Phylogenetic analysis

Identification and phylogenetic analysis of a sheep pox virus isolated from the Ningxia Hui Autonomous Region of China

X. L. Zhu, Yang, F., Li, H. X., Dou, Y. X., Meng, X. L., Li, H., Luo, X. N., and Cai, X. P., Identification and phylogenetic analysis of a sheep pox virus isolated from the Ningxia Hui Autonomous Region of China, vol. 12, pp. 1670-1678, 2013.

An outbreak of sheep pox was investigated in the Ningxia Hui Autonomous Region in China. Through immunofluorescence testing, isolated viruses, polymerase chain reaction identification, and electron microscopic examination, the isolated strain was identified as a sheep pox virus. The virus was identified through sequence and phylogenetic analysis of the P32 gene, open reading frame (ORF) 095, and ORF 103 genes. This study is the first to use the ORF 095 and ORF 103 genes as candidate genes for the analysis of sheep pox.

Complete mitochondrial genomes of the Bright Sunbeam Curetis bulis and the Small Copper Lycaena phlaeas (Lepidoptera: Lycaenidae) and their phylogenetic implications

L. L. Zhang, Hao, J. S., Huang, D. Y., Sun, X. Y., Hao, J. J., Peng, C. M., and Yang, Q., Complete mitochondrial genomes of the Bright Sunbeam Curetis bulis and the Small Copper Lycaena phlaeas (Lepidoptera: Lycaenidae) and their phylogenetic implications, vol. 12, pp. 4434-4445, 2013.

In this study, the complete mitochondrial genomes of Curetis bulis and Lycaena phlaeas were determined and analyzed. The circular genomes are 15,162 bp long for C. bulis and 15,280 bp long for L. phlaeas, with a total A+T content of 82.6 and 83.1%, respectively. Both mitogenomes contain 37 genes, and their gene orders are similar to those of other lepidopterans.

Genome-wide analysis of the auxin response factor gene family in cucumber

S. Q. Liu and Hu, L. F., Genome-wide analysis of the auxin response factor gene family in cucumber, vol. 12, pp. 4317-4331, 2013.

Auxin response factors (ARFs) participate in the transcriptional regulation of a series of biological processes related to growth and development. The ARF genes comprise a large multigene family in plants. Recently, a draft of the full cucumber (Cucumis sativus) genome assembly has been released; however, none of the ARF genes have been characterized. We made a comprehensive analysis of ARF genes in this species. Fifteen ARF genes were identified and could be divided into three classes.

Identification of marker genes in diabetic wounds by DNA microarray study

T. Ni, Wang, N., Mao, Z. G., and Yao, M., Identification of marker genes in diabetic wounds by DNA microarray study, vol. 12, pp. 5348-5355, 2013.

This study aimed to identify marker genes in diabetic wounds using a dataset based on a DNA microarray of dermal lymphatic endothelial cells, and our results provide a basic understanding of diabetic wounds through further study of these differentially expressed genes (DEGs). From the Gene Expression Omnibus database, we downloaded a gene expression microarray (GSE38396) that includes 8 samples: 4 normal controls and 4 disease samples (type II diabetes).

Phylogenetic analysis of substrate-binding subunits in an osmoprotectant system

T. J. D. Coutinho, Rodrigues, N. F., and Farias, S. T., Phylogenetic analysis of substrate-binding subunits in an osmoprotectant system, vol. 12, pp. 5743-5757, 2013.

Substrate-binding subunits are important components of the solute importation system, known as the osmoprotectant system, which consists of a membrane protein belonging to the ABC superfamily. These molecules recognize specific substrates that have different physiological roles in prokaryotes, i.e., roles that contribute to the survival of these organisms in environments with high concentrations of salt.

VP6 gene diversity in Brazilian strains of porcine group C rotavirus

K. C. Médici, Barry, A. F., Alfieri, A. F., and Alfieri, A. A., VP6 gene diversity in Brazilian strains of porcine group C rotavirus, vol. 9, pp. 506-513, 2010.

Group C rotavirus (RV-C) has been found in Brazilian pig herds; however, wild-type strains have not yet been characterized. We made a molecular analysis of a region of gene 5 in Brazilian RV-C strains. Stool samples from 11 piglets (diarrheic and with normal consistency) positive for the RV-C VP6 gene in an RT-PCR assay were sequenced. A 270-bp amplicon of nine sequences was analyzed. All sequences showed high identity to the Cowden strain of the porcine RV-C prototype and 81.3 to 94.3% to each other (230 nucleotide fragment).

Genome-wide analysis of cyclins in maize (Zea mays)

X. Hu, Cheng, X., Jiang, H., Zhu, S., Cheng, B., and Xiang, Y., Genome-wide analysis of cyclins in maize (Zea mays), vol. 9, pp. 1490-1503, 2010.

Cyclins are primary regulators of the activity of cyclin-dependent kinases and play crucial roles in cell cycle progression in eukaryotes. Although extensive studies have revealed the roles of some cyclins and underlying mechanisms in plants, relatively few cyclins have been functionally analyzed in maize. We identified 59 cyclins in the maize genome, distributed on 10 chromosomes; these were grouped into six types by phylogenetic analysis. The cyclin genes in the maize genome went through numerous tandem gene duplications on five chromosomes.

Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene

S. Y. Chee, Devakie, M. N., and Azizah, M. N. Siti, Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene, vol. 10, pp. 1237-1244, 2011.

Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T.

mtDNA variation of the critically endangered hawksbill turtle (Eretmochelys imbricata) nesting on Iranian islands of the Persian Gulf

M. Tabib, Zolgharnein, H., Mohammadi, M., Salari-Aliabadi, M. A., Qasemi, A., Roshani, S., Rajabi-Maham, H., and Frootan, F., mtDNA variation of the critically endangered hawksbill turtle (Eretmochelys imbricata) nesting on Iranian islands of the Persian Gulf, vol. 10, pp. 1499-1503, 2011.

Genetic diversity of sea turtles (hawksbill turtle) was studied using sequencing of mitochondrial DNA (mtDNA, D-loop region). Thirty dead embryos were collected from the Kish and Qeshm Islands in the Persian Gulf. Analysis of sequence variation over 890 bp of the mtDNA control region revealed five haplotypes among 30 individuals. This is the first time that Iranian haplotypes have been recorded. Nucleotide and haplotype diversity was 0.77 and 0.001 for Qeshm Island and 0.64 and 0.002 for Kish Island, respectively.

Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber

S. Q. Liu, Liu, X. H., and Jiang, L. W., Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber, vol. 10, pp. 2613-2636, 2011.

Plant lipoxygenase (LOX) is involved in growth and developmental control processes, through the biosynthesis of regulatory molecules and defense responses to pathogens, wounding and stress. To date, few LOX proteins and little tissue expression profiling have been reported in detail for cucumber (Cucumis sativus L.). Recent completion of the cucumber genome sequence now permits genome-wide analysis of the LOX gene family in cucumber as well as comparison with LOX in Arabidopsis and rice.

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