Phylogenetic analysis

Extracellular enzymatic profiles and taxonomic identification of endophytic fungi isolated from four plant species

R. N. Alberto, Costa, A. T., Polonio, J. C., Santos, M. S., Rhoden, S. A., Azevedo, J. L., Pamphile, J. A., Alberto, R. N., Costa, A. T., Polonio, J. C., Santos, M. S., Rhoden, S. A., Azevedo, J. L., and Pamphile, J. A., “Extracellular enzymatic profiles and taxonomic identification of endophytic fungi isolated from four plant species”, vol. 15, no. 4, p. -, 2016.

INTRODUCTION

Endophytic fungi exhibit complex interactions with their hosts. This fact has recently triggered several studies exploring their utilization as sources of novel bioactive natural products. Although the production of metabolites depends on several factors, fungi employ molecular pathways resulting in specific compounds. The products of these metabolic processes include important drugs such as penicillin and statins, and toxic substances such as aflatoxins (Keller et al., 2005).

Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus samples obtained from farms in Gansu, China

M. Z. Huang, Wang, H., Wang, S. Y., Cui, D. A., Tuo, X., Liu, Y. M., Huang, M. Z., Wang, H., Wang, S. Y., Cui, D. A., Tuo, X., Liu, Y. M., Huang, M. Z., Wang, H., Wang, S. Y., Cui, D. A., Tuo, X., and Liu, Y. M., “Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus samples obtained from farms in Gansu, China”, vol. 15, p. -, 2016.

Porcine epidemic diarrhea poses significant sanitation problems in the porcine industry, and has negatively affected the economy in recent years. In this study, 48 fecal specimens were collected from piglets from four intensive swine farms located in the Gansu Province of China. The molecular diversity and phylogenetic relationships between porcine epidemic diarrhea viruses (PEDV) prevalent in Gansu were probed, and the resultant proteins were characterized.

Cloning, sequence characterization, and expression patterns of members of the porcine TSSK family

P. Wang, Huo, H. L., Wang, S. Y., Miao, Y. W., Zhang, Y. Y., Zhang, Q. L., Li, F. Q., Liu, L. X., Li, W. Z., Zeng, Y. Z., Huo, J. L., and Xiao, H., “Cloning, sequence characterization, and expression patterns of members of the porcine TSSK family”, vol. 14, pp. 14908-14919, 2015.

Testis-specific serine kinases (TSSKs) are a family of serine/threonine kinases highly expressed in the testes that are responsible for regulating many spermatogenesis-related protein activities. Mutations in this family have a positive relationship with oligospermia and azoospermia in human and mouse. Here, five members of the TSSK family from a Banna mini-pig inbred line (BMI) were cloned, sequenced, and characterized.

Homology-based analysis of the GRAS gene family in tobacco

Y. Q. Chen, Tai, S. S., Wang, D. W., Ding, A. M., Sun, T. T., Wang, W. F., and Sun, Y. H., “Homology-based analysis of the GRAS gene family in tobacco”, vol. 14, pp. 15188-15200, 2015.

Members of the GRAS gene family are important transcriptional regulators. In this study, 21 GRAS genes were identified from tobacco, and were classified into eight subgroups according to the classification of Arabidopsis thaliana. Here, we provide a preliminary overview of this gene family in tobacco, describing the gene structure, gene expression, protein motif organization, phylogenetic analysis, and comparative analysis in tobacco, Arabidopsis, and rice.

Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research

Y. C. Yang, Kung, T. L., Hu, C. Y., and Lin, S. F., “Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research”, vol. 14, pp. 14857-14870, 2015.

Variation in the chloroplast DNA sequence is useful for plant phylogenetic studies. However, the number of variable sequences provided by chloroplast DNA for suggested genes or genomic regions in plant phylogenetic analyses is often inadequate.

Molecular cloning and evolutionary analysis of captive forest musk deer bitter taste receptor gene T2R16

G. J. Zhao, Wu, N., Li, D. Y., Zeng, D. J., Chen, Q., Lu, L., Feng, X. L., Zhang, C. L., Zheng, C. L., and Jie, H., “Molecular cloning and evolutionary analysis of captive forest musk deer bitter taste receptor gene T2R16”, vol. 14, pp. 16185-16195, 2015.

Sensing bitter tastes is crucial for most animals because it can prevent them from ingesting harmful food. This process is mainly mediated by the bitter taste receptors (T2R) that are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires. Marked variation in repertoire size has been noted among species. However, research on T2Rs is still limited and the mechanisms underlying the evolution of vertebrate T2Rs remain poorly understood.

Sequence variation in the Toxoplasma gondii ROP20 gene among strains from different hosts and geographical locations

H. R. Ning, .L.Wang, J., Qin, S. Y., Huang, S. Y., Lou, Z. L., Hu, L. Y., and Zhu, X. Q., “Sequence variation in the Toxoplasma gondii ROP20 gene among strains from different hosts and geographical locations”, vol. 14, pp. 8414-8419, 2015.

Toxoplasma gondii, an opportunistic protozoan parasite, infects almost all warm-blooded animals. In this study, we examined the sequence variation in rhoptry protein 20 (ROP20) genes among 18 T. gondii isolates collected from different hosts and geographical regions. Full length ROP20 genes were amplified and sequenced. The results showed that the genes were 1659 bp in length and contained only a single exon, and that the A+T content varied from 46.68 to 47.20% among the 18 strains.

In silico analysis of the 16S rRNA gene of endophytic bacteria, isolated from the aerial parts and seeds of important agricultural crops

C. Bredow, Azevedo, J. L., Pamphile, J. A., Mangolin, C. A., and Rhoden, S. A., “In silico analysis of the 16S rRNA gene of endophytic bacteria, isolated from the aerial parts and seeds of important agricultural crops”, vol. 14, pp. 9703-9721, 2015.

Because of human population growth, increased food production and alternatives to conventional methods of biocontrol and development of plants such as the use of endophytic bacteria and fungi are required. One of the methods used to study microorganism diversity is sequencing of the 16S rRNA gene, which has several advantages, including universality, size, and availability of databases for comparison. The objective of this study was to analyze endophytic bacterial diversity in agricultural crops using published papers, sequence databases, and phylogenetic analysis.

Genome-wide identification and characterization of the Dof gene family in Medicago truncatula

Y. J. Shu, Song, L. L., Zhang, J., Liu, Y., and Guo, C. H., “Genome-wide identification and characterization of the Dof gene family in Medicago truncatula”, vol. 14, pp. 10645-10657, 2015.

The DNA-binding one zinc finger (Dof) family is a classic plant-specific zinc-finger transcription factor family, which is involved in many important processes, including seed maturation and germination, plant growth and development, and light responses. Investigation of the Medicago truncatula genome revealed 42 putative Dof genes, each of which holds one Dof domain. These genes were classified into four groups based on phylogenetic analysis, which are similar to the groups reported for Arabidopsis and rice.

Conservation and population genetic diversity of Curcuma wenyujin (Zingiberaceae), a multifunctional medicinal herb

W. H. Zheng, Zhuo, Y., Liang, L., Ding, W. Y., Liang, L. Y., and Wang, X. F., “Conservation and population genetic diversity of Curcuma wenyujin (Zingiberaceae), a multifunctional medicinal herb”, vol. 14, pp. 10422-10432, 2015.

Curcuma wenyujin is an important multifunctional medicinal herb in China. Currently, populations of C. wenyujin are decreasing, and wild individuals have almost disappeared from their natural habitats. Moreover, little is known regarding the molecular characteristics of this plant. In this study, we investigated the genetic diversity and variation of five populations of C. wenyujin, using ran­dom amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers.

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