http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.863287
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae Tai-Cheng Zhou1,2*, Tao Sha1*, David M. Irwin2,3, and Ya-Ping Zhang1,2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Alabama on 03/30/15 For personal use only.
1
Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China, 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China, and 3Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Abstract
Keywords
Pavo cristatus, known as the Indian peafowl, is endemic to India and Sri Lanka and has been domesticated for its ornamental and food value. However, its phylogenetic status is still debated. Here, to clarify the phylogenetic status of P. cristatus within Phasianidae, we analyzed its mitochondrial genome (mtDNA). The complete mitochondrial DNA (mtDNA) genome was determined using 34 pairs of primers. Our data show that the mtDNA genome of P. cristatus is 16,686 bp in length. Molecular phylogenetic analyses of P. cristatus was performed along with 22 complete mtDNA genomes belonging to other species in Phasianidae using Bayesian and maximum likelihood methods, where Aythya americana and Anas platyrhynchos were used as outgroups. Our results show that P. critatus has its closest genetic affinity with Pavo muticus and belongs to clade that contains Gallus, Bambusicola and Francolinus.
Complete mitochondrial genome, molecular phylogeny, Pavo cristatus
The Indian peafowl (Pavo cristatus), which belongs to the family Phasianidae, is the national bird of India and is endemically distributed to the deciduous open forest regions of India and Sri Lanka (Brickle, 2002). The beautiful appearance with a elaborate train, which is related to sexual advertisements (Loyau et al., 2005), makes it of great ornamental value, while the high protein, low fat and low cholesterol meat of the Indian peafowl is of value as food. In addition, the peafowl can be easily cultivated, as it has low demands, and recently been extensively propagated. However, very little genetic data on this species has been published, especially on its phylogenetic status. In this study, we determined the complete mtDNA genome of an Indian peafowl obtained from the Kunming haigeng Cssela Bird and Nature Park in Yunnan Province, China. The genome was amplified from 34 overlapping fragments by the polymerase chain reaction (PCR) amplification using specific primers designed in this and previous studies (available from the authors on request). Purified PCR fragments were directly sequenced using an ABI 3730 automatic sequencer (Applied Biosystems, Foster City, CA). The complete
*These authors contributed equally to this work. Correspondence: Yaping Zhang, State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan Province, China. Tel: (+86) 871-5190761. Fax: (+86) 871-5195430. E-mail: zhangyp@ mail.kiz.ac.cn
History Received 10 October 2013 Revised 25 October 2013 Accepted 3 November 2013 Published online 10 January 2014
mitochondrial genome sequence of P. cristatus (16,686 bp; GenBank accession no: KF444060) consists of 13 proteincoding genes, 22 tRNA genes and 2 rRNA genes, and a displacement loop (D-loop). The organization and gene order of the mtDNA genome are similar to those of other Phasianidae mitochondrial genomes (Nishibori et al., 2002, 2004). A phylogenetic analysis was performed using the complete mtDNA genome of P. cristatus and complete mtDNA genomes of 22 other species from Phasianidae (Figure 1). The aligned genomes contained 16,944 base pairs, of which 5779 were parsimony-informative. The best fitting model (GTRþIþG) of sequence evolution for Bayesian analysis was identified using Modeltest 3.7 (Posada & Crandall, 1998) under the Akaike information criterion. Both the Bayesian (BI) and maximum likelihood (ML) analyses produced similar phylogenetic trees for Phasianidae (Figure 1) by taking Aythya Americana and Anas platyrhynchos as outgroups. The Phasianidae contains six lineages: Group 1 contains Coturnix and Alectoris; Group 2 includes Pavo; Group 3 holds Gallus, Bambusicola, and Francolinus; Group 4 has Tetraophasis; Group 5 is composed of Crossoptilon, Lophura and Phaianus; and Group 6 contained Perdix (Figure 1). The newly determined P. critatus clusters with P. muticus with very high BSPs (BS ¼ 100%, PP ¼ 1.00). Our results also show that Gallus, Bambusicola and Francolinus form a clade that is a sister group to the Pavo from the complete mtDNA genome perspective. Our phylogenetic position for Pavo is inconsistent with some previous studies (Johnsgard, 1986; Kimball et al., 2011), but is consistent with one recent study (Eo et al., 2009; Li et al., 2011; Ma et al., 2010). The inconsistency between studies may be due to differences in the genetic markers used for the phylogenetic analyses. In this study, the amount of sequence data should be reasonable for examining mitogenomic relationships within Phasianidae.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Alabama on 03/30/15 For personal use only.
2
T.-C. Zhou et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree derived from 23 complete mitochondrial genomes of Phasianidae using BI and ML analyses. Bayesian posterior probability 470%, and maximum likelihood bootstrap proportions 450% are indicated on the branches.
Acknowledgements We thank Zhu-Gang Wu for collecting the sample used in this study.
Declaration of interest The authors declared no conflict of interest.
References Brickle NW. (2002). Habitat use, predicted distribution and conservation of green peafowl (Pavo muticus) in Dak Lak Province. Vietnam. Biol Conserv 105:189–97. Eo SH, Bininda-Emonds OR, Carroll JP. (2009). A phylogenetic supertree of the fowls (Galloanserae, Aves). Zool Scr 38:465–81. Johnsgard P. (1986). The pheasants of the world. Oxford University Press, Oxford. p 300. Kimball RT, Mary CMS, Braun EL. (2011). A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes). Int J Evol Biol 2011:423938 (1–16).
Li HM, Shi JP, Zeng DL, Zeng ZH, Qin XM. (2011). The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species. Mitochondrial DNA 22:159–61. Loyau A, Saint Jalme M, Cagniant C, Sorci G. (2005). Multiple sexual advertisements honestly reflect health status in peacocks (Pavo cristatus). Behav Ecol Socibiol 58:552–7. Ma LL, Zhang XY, Yue BS, Ran JH. (2010). Complete mitochondrial genome of the Chinese Monal pheasant Lophophorus lhuysii, with phylogenetic implication in Phasianidae. Mitochondrial DNA 21:5–7. Nishibori M, Hayashi T, Yasue H. (2004). Complete nucleotide sequence of Numida meleagris (Helmeted Guineafowl) mitochondrial genome. J Poult Sci 41:259–68. Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, Yasue H. (2002). Complete nucleotide sequence of the Coturnix chinensis (Blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species. J Hered 93:439–44. Posada D, Crandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae Tai-Cheng Zhou1,2*, Tao Sha1*, David M. Irwin2,3, and Ya-Ping Zhang1,2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Alabama on 03/30/15 For personal use only.
1
Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China, 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China, and 3Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Abstract
Keywords
Pavo cristatus, known as the Indian peafowl, is endemic to India and Sri Lanka and has been domesticated for its ornamental and food value. However, its phylogenetic status is still debated. Here, to clarify the phylogenetic status of P. cristatus within Phasianidae, we analyzed its mitochondrial genome (mtDNA). The complete mitochondrial DNA (mtDNA) genome was determined using 34 pairs of primers. Our data show that the mtDNA genome of P. cristatus is 16,686 bp in length. Molecular phylogenetic analyses of P. cristatus was performed along with 22 complete mtDNA genomes belonging to other species in Phasianidae using Bayesian and maximum likelihood methods, where Aythya americana and Anas platyrhynchos were used as outgroups. Our results show that P. critatus has its closest genetic affinity with Pavo muticus and belongs to clade that contains Gallus, Bambusicola and Francolinus.
Complete mitochondrial genome, molecular phylogeny, Pavo cristatus
The Indian peafowl (Pavo cristatus), which belongs to the family Phasianidae, is the national bird of India and is endemically distributed to the deciduous open forest regions of India and Sri Lanka (Brickle, 2002). The beautiful appearance with a elaborate train, which is related to sexual advertisements (Loyau et al., 2005), makes it of great ornamental value, while the high protein, low fat and low cholesterol meat of the Indian peafowl is of value as food. In addition, the peafowl can be easily cultivated, as it has low demands, and recently been extensively propagated. However, very little genetic data on this species has been published, especially on its phylogenetic status. In this study, we determined the complete mtDNA genome of an Indian peafowl obtained from the Kunming haigeng Cssela Bird and Nature Park in Yunnan Province, China. The genome was amplified from 34 overlapping fragments by the polymerase chain reaction (PCR) amplification using specific primers designed in this and previous studies (available from the authors on request). Purified PCR fragments were directly sequenced using an ABI 3730 automatic sequencer (Applied Biosystems, Foster City, CA). The complete
*These authors contributed equally to this work. Correspondence: Yaping Zhang, State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan Province, China. Tel: (+86) 871-5190761. Fax: (+86) 871-5195430. E-mail: zhangyp@ mail.kiz.ac.cn
History Received 10 October 2013 Revised 25 October 2013 Accepted 3 November 2013 Published online 10 January 2014
mitochondrial genome sequence of P. cristatus (16,686 bp; GenBank accession no: KF444060) consists of 13 proteincoding genes, 22 tRNA genes and 2 rRNA genes, and a displacement loop (D-loop). The organization and gene order of the mtDNA genome are similar to those of other Phasianidae mitochondrial genomes (Nishibori et al., 2002, 2004). A phylogenetic analysis was performed using the complete mtDNA genome of P. cristatus and complete mtDNA genomes of 22 other species from Phasianidae (Figure 1). The aligned genomes contained 16,944 base pairs, of which 5779 were parsimony-informative. The best fitting model (GTRþIþG) of sequence evolution for Bayesian analysis was identified using Modeltest 3.7 (Posada & Crandall, 1998) under the Akaike information criterion. Both the Bayesian (BI) and maximum likelihood (ML) analyses produced similar phylogenetic trees for Phasianidae (Figure 1) by taking Aythya Americana and Anas platyrhynchos as outgroups. The Phasianidae contains six lineages: Group 1 contains Coturnix and Alectoris; Group 2 includes Pavo; Group 3 holds Gallus, Bambusicola, and Francolinus; Group 4 has Tetraophasis; Group 5 is composed of Crossoptilon, Lophura and Phaianus; and Group 6 contained Perdix (Figure 1). The newly determined P. critatus clusters with P. muticus with very high BSPs (BS ¼ 100%, PP ¼ 1.00). Our results also show that Gallus, Bambusicola and Francolinus form a clade that is a sister group to the Pavo from the complete mtDNA genome perspective. Our phylogenetic position for Pavo is inconsistent with some previous studies (Johnsgard, 1986; Kimball et al., 2011), but is consistent with one recent study (Eo et al., 2009; Li et al., 2011; Ma et al., 2010). The inconsistency between studies may be due to differences in the genetic markers used for the phylogenetic analyses. In this study, the amount of sequence data should be reasonable for examining mitogenomic relationships within Phasianidae.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Alabama on 03/30/15 For personal use only.
2
T.-C. Zhou et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree derived from 23 complete mitochondrial genomes of Phasianidae using BI and ML analyses. Bayesian posterior probability 470%, and maximum likelihood bootstrap proportions 450% are indicated on the branches.
Acknowledgements We thank Zhu-Gang Wu for collecting the sample used in this study.
Declaration of interest The authors declared no conflict of interest.
References Brickle NW. (2002). Habitat use, predicted distribution and conservation of green peafowl (Pavo muticus) in Dak Lak Province. Vietnam. Biol Conserv 105:189–97. Eo SH, Bininda-Emonds OR, Carroll JP. (2009). A phylogenetic supertree of the fowls (Galloanserae, Aves). Zool Scr 38:465–81. Johnsgard P. (1986). The pheasants of the world. Oxford University Press, Oxford. p 300. Kimball RT, Mary CMS, Braun EL. (2011). A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes). Int J Evol Biol 2011:423938 (1–16).
Li HM, Shi JP, Zeng DL, Zeng ZH, Qin XM. (2011). The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species. Mitochondrial DNA 22:159–61. Loyau A, Saint Jalme M, Cagniant C, Sorci G. (2005). Multiple sexual advertisements honestly reflect health status in peacocks (Pavo cristatus). Behav Ecol Socibiol 58:552–7. Ma LL, Zhang XY, Yue BS, Ran JH. (2010). Complete mitochondrial genome of the Chinese Monal pheasant Lophophorus lhuysii, with phylogenetic implication in Phasianidae. Mitochondrial DNA 21:5–7. Nishibori M, Hayashi T, Yasue H. (2004). Complete nucleotide sequence of Numida meleagris (Helmeted Guineafowl) mitochondrial genome. J Poult Sci 41:259–68. Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, Yasue H. (2002). Complete nucleotide sequence of the Coturnix chinensis (Blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species. J Hered 93:439–44. Posada D, Crandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18.
