Phylogenetic analysis

Phylogenetic analysis of widely cultivated Ganoderma in China based on the mitochondrial V4-V6 region of SSU rDNA

X. W. Zhou, Su, K. Q., and Zhang, Y. M., “Phylogenetic analysis of widely cultivated Ganoderma in China based on the mitochondrial V4-V6 region of SSU rDNA”, vol. 14, pp. 886-897, 2015.

Ganoderma mushroom is one of the most prescribed traditional medicines and has been used for centuries, particularly in China, Japan, Korea, and other Asian countries. In this study, different strains of Ganoderma spp and the genetic relationships of the closely related strains were identified and investigated based on the V4-V6 region of mitochondrial small subunit ribosomal DNA of the Ganoderma species. The sizes of the mitochondrial ribosomal DNA regions from different Ganoderma species showed 2 types of sequences, 2.0 or 0.5 kb.

Sequence characterization and phylogenetic analysis of toll-like receptor (TLR) 4 gene in the Tibetan macaque (Macaca thibetana)

Q. X. Dai, Yao, Y. F., Qi, Z. C., Huang, Y., Ni, Q. Y., Zhang, M. W., and Xu, H. L., “Sequence characterization and phylogenetic analysis of toll-like receptor (TLR) 4 gene in the Tibetan macaque (Macaca thibetana)”, vol. 14, pp. 1875-1886, 2015.

In this study, the complete coding region sequence of an innate immune-related TLR4 gene was obtained from the Tibetan macaque (Macaca thibetana) genome via PCR and direct sequencing. The sequence had a total length of 2481 bp, contained 3 complete exons, and encoded 826 amino acids (AAs); its isoelectric point was 5.703, and the molecular weight was 94.72 kDa. The high structure prediction showed that the protein was comprised of one extracellular region, one transmembrane region, and one intracellular region.

Evaluation of the genetic diversity of Bupleurum using amplified fragment length polymorphism analysis

S. Y. Ke, Shi, L. L., Ma, Y. Z., and Zhou, X. J., “Evaluation of the genetic diversity of Bupleurum using amplified fragment length polymorphism analysis”, vol. 14, pp. 2590-2599, 2015.

Radix bupleuri (Chaihu), the dried root of the Bupleurum plant, is an important component of traditional Chinese medicine. In this study, we examined the genetic diversity of 11 Bupleurum strains, originating from 7 provinces in China, using amplified fragment length polymorphism analysis. A total of 274 polymorphic bands were obtained using 6 primer combinations, indicating a high level of polymorphism across all strains.

Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis)

X. Y. Huang, Tao, P., Li, B. Y., Wang, W. H., Yue, Z. C., Lei, J. L., and Zhong, X. M., “Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis)”, vol. 14, pp. 2189-2204, 2015.

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetable crops grown worldwide, and various methods exist for selection, propagation, and cultivation. The entire Chinese cabbage genome has been sequenced, and the heat shock transcription factor family (Hsfs) has been found to play a central role in plant growth and development and in the response to biotic and abiotic stress conditions, particularly in acquired thermotolerance. We analyzed heat tolerance mechanisms in Chinese cabbage.

Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya

C. T. Chiu, Wang, C. W., Chen, F. C., Chin, S. W., Liu, C. C., Lee, M. J., Chung, W. C., Chien, Y. W., Chang, H. J., and Lee, C. Y., “Sexual genetic and simple sequence repeat (SSR) analysis for molecular marker development on the all hermaphrodite papaya”, vol. 14, pp. 2502-2511, 2015.

The papaya (Carica papaya L.) is one of the most important economic tropical fruits in the world, and the hermaphrodite is the preferred type in field cultures. We analyzed the sexual ratio of offspring from the cultivar ‘Taiwan Seed Station No. 7’ (T7) by a self-cross and its cross with Taichung Sunrise (TS). Female progeny from the T7 self-crossing were not observed. This finding may be caused by a lethal gene that is linked to females. In this study, we selected 192 simple sequence repeats (SSRs) to analyze the polymorphism between T7 and TS.

Phylogeographic analysis of African swine fever virus based on the p72 gene sequence

Y. Muangkram, Sukmak, M., and Wajjwalku, W., “Phylogeographic analysis of African swine fever virus based on the p72 gene sequence”, vol. 14, pp. 4566-4574, 2015.

African swine fever virus (ASFV) outbreak has been considered as an emerging and re-emerging disease for almost a century. Diagnostically, simple polymerase chain reaction and sequencing-based molecular detection could be employed for both viral identification and genotyping. This study established a novel phylogenetic analysis and epidemiology comparison based on 205 bp of p72 gene sequences. Based on this partial p72 fragment, an updated list of 44 different genotypes from a total of 516 ASFV sequences compiled from GenBank was generated.

Cloning and sequence analysis of the safflower betaine aldehyde dehydrogenase gene

Y. B. Wang, Guan, L. L., Xu, Y. W., Shen, H., and Wu, W., “Cloning and sequence analysis of the safflower betaine aldehyde dehydrogenase gene”, vol. 13, pp. 344-353, 2014.

In response to salinity or drought stress, many plants accumulate glycine betaine, which is a regulator of osmosis. In plants, the last step in betaine synthesis is catalyzed by betaine aldehyde dehydrogenase (BADH), a nuclear-encoded chloroplastic enzyme. Based on the conserved oligo amino acid residues of the published BADH genes from other higher plant species, a cDNA sequence, designated CtBADH, was isolated from safflower (Carthamus tinctorius L.) using a polymerase chain reaction approach.

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

C. H. Zhang, Ma, R. J., Shen, Z. J., Sun, X., Korir, N. K., and Yu, M. L., “Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)”, vol. 13, pp. 2654-2668, 2014.

In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths.

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Q. J. Chao, Li, Y. D., Geng, X. X., Zhang, L., Dai, X., Zhang, X., Li, J., and Zhang, H. J., “Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia”, vol. 13, pp. 2739-2751, 2014.

This is the first report of a complete mitochondrial genome sequence from Himalayan marmot (Marmota himalayana, class Marmota). We determined the M. himalayana mitochondrial (mt) genome sequence by using long-PCR methods and a primer-walking sequencing strategy with genus-specific primers. The complete mt genome of M. himalayana was 16,443 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (CR).

Sequence variation in the Toxoplasma gondii eIF4A gene among strains from different hosts and geographical locations

J. Chen, Fang, S. F., Zhou, D. H., Li, Z. Y., Liu, G. H., and Zhu, X. Q., “Sequence variation in the Toxoplasma gondii eIF4A gene among strains from different hosts and geographical locations”, vol. 13, pp. 3356-3361, 2014.

Toxoplasma gondii is an opportunistic protozoan parasite that infects a wide range of animals, including humans. The T. gondii eukaryotic translation initiation factor 4A (eIF4A) protein is expressed in the tachyzoite, but its expression is markedly downregulated in the bradyzoite, and it is therefore considered to be associated with tachyzoite virulence.

Phylogenetic analysis