Genetic diversity and matrilineal structure in Chinese tree shrews inhabiting Kunming,China

Due to their special phylogenetic position in the Euarchontoglires and close affinity to primates,tree shrews have been proposed as an alternative experimental animal to primates in biomedical research.However,the population genetic structure of tree shrews has largely remained unknown and this has hindered the development of tree shrew breeding and selection.Here we sampled 80 Chinese tree shrews（Tupaia belangeri chinensis） in Kunming,China,and analyzed partial mtDNA control region sequence variation.Based on our samples and two published sequences from northern tree shrews（T.belangeri）,we identified 29 substitutions in the mtDNA control region fragment（～ 604 bp） across 82 individuals and defined 13 haplotypes.Seventeen samples were selected for sequencing of the cytochrome b（Cyt b;1134 bp） gene based on control region sequence variation and were analyzed in combination with 34 published sequences to solidify the phylogenetic pattern obtained from control region data.Overall,tree shrews from Kunming have high genetic diversity and present a remarkable long genetic distance to the two reported northern tree shrews outside China.Our results provide some caution when using tree shrews to establish animal models because of this apparent genetic difference.In addition,the high genetic diversity of Chinese tree shrews inhabiting Kunming suggests that systematic genetic investigations should be conducted before establishing an inbred strain for medical and biological research.

Creating animal models, why not use the Chinese tree shrew ( Tupaia belangeri chinensis)？

The Chinese tree shrew （Tupaia belangeri chinensis） a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew （Tupaia belangeri） aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database （www.treeshrewdb.org） has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 （HSV-1） and hepatitis C virus （HCV） infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis)

The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew(Tupaia belangeri chinensis)

The Chinese tree shrew(Tupaia belangeri chinensis)is a small experimental animal with a close affinity to primates.This species has long been proposed to be an alternative experimental animal to primates in biomedical research.Despite decades of study,there is no pure breed for this animal,and the overall genetic diversity of wild tree shrews remains largely unknown.In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations,we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew.An analysis of a wild population of 117 individuals collected from the suburb of Kunming,China,showed that these loci exhibited a highly expected heterozygosity(0.616).These 12 microsatellites were sufficient for individual identification and parentage analysis.The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.

Positively selected genes of the Chinese tree shrew （Tupaia belangeri chinensis） locomotion system

While the recent release of the Chinese tree shrew （Tupaia belangeri chinensis） genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals （human, rhesus monkey, mouse, rat and dog） and the Chinese tree shrew. Our analyses identified 29 genes with significantly high co （Ka/Ks ratio） values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6 （homeobox A6） and AVP （arginine vasopressin）, play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew.

Age-related changes of corneal endothelial cell in healthy Chinese tree shrew measured by non-contact specular microscope

AIM：To determine the impact of age on the morphology of endothelial cells and central corneal thickness（CCT） in Chinese tree shrew.METHODS：One-hundred and twenty eyes of 60 healthy Chinese tree shrews were studied.Based on age,the tree shrews were divided into four groups.After general anesthesia,the images of endothelium were acquired using non-contact specular microscope Topcon 3000 P.Eight parameters of corneal endothelial cells were measured by built-in software,including CCT,endothelial cell density（ECD）,percent hexagonality（HG%）,coeffi cient of variability（CV）,size of minimal cell（Smin）,size of maximal cell（Smax）,average cells size（Savg） and size standard deviation（Ssd）.Data were analyzed using STATA software.The differences of eight parameters among groups and correlations with age were analyzed.RESULTS：In all studied animals,the average CCT was 2 4 9.6 ± 2 .29 μ m（202-301 μm）,ECD was 308 0.72 ± 460.76 cells/mm^2（1239.6-4047.6 cells/mm^2） and CV was 29.10±7.60（13.6-54.6）.CV was significantly different among different groups（P〈0.001）.Strong correlation with age was found in ECD,Smax,Savg,Ssd and CV.CONCLUSION：Cornea of Chinese tree shrews had half CCT of human cornea and similar ECD,CV and size of corneal endothelial cells.Young adult tree shrews had higher ECD,HG% and low CV.ECD,Smax,Savg,Ssd and CV correlated with age signifi cantly.

Evaluating the Phylogenetic Position of Chinese Tree Shrew(Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome:Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research

Tree shrew （Tupaia belangeri） is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews （T. belangeri chinensis） and one Malayan flying lemur （Galeopterus variegatus）. Combined with the published data for species in Euarchonta, we intended to diseen] the phylogenetic relationship among representative species of Dermoptera, Scandentia and Primates. The mtDNA genomes of Chinese tree shrews and Malayan flying lemur shared similar gene organization and structure with those of other mammals. Phylogenetic analysis based on 12 concatenated mitochondrial proteinencoding genes revealed a closer relationship between species of Scandentia and Glires, whereas species of Dermoptera were clustered with Primates. This pattern was consistent with previously reported phylogeny based on mtDNA data, but differed from the one reconstructed on the basis of nuclear genes. Our result suggested that the matrilineal affinity of tree shrew to primates may not be as close as we had thought. The ongoing project for sequencing the entire genome of Chinese tree shrew will provide more information to clarify this important issue.

Proteomic characteristics of the liver and skeletal muscle in the Chinese tree shrew(Tupaia belangeri chinensis)

Valid animal models are useful for studying the pathophysiology of specific disorders,such as neural disease,diabetes and cancer.Previous molecular phylogeny studies indicate that the tree shrew is in the same order as(or a close sister to)primates,and thus may be an ideal model in which to study human disease.In this study,the proteome of liver and muscle tissue in tree the shrew was identified by combining peptide fractionation and LC-MS/MS identification.In total,2146 proteins were detected,including 1759 proteins in liver samples and 885 proteins in skeletal muscle samples from the tree shrew.Further sub-source analysis revealed that nearly half of the identified proteins(846 proteins and 418 proteins)were derived from human database.In this study,we are the first to describe the characteristics of the proteome from the liver and skeletal muscle of the tree shrew.Phylogenetic tree analysis based on these proteomic data showed that the tree shrew is closer to primates(human)than to glires(the mouse and rat).

Why can the antiviral gene RIG-Ⅰ be lost in the Chinese tree shrew?

,this study uncovered a previously unknown evolutionary signal in response to RIG-I loss in the tree shrew and provided insights into the evolutionary adaptation and functional diversity of antiviral activity in vertebrates.