Sequence analysis and phylogenetic evolution study of lysozyme gene on six populations in bovinae.
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The nucleotide sequence of coding region of the lysozyme gene on six populations in Bovinae was analyzed using the methods of PCR amplification and sequencing,and the nucleotide sequence of coding region was compared with the homologous lysozyme gene on Hereford retrieved from the GenBank.Phylogenetic tree was constructed by Neighbour-Joining method.The results showed that 5 nucleotide polymorphic sites were observed with 9 haplotypes in the 5 Bovinae populations(except Bubalis).The nucleotide diversities ranged from 0.00000 to 0.00196,indicating a low intrapopulation genetic diversity.Constructing molecular phylogenetic tree showed that Bos indicus,Menggu cattle and Luxi cattle were more closed,the relationships of Bos indicus,B.taurus and B.grunniens were comparatively closer than that of B.frontalis.Keywords:
Nucleotide diversity
Coding region
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Sequence (biology)
Phylogenetic relationship
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ABSTRACT We tested whether comparative sequence analysis of the mitochondrion-encoded cytochrome c oxidase subunit 2 gene ( COX2 ) could be used to distinguish intraspecific variants of Candida glabrata . Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intraspecific variation. For this survey we used 11 clinical isolates of C. glabrata from three different geographical locations in Brazil, 10 isolates from one location in the United States, 1 American Type Culture Collection strain as an internal control, and the published sequence of strain CBS 138. The complete coding region of COX2 was amplified from total cellular DNA, and both strands were sequenced twice for each strain. These sequences were aligned with published sequences from other fungi, and the numbers of substitutions and phylogenetic relationships were determined. Typing of these strains was done by using 17 substitutions, with 8 being nonsynonymous and 9 being synonymous. Also, cDNAs made from purified mitochondrial polyadenylated RNA were sequenced to confirm that our sequences correspond to the expressed copies and not nuclear pseudogenes and that a frameshift mutation exists in the 3′ end of the coding region (position 673) relative to the Saccharomyces cerevisiae sequence and the previously published C. glabrata sequence. We estimated the average evolutionary rate of COX2 to be 11.4% sequence divergence/10 8 years and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of COX2 sequences enables typing of C. glabrata strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphism that discriminates strains isolated in the United States and strains isolated in Brazil. This provides for the first time a means of typing of Candida strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.
Pseudogene
Candida glabrata
Nonsynonymous substitution
Coding region
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[Objective] The aim was to prove that the mitochondrial genes of Cyt b and 12S rRNA with different evolutional rates have effects on the topological structures of phylogenetic trees.[Method] The complete sequences of Cyt b and 12S rRNA from 15 species in 12 families of snakes were downloaded and extracted from GenBank,while their molecular phylogenetic trees were constructed by Maximum Likelihood(ML) method with GTR+I+G substitute model based on PAUP4.0 software.[Result] With the same software,methods and species,the difference in topological structures of phylogenetic trees was mainly due to different evolutional rates of Cyt b and 12S rRNA genes.[Conclusion] In studies on phylogenetic trees,aimed to different research species and purposes,phylogenetic trees should be constructed by choosing the correct and appropriate genes.
Phylogenetic relationship
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In this study,we designed primers according to sable gene and obtained the complete mitochon-drial 12S rRNA gene sequences of 7 breeds of mink by PCR amplification,sequencing and assembling.Sequence analysis revealed that 12S rRNA gene of minks was 960 or 962 bp in length,the composition of the nucleotides was 37.50%A,17.60%G,22.19%T and 22.71%C.8 variable sites were observed,and the transition/transversion(Ts/Tv)was 3.Given sable as outgroup and homologous sequences of 11 species in the mustela retrieved from GenBank,the phylogenetic trees were constructed respectively by N-J and MP methods.The results indicated that minks in China compared with American minks had closer relationship than that with European mink.
Transversion
Sequence (biology)
Maximum parsimony
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To study the differences and evolutionary relationships of the 16 S rRNA gene sequences among the four main meat species including Bos taurus,Ovis aries,Gallus gallus,and Sus scrofa,and to establish a basis for the identification method of the meat sold in the restaurant market. A pair of universal primers of the 16 S rRNA gene was synthesized,and then the 16 S rRNA genes in the muscle tissue from the four animals including Bos taurus,Ovis aries,Gallus gallus,and Sus scrofa were amplified using PCR method for sequence analysis and phylogenetic tree analysis. The results showed that the 16 S rRNA genes from the four animals could be well amplified using the PCR amplification system and conditions. Compared with the standard sequences published in Gen Bank,respectively,each of the four main meat species shared more than99% homology,showing higher homology; there were differences or indels on the 174 sites in between the sequences of the species,which shared lower homology. On the evolutionary relationship of the species,Bos Taurus and Ovis aries had the nearest relationship,followed by Sus scrofa and Gallus gallus. The results indicate that there is a significant species- specific difference in the 16 S rRNA gene,which can be used as a candidate gene for gene barcode. The 16 S rRNA gene can be used to establish the appropriate molecular diagnostic methods,for the identification of meat species and clinical detection.
Ovis
Homology
Indel
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Flammulina
Sequence (biology)
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rpoB sequences encoding the β-subunit of RNA polymerase were determined in 26 Mycoplasma species for phylogenetic study. The portion of rpoB DNA used in this study showed a high degree of variation in terms of size and sequence among species. The rpoB phylogenies inferred from amino acid and nucleotide sequences were used to divide the mycoplasmas into two groups, a 'pneumoniae group' and a 'hominis group', which was consistent with the result from 16S rDNA sequence analysis. However, phylogenetic relationships within these groups differed in the two gene trees, which were supported by the incongruence length difference (ILD) test. This indicates that multiple gene sequences must be applied to infer accurate phylogenetic relationships among the mycoplasmas. The rpoB sequence, and especially the deduced amino acid sequence, offers a good alternative marker.
rpoB
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Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode. Key words: Theileria sp., 28S rRNA, phylogeny, cattle, sheep, China
Theileria
28S ribosomal RNA
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The genomic DNA of Eperthrozoon ovis was extracted from blood samples of sheeps naturally infected with eperthrozoons in Shihezi and Hangzhou districts and was amplified with PCR by a pair of primers designed according to the published genomic sequence of 16S rRNA of eperthrozoon gene locating in the conserved region of the corresponding sequence of haematophilic bacteria.In this way,a target fragment with size about 1 100 bps was amplified.The amplified fragments were cloned and sequenced and the sequencing result showed that this fragments comprised of two sequences of 1 080 bps and 1 079 bps respectively(GenBank No.EU916726 and FJ440328).The result in phylogenetic analysis indicated that these two sequences were 99.7% identical to the published reference sequence AF338268.These sequences were compared with those sequences of 5 mycoplasma,14 haematophilic bacteria and rickettsia available in GenBank,thus the phylogenetic tree was established,in which they formed a large phylogenetic branch with other haematophilic bacteria and were very close to the Mycoplasma genus of Mycoplasmataloes as proposed by Neimark et al.This result of analysis sustains the advice that Erthrozoon and Haemobartonella genera should be reclassified in Mycoplasma genus of mycoplasmatales.
genomic DNA
Mega-
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