Phylogenetic analysis

Complete mitochondrial genome of a natural triploid crucian carp mutant, Carassius auratus var. pingxiangnensis, and phylogenetic analysis of different ploidies in crucian carp

J. Q. Sheng, Wang, J. H., He, S. H., Zeng, L. G., Peng, K., and Hong, Y. J., Complete mitochondrial genome of a natural triploid crucian carp mutant, Carassius auratus var. pingxiangnensis, and phylogenetic analysis of different ploidies in crucian carp, vol. 13, pp. 5849-5864, 2014.

Carassius auratus var. pingxiangnensis is a natural triploid crucian carp mutant. In order to understand its placement and genetic background at the gene level, the characteristics of mitochondrial DNA sequences and phylogenetic relationship were examined. The results showed that the mitochondrial DNA is a circular double-stranded DNA molecule that is 16,576 bp in length with 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding control region.

Characterization of the Toxoplasma gondii hsp60 gene sequences from different hosts and geographical locations

J. Lu, Zhou, D. H., Chen, J., Zhang, N. Z., Wang, R. A., Weng, Y. B., and Zhu, X. Q., Characterization of the Toxoplasma gondii hsp60 gene sequences from different hosts and geographical locations, vol. 13, pp. 6906-6911, 2014.

The intracellular protozoan Toxoplasma gondii is one of the most successful parasites, with the ability to invade all warm-blooded animals, including humans. T. gondii heat shock protein 60 (TgHSP60) plays an important role in intracellular survival and in the differentiation of the parasite, and is also recognized as being associated with its virulence. In the present study, we examined sequence variation in the hsp60 coding region among five T.

Genome-wide identification and phylogenetic analysis of the SBP-box gene family in melons

Y. Ma, Guo, J. W., Bade, R., Men, Z. H., and Hasi, A., Genome-wide identification and phylogenetic analysis of the SBP-box gene family in melons, vol. 13, pp. 8794-8806, 2014.

The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants, including green algae, moss, silver birch, snapdragon, Arabidopsis, rice, and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in melon.

Genome-wide survey and phylogenetic analysis on subunit sequences of eukaryotic DNA polymerase delta

H. F. Song, Chen, H. Q., Wang, Y., and Zhou, Y. J., Genome-wide survey and phylogenetic analysis on subunit sequences of eukaryotic DNA polymerase delta, vol. 13, pp. 9558-9568, 2014.

DNA polymerase d is not only the major replicative enzyme in eukaryotic chromosomal DNA synthesis but is also the primary polymerase for most DNA repair pathways. However, the subunit composition of polymerase d varies in different organisms. While polymerase d in many eukaryotic species has all 4 subunits (POLD1, 2, 3, and 4), many other organisms do not possess POLD4. Whether POLD4 is indispensable and why these differences exist are unknown.

Cloning and sequence analysis of the Blumea balsamifera DC farnesyl diphosphate synthase gene

Y. X. Pang, Guan, L. L., Wu, L. F., Chen, Z. X., Wang, K., Xie, X. L., Yu, F. L., Chen, X. L., Zhang, Y. B., and Jiang, Q., Cloning and sequence analysis of the Blumea balsamifera DC farnesyl diphosphate synthase gene, vol. 13, pp. 9874-9882, 2014.

Blumea balsamifera DC is a member of the Compositae family and is frequently used as traditional Chinese medicine. Blumea balsamifera is rich in monoterpenes, which possess a variety of pharmacological activities, such as antioxidant, anti-bacteria, and anti-viral activities. Farnesyl diphosphate synthase (FPS) is a key enzyme in the biosynthetic pathway of terpenes, playing an important regulatory role in plant growth, such as resistance and secondary metabolism.

FastJoin, an improved neighbor-joining algorithm

J. Wang, Guo, M. - Z., and Xing, L. L., FastJoin, an improved neighbor-joining algorithm, vol. 11. pp. 1909-1922, 2012.

Reconstructing the evolutionary history of a set of species is an elementary problem in biology, and methods for solving this problem are evaluated based on two characteristics: accuracy and efficiency. Neighbor-joining reconstructs phylogenetic trees by iteratively picking a pair of nodes to merge as a new node until only one node remains; due to its good accuracy and speed, it has been embraced by the phylogeny research community. With the advent of large amounts of data, improved fast and precise methods for reconstructing evolutionary trees have become necessary.

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica)

C. H. Zhang, Shangguan, L. F., Ma, R. J., Sun, X., Tao, R., Guo, L., Korir, N. K., and Yu, M. L., Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica), vol. 11, pp. 4789-4809, 2013.

We identified 131 AP2/ERF (APETALA2/ethylene-responsive factor) genes in material from peach using the gene sequences of AP2/ERF amino acids of Arabidopsis thaliana (Brassicaceae) as probes. Based on the number of AP2/ERF domains and individual gene characteristics, the AP2/ERF superfamily gene in peach can be classified broadly into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), containing 104, 5, and 21 members, respectively, along with a solo gene (ppa005376m).

Entropy-based approach for selecting informative regions in the L1 gene of bovine papillomavirus for phylogenetic inference and primer design

M. V. A. Batista, Freitas, A. C., and Balbino, V. Q., Entropy-based approach for selecting informative regions in the L1 gene of bovine papillomavirus for phylogenetic inference and primer design, vol. 12, pp. 400-407, 2013.

Bovine papillomaviruses (BPVs) cause many benign and malignant lesions in cattle and other animals. Twelve BPV types have been identified so far, and several putative novel BPV types have been detected based on the analysis of L1 gene fragments, generated by FAP59/64 and MY11/09 primers. Phylogenetic trees are important in studies that describe novel BPV types. However, topological mistakes could be a problem in such studies. Therefore, we made use of entropy to find phylogenetic informative regions in the BPV L1 gene sequences from all 12 BPVs.

In silico analysis of diverse endophytic fungi by using ITS1-5,8S-ITS2 sequences with isolates from various plant families in Brazil

S. A. Rhoden, Garcia, A., Azevedo, J. L., and Pamphile, J. A., In silico analysis of diverse endophytic fungi by using ITS1-5,8S-ITS2 sequences with isolates from various plant families in Brazil, vol. 12, pp. 935-950, 2013.

Brazil has a great diversity of plants, and considering that all plant species studied to date have endophytic microorganisms (bacteria or fungi), the country is a resource in the search for bioactive compounds. Endophytes live within plants without causing damage and may be in dynamic equilibrium with the health of the plant. Endophytic fungi can be identified by sequencing the region corresponding to internal transcribed spacer 1-5,8S-internal transcribed spacer 2 ribosomal DNA, and carrying out phylogenetic analyses of these sequences helps to identify species.

Isolation and phylogenetic analysis of novel γ-gliadin genes in genus Dasypyrum

G. R. Li, Liu, C., Yang, E. N., and Yang, Z. J., Isolation and phylogenetic analysis of novel γ-gliadin genes in genus Dasypyrum, vol. 12, pp. 783-790, 2013.

As the most ancient member of the wheat gluten family, the γ-gliadin genes are suitable for phylogenetic analysis among wheat and related species. Species in the grass genus Dasypyrum have been widely used for wheat cross breeding. However, the genomic relationships among Dasypyrum species have been little studied. We isolated 22 novel γ-gliadin gene sequences, among which 10 are putatively functional. The open reading frame lengths of these sequences range from 642 to 933 bp, and these putative proteins consist of five domains.

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