The complete mitochondrial genome of water deer in Liaoning, China (original) (raw)
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Gene Reports
The complete mitochondrial genome of Eld's deer (Rucervus eldii eldii) has been sequenced, assembled and characterized for the first time using 25 sets of published primers. The Eld's deer, famously known as Sangai or Manipur's brow-antlered deer belongs to the family cervidae and is critically endangered species in India which needs immediate attention and concern for wildlife conservation. The 16,357 bp long complete mitogenome of R. e. eldii was very similar to most vertebrates in organisation with 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and a typical non-coding control region. Its protein-coding region exhibits codon usage common to all mammals. A detailed characterization of the available mitogenomes of Artiodactyla suggested conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins. A detailed characterization of the available mitogenomes of Artiodactyla, suggested conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins. The complete mitogenome and proteincoding genes of R. e. eldii were found to be highly A+T biased. Rate of protein evolution was highest in nad6 and lowest in cox1. The phylogenetic analyses based on concatenated amino acid and nucleotide sequences of 13 protein-coding genes provided a well-supported broader outline of cervidae, which agree with the previously described traditional morphological classification. Besides, the well supported phylogeny of artiodactyls mitochondrial genomes helped to resolve relationships between Rucervus eldii eldii (India) and Rucervus eldii hainanus (China) being the other two Eld's deer species remains unresolved ie. Rucervus eldii thamin (Myanmar)
Journal of Mammalogy, 2015
The white-tailed deer (Odocoileus virginianus) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/ COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies. El venado cola blanca es una de las especies de mayor importancia dentro del aprovechamiento de la fauna silvestre de México, donde se distribuyen de manera natural 14 subespecies. Actualmente, estas subespecies se han clasificado de acuerdo a sus variaciones fenotípicas que presentan a lo largo de su rango de distribución, sin embargo no se ha establecido la caracterización genética completa de las mismas. Es por esto que el objetivo del presente estudio es reportar los mitogenomas de 9 de las 14 subespecies de venado cola blanca, así como identificar las variaciones únicas de cada subespecie. En las 9 subespecies se observó la estructura típica de los mitogenomas de vertebrados (13 genes que codifican para proteínas, 22 ARNt, 2 ARNr). Los genes con mayor polimorfismo fueron D-loop, ND4, ND5, CYTB/COI, ATP6 y COIII. El análisis filogenético mostró la separación de las subespecies del sur y sureste de las subespecies del centro y norte del país, a su vez las distancias genéticas entre estos dos grupos fueron las más altas. Estas variaciones subespecie-específicas podrían ser útiles para diseñar una estrategia para caracterizar genéticamente las subespecies estudiadas.
Acta biologica Hungarica, 2016
Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebra...
Pakistan Journal of Zoology, 2022
Authors' Contribution WN gave the idea and provided the facilities and guidance and also helped in writing the manuscript. BB collected the samples and provided the data. NQ and JG performed the experiments and wrote the manuscript. ED analyzed the data. SW helped in writing the manuscript. CG helped in experimentation. HG helped in bioinformatics analysis. HJ helped in sample collection. BR helped in figure preparation. TH helped in data analysis. All authors reviewed the article.
Mitochondrial 12S rRNA has proven to be a useful molecular marker for better conservation and management of the endangered species. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the mitochondrial 12S rRNA gene has proven to be a reliable and efficient tool for the identification of different Indian deer species of family cervidae. In the present study, mitochondrial 12S rRNA gene sequence of mouse deer (Moschiola indica) belonging to the family Tragulidae was characterized and analysed in silico for its use in species identification. Genomic DNA was isolated from the hair follicles and mitochondrial 12S rRNA gene was amplified using universal primers. PCR product was cloned and sequenced for the first time. The sequence of mouse deer showed 90. 04, 90.08, 90.04, 91.2, 90.04, and 90.08% identities with sika deer, sambar, hog deer, musk deer, chital, and barking deer, respectively. Restriction mapping in Lasergene (DNAstar Inc., Madison, WI, USA) revealed that mouse deer mitochondrial 12S rRNA gene sequence can be differentiated from the other deer species in PCR-RFLP using RsaI, DdeI, BsrI, and BstSFI. With the help of predicted pattern, mouse deer can be identified using genomic DNA from a variety of biomaterials, thereby providing molecular aid in wildlife forensics and conservation of the species.
Journal of Heredity, 2006
Deer in the genera Mazama and Odocoileus generally have two copies of a 75-base-pair (bp) repeat in the left domain of the control region of the mitochondrial DNA (mtDNA). Phylogenetic analyses further suggest an ancient origin for the duplication supporting a previously stated contention that this event occurred before the separation of Mazama and Odocoileus. However, white-tailed deer (Odocoileus virginianus) had three or four copies of a 75-bp repeat in the control region of their mtDNA in 7.8% of the individuals analyzed, and all of these animals were from the coastal plain of the southeastern United States. When copy 3 is present, it is very similar in sequence to copy 2, but variation suggests that copy 3 probably evolved multiple times from copy 2. The pattern of phylogenetic clustering of the haplotypes from across the coastal plain also suggests that phenotypes with three or four copies of the repeat have originated multiple times. The 44 observed haplotypes showed strong spatial subdivision across the area with subpopulations frequently showing complete shifts in haplotype frequencies from others taken from nearby areas. Many of the subpopulations right along the coast or on adjacent barrier islands have a limited number of haplotypes as would occur in populations undergoing drift because of small numbers of breeding females and limited female dispersal.
Mitochondrial Dna Variation in Roe Deer Population from Lithuania
2014
In order to investigate the roe deer population from Lithuania, data on the 457 bp mtDNA control region sequences were analysed. In the samples of 20 roe deer from Lithuania we found 6 different haplotypes, based on 38 variable sites, and observed haplotypes belonged to two haplogroups. Genetic diversity was estimated by haplotype diversity H d =0.800, nucleotide diversity P i =0.03031, average number of nucleotide differences k=13.853, and sequence conservation C=0.917. Haplotypes Hap_1 and Hap_2 were the most common in Lithuanian roe deer population. Comparative analysis of the data was performed using homologous mtDNA control region sequences downloaded in GenBank database. Analyses of control region mtDNA sequences indicated widespread introgression of Siberian roe deer ( C. pygargus ) mtDNA in the European roe deer genome, and introgressed individuals constituted 20% of the deer studied. Phylogenetic findings demonstrated distinction between two clades. Hap_2, Hap_3 and Hap_4 h...
Genes & genetic systems, 2014
The water deer (Hydropotes inermis) is one of the rarest species of deer in the family Cervidae. Only two subspecies exist in East Asia, and few studies have examined the genetic characteristics of the species. Here, we investigated the genetic diversity, phylogeny and population differentiation of the Korean subspecies (H. inermis argyropus). Seventeen mitochondrial D-loop haplotypes (822 bp) were detected and analyzed from 107 individual samples, together with a Chinese subspecies (H. inermis inermis) haplotype. The genetic diversity of the Korean subspecies is lower (π = 0.756%, h = 0.867) than that of the Chinese subspecies estimated in a previous study. This low genetic diversity may result from historical anthropogenic disturbances and/or a founder effect during the glacial period. The phylogenetic tree and median-joining network showed no location-specific distribution of D-loop haplotypes, but revealed two major lineages, A and B, of water deer. The A and B lineages were sep...
SEQUENCE DIVERSITY AND PHYLOGENETIC ANALYSIS IN PAKISTANI SPOTTED DEER (Axis axis)
Pakistan Journal of Agricultural Sciences, 2016
Spotted deer or "Chital" are one of the most common wild herbivore found in forests. The main objective of the study was to assess the genetic variations in mitochondrial cytochrome-b gene, mitochondrial cytochrome-c gene and mitochondrial d-loop region in Pakistani spotted deer. DNA was extracted from fecal samples of unrelated animals of spotted deer from different localities. PCR primers were designed by Primer software and amplification of gene was done by Polymerase Chain Reaction. The PCR products were sequenced. Variations in nucleotide were identified by alignment. Blast 2 sequences, Clustal W, MEGA 3, Bioconductor in "R" were used for analysis. Multidimensional scaling plot of mitochondrial cytochrome-b, c and dloop region, Pair Wise Evolutionary Distance and Phylogenetic Tree was constructed. Variable sites in Cytochrome-b, Cytochrome-c and d-loop region were identified in spotted deer. Allele frequency of all variations was calculated and low mutant allele frequency was observed. High homozygosity was observed in all spotted deer and differences were very low. This is the first report on molecular genetics of spotted deer from Pakistan. The finding of this research is prerequisite for future research.