tiffani LW: Big cat phylogenies, consensus trees, and computational thinking. J Comput Biol. 2011, 18 (7): 895-906. 10.1089/cmb.2010.0199.View Article
- Burger J, Rosendahl W, Loreille O, Hemmer H, Eriksson T, Götherström A, Hiller J, Collins MJ, Wess T, Alt KW: Molecular phylogeny of the extinct cave lion Panthera leo persica spelaea. Mol Phylogenet Evol. 2004, 30 (3): 841-849. 10.1016/j.ympev.2003.07.020.View ArticlePubMed
- Singh HS, Gibson L: A conservation success story in the otherwise dire megafauna extinction crisis: the Asiatic lion (Panthera leo persica) of Gir forest. Biol Conserv. 2011, 144 (5): 1753-1757. 10.1016/j.biocon.2011.02.009.View Article
- Stephen JO, Janice SM, Craig P, Lawrence H, Valerius D, Paul J, Janis O, David EW, Mitchell B: Biochemical genetic variation in geographic isolates of African and Asiatic lions. Natl Geogr Res. 1987, 3 (1): 114-124.
- Singh A, Shailaja A, Singh A, Shailaja A, Gaur L, Singh V: Development and characterization of novel microsatellite markers in the Asiatic lion (Panthera leo persica). Mol Ecol Resour. 2002, 2 (4): 542-554.
- Dianne NJ, William SM, Stephens JC, O’Brien SJ: Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae. Mol Phylogenet Evol. 1995, 12 (4): 690-707.
- Michelle YM, Deborah AM: Phylogeny and speciation of felids. Cladistics. 2000, 16 (2): 232-253. 10.1111/j.1096-0031.2000.tb00354.x.View Article
- Jae-Heup K, Eizirik E, O'Brien SJ, Johnson WE: Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats. Mitochondr DNA. 2001, 1 (3): 279-292. 10.1016/S1567-7249(01)00027-7.View Article
- Zhang W, Zhang Z, Shen F, Hou R, Lv X, Yue B: Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris). J Genet. 2006, 85 (2): 107-116. 10.1007/BF02729016.View ArticlePubMed
- Boore JL, Macey JR, Medina M: Sequencing and comparing whole mitochondrial genomes of animals. Methods Enzymol. 2005, 395: 311-348.View ArticlePubMed
- Hebert PD, Cywinska A, Ball SL, deWaard JR: Biological identifications through DNA barcodes. Proc Biol Sci. 2003, 270 (1512): 313-322. 10.1098/rspb.2002.2218.PubMed CentralView ArticlePubMed
- Davis BW, Li G, Murphy WJ: Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, panthera (carnivora: Felidae). Mol Phylogenet Evol. 2010, 56 (1): 64-76. 10.1016/j.ympev.2010.01.036.View ArticlePubMed
- MITOS. [http://mitos.bioinf.uni-leipzig.de]
- Kim KS, Seong EL, Ho WJ, Ji HH: The complete nucleotide sequence of the domestic dog (Canis familiariz) mitochondrial genome. Mol Phylogenet Evol. 1998, 10 (2): 210-220. 10.1006/mpev.1998.0513.View ArticlePubMed
- Ursing BM, Arnason U: The complete mitochondrial DNA sequence of the pig (Sus scrofa). J Mol Evol. 1998, 47 (3): 302-306. 10.1007/PL00006388.View ArticlePubMed
- Gissi C, Gullberg A, Arnason U: The complete mitochondrial DNA sequence of the rabbit (Oryctolagus cuniculus). Genomics. 1998, 50 (2): 161-169. 10.1006/geno.1998.5282.View ArticlePubMed
- Sumida M, Kanamori Y, Kaneda H, Kato Y, Nishioka M, Hasegawa M, Yonekawa H: Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet Syst. 2001, 76 (5): 311-325. 10.1266/ggs.76.311.View ArticlePubMed
- Wu XB, Wang YQ, Zhou KY, Zhu WQ, Nie JS, Wang CL: Complete mitochondrial DNA sequence of Chinese alligator, Alligator sinensis, and phylogeny of crocodiles. Chin Sci Bull. 2003, 48 (19): 2050-2054. 10.1360/03wc0076.View Article
- Douglas DA, Gower DJ: Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution. BMC Genomics. 2010, 11: 14-10.1186/1471-2164-11-14.PubMed CentralView ArticlePubMed
- Sun Y, Ma F, Xiao B, Zheng JJ, Yuan XD, Tang MQ, Wang L, Yu YF, Li QW: The complete mitochondrial genomes sequences of Asio flammeus and Asio otus and comparativeanalysis. Sci China Ser C Life Sci. 2004, 47 (6): 510-520. 10.1360/04yc0117.View Article
- Hu M, Chilton NB, Gasser RB: The mitochondrial genome of Strongyloides stercoralis (Nematoda)—idiosyncratic gene order and evolutionary implications. Int J Parasitol. 2003, 33 (12): 1393-1408. 10.1016/S0020-7519(03)00130-9.View ArticlePubMed
- Man Z, Yishu W, Peng Y, Xiaobing W: Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae. Mol Phylogenet Evol. 2011, 60 (2011): 62-67.View ArticlePubMed
- Wei L, Xiaobing E, Jiang Z: The complete mitochondrial genome structure of snow leopard Panthera uncia. Mol Biol Rep. 2009, 36 (3): 871-878.View ArticlePubMed
- Wu X, Yan P, Hu L, Su X, Jiang Z: Complete nucleotide sequences and gene organization of mitochondrial genome of Bufo gargarizans. Mitochondrion. 2006, 6 (4): 186-193. 10.1016/j.mito.2006.07.003.View ArticlePubMed
- Jae-Heup K, Eizirik E, O'Brien SJ, Johnson WE: Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats. Mitochondrion. 2001, 1 (3): 279-292. 10.1016/S1567-7249(01)00027-7.View ArticlePubMed
- Lei WEI, XiaoBing WU, LiXin ZHU, ZhiGang JIANG: Mitogenomic analysis of the genus Panthera. Sci China Life Sci. 2011, 54 (10): 917-930. 10.1007/s11427-011-4219-1.View Article
- O'Brien SJ, Johnson WE: The evolution of cats. Genomic paw prints in the DNA of the world's wild cats have clarified the cat family tree and uncovered several remarkable migrations in their past. Sci Am. 2007, 297 (1): 68-75.View ArticlePubMed
- Johnson WE, Eizirik E, Pecon-Slattery J, Murphy WJ, Antunes A, Teeling E, O'Brien SJ: The late miocene radiation of modern felidae: a genetic assessment. Science. 2006, 311 (5757): 73-77. 10.1126/science.1122277.View ArticlePubMed
- Janczewski DN, Modi WS, Stephens JC: Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the Pantherine lineage of Felidae. Mol Biol Evol. 1995, 12 (4): 690-707.PubMed
- Frazer-Abel AA, Hagerman PJ: Determination of the angle between the acceptor and anticodon stems of a truncated mitochondrial tRNA. Mol Biol. 1999, 85 (2): 581-593.View Article
- CLC Genomics Workbench v 5.0.http://www.clcbio.com/products/clc-genomics-workbench/,
- Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27 (2): 573-580. 10.1093/nar/27.2.573.PubMed CentralView ArticlePubMed
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28 (10): 2731-2739. 10.1093/molbev/msr121.PubMed CentralView ArticlePubMed
- Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186/1471-2148-7-214.PubMed CentralView ArticlePubMed
- Anne CS, Fabia UB, Laura SK, George HP, Evan T, Hsiuman L, Sudhir K: More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci. 2010, 365 (1556): 3277-3288. 10.1098/rstb.2010.0096.View Article
- FigTree v1.3.http://tree.bio.ed.ac.uk/software/figtree/,
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.