TY - JOUR
T1 - Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia
AU - Meganathan, P. R.
AU - Dubey, Bhawna
AU - Batzer, Mark A.
AU - Ray, David A.
AU - Haque, Ikramul
N1 - Funding Information:
The authors are thankful to Nehru Zoological Park, Hyderabad, Andhra Pradesh, India and Madras Crocodile Bank Trust (MCBT), Mamallapuram, Tamil Nadu, India for providing authenticated crocodilian samples for this study. We gratefully acknowledge Dr. B. N. Sarkar, Anthorpological Survey of India, Kolkata, India for providing equipment facilities to standardize the primers. Part of this work was carried out by using the resources of the Computational Biology Service Unit from Cornell University which is partially funded by Microsoft Corporation. This study was funded by Directorate of Forensic Sciences, Ministry of Home Affairs, Govt. of India, New Delhi (P. R. M., B. D., and I. H). This research was supported by the Louisiana Board of Regents Governor's Biotechnology Initiative GBI (2002-005) (M.A.B.) and by the National Science Foundation ( MCB-0841821 and DEB-1020865 ) (D.A.R).
PY - 2011/6/1
Y1 - 2011/6/1
N2 - Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827. bp, 16,851. bp and 16,852. bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution.
AB - Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827. bp, 16,851. bp and 16,852. bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution.
KW - Codon usage
KW - Crocodylus johnstoni
KW - Crocodylus moreletii
KW - Crocodylus palustris
KW - Mitochondrial genome
KW - Phylogenetic relationships
UR - http://www.scopus.com/inward/record.url?scp=79955012355&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2011.01.012
DO - 10.1016/j.gene.2011.01.012
M3 - Article
C2 - 21310220
AN - SCOPUS:79955012355
VL - 478
SP - 35
EP - 41
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -