Molecular characterization, balancing selection, and genomic organization of the tree shrew (Tupaia belangeri) MHC class I gene

Zhang, Xihe; Dai, Zheng-Xi; Zhang, Gao-Hong; Han, Jian; Zheng, Yong‐Tang

doi:10.1016/j.gene.2013.03.113

Cited by 24 publications

(14 citation statements)

References 42 publications

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“…In our diagram of phylogenetic tree, Feliformia (cat), Lagomorpha (rabbit) and Caniformia (dog) as the closer specie to the tree shrew than Primates ; and tree shrew is closer to Primates than Lagomorpha (Rabbit) and Rodentia (mouse, rat, and guinea pig) those were generally used as experimental animals. This is in consistent with previous studies in tree shrew MHC class I gene [25], [26].…”

Section: Resultssupporting

confidence: 94%

Identification of Glyceraldehyde 3-Phosphate Dehydrogenase Sequence and Expression Profiles in Tree Shrew (Tupaia belangeri)

et al. 2014

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The tree shrews (Tupaia belangeri) diverged from the primate order (Primates) and are classified as Scandentia, a separate taxonomic group of mammals. The tree shrew has been suggested to use an animal model to study human disease but the genomic sequences of tree shrew is largely unidentified. Here we identified the full-length cDNA sequence of a housekeeping gene, Glyceraldehyde 3-phosphate Dehydrogenase (GAPDH), in tree shrew. We further constructed a phylogenetic family tree base on GAPDH molecules of various organisms and compared GAPDH sequences with human and other small experimental animals. These study revealed that tree shrew was closer to human than mouse, rat, rabbit and guinea pig. The Quantitative Reverse Transcription PCR and western blot analysis further demonstrated that GAPDH expressed in various tissues in tree shrew as a general conservative housekeeping proteins as in human. Our findings provide the novel genetic knowledge of the tree shrew and strong evidences that tree shrew can be an experimental model system to study human disorders.

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Section: Resultssupporting

confidence: 94%

Identification of Glyceraldehyde 3-Phosphate Dehydrogenase Sequence and Expression Profiles in Tree Shrew (Tupaia belangeri)

et al. 2014

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“…As shown in the cladogram (Fig. 2), the closest phylogenetic relatives to the tree shrew, not belonging to the order of Primates, are the rabbit (Oryctolagus cuniculus) and horse (Equus caballus), which is consistent with the results of previous studies on the tree shrew MHC gene (33,34). Our results support the current classification of the tree shrew, namely that the tree shrew is a small-sized mammal phylogenetically closer to humans than other small-sized experimental animals, such as the mouse, rat, rabbit and guinea pig, but phylogenetically farther than non-human primates, such as the chimpanzee and monkey.…”

Section: Discussionsupporting

confidence: 91%

Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri)

Zheng

Yun

Wang

et al. 2014

International Journal of Molecular Medicine

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The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

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“…It was found that the highest time of divergence of the GAPDH gene occurred between sheep and common chimpanzee but least time of divergence of the GAPDH gene is observed between killer whale and dolphin. The phylogenetic analysis of this study was showed in Fig 4. It was observed that GAPDH gene of the herbivorous animals (sheep, goat, cattle, w. buffalo) are clustered together due to closer identity and similarity percentage but however, Human, rhesus monkey, chimpanzee and cat are more closer in the phylogenetic tree which can be inferred that this enzyme can be considered as housekeeping gene in all domestic animals which is in accordance with the previous studies (Zhang et al, 2013).…”

Section: Structural Analysissupporting

confidence: 88%

In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

Sahoo

Mishra

Mohapatra

et al. 2019

IJAR

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This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

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Molecular characterization, balancing selection, and genomic organization of the tree shrew (Tupaia belangeri) MHC class I gene

Cited by 24 publications

References 42 publications

Identification of Glyceraldehyde 3-Phosphate Dehydrogenase Sequence and Expression Profiles in Tree Shrew (Tupaia belangeri)

Identification of Glyceraldehyde 3-Phosphate Dehydrogenase Sequence and Expression Profiles in Tree Shrew (Tupaia belangeri)

Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri)

In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

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