scholarly journals A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca) 

2020 ◽  
Author(s):  
Matyas Cserhati
Keyword(s):  
Giant Panda ◽  
Ailuropoda Melanoleuca ◽  
Whole Genome ◽  
Genetic Studies ◽  
Stochastic Error ◽  
Red Panda ◽  
Genome Study ◽  
Ailurus Fulgens ◽  
Genome Level ◽  
Species Being

Abstract Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results: A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as A. fulgens were also aligned to draw further phylogenetic inferences. The results from the whole genome study show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place A. fulgens into its own group.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that A. fulgens belongs to the mustelid clade.

scholarly journals A Tail of Two Pandas: Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca)

2020 ◽  
Author(s):  
Matyas Cserhati
Keyword(s):  
Giant Panda ◽  
Ailuropoda Melanoleuca ◽  
Whole Genome ◽  
Geographic Isolation ◽  
Genetic Studies ◽  
Stochastic Error ◽  
Red Panda ◽  
Ailurus Fulgens ◽  
Genome Level ◽  
Species Being

Abstract Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid or a member of its own family. Previous genetic studies have given contradictory results as to its phylogenetic placement.Results: Therefore, a recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum.The results show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. This study is more substantial because it takes the whole genome into account.

scholarly journals A tail of two pandas— whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matyas Cserhati
Keyword(s):  
Maximum Likelihood ◽  
Giant Panda ◽  
Monophyletic Group ◽  
Ailuropoda Melanoleuca ◽  
Whole Genome ◽  
Neighbor Joining ◽  
Stochastic Error ◽  
Red Panda ◽  
Maximum Likelihood Methods ◽  
Ailurus Fulgens

Abstract Background The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences. The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak. Conclusions The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise.

scholarly journals Isolation and Identification of Kidney-derived Pathogenic Escherichia coli from Red Panda (Ailurus fulgens)

2020 ◽  
Author(s):  
Songrui Liu ◽  
Yunli Li ◽  
Chanjuan Yue ◽  
Dongsheng Zhang ◽  
Xiaoyan Su ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Infection ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Ex Situ ◽  
Type I ◽  
Pathogenicity Test ◽  
Whole Genome ◽  
Red Panda ◽  
Ailurus Fulgens

Abstract Background Disease prevention and control is a significant part during the ex-situ conservation of the red panda (Ailurus fulgens) with bacterial infection being one of the important threats to the health of the captive population. So far, there was no systematic and detailed publications about the red panda-related E. coli disease. This study was conducted for the purpose of determining the cause of death, etiology and pathogenesis on a red panda through clinical symptoms, complete blood count, biochemical analysis, pathological diagnosis, antimicrobial susceptibility test, mouse pathogenicity test, and bacterial whole genome sequencing.Results A bacterial strain confirmed as Uropathogenic Escherichia coli (UPEC) was isolated from one captive dead red panda, which is resistant to most of the β-lactam drugs and a small number of aminoglycoside medications. The mouse pathogenicity test results showed the strains isolated postmortem from mice were the same as from the dead red panda, and the pathological findings were similar to the red panda while they were not completely the same. These pathological differences between red panda and mice may be related to the routes of infection and perhaps species differences and tolerance. The whole genome sequencing results showed that the isolated strain contained P pili, type I pili and iron uptake system related factors, which were closely related to its nephrotoxicity. Conclusion The red panda died of bacterial infection which was identified as Uropathogenic Escherichia coli. The pathogenic mechanisms of the strain are closely related to the expression of specific virulence genes.

Microhabitat separation during winter among sympatric giant pandas, red pandas, and tufted deer: the effects of diet, body size, and energy metabolism

2004 ◽  
Vol 82 (9) ◽  
pp. 1451-1458 ◽  
Author(s):  
Zejun Zhang ◽  
Fuwen Wei ◽  
Ming Li ◽  
Baowei Zhang ◽  
Xuehua Liu ◽  
...  
Keyword(s):  
Body Size ◽  
Energy Metabolism ◽  
Giant Panda ◽  
Sichuan Province ◽  
Ailuropoda Melanoleuca ◽  
Giant Pandas ◽  
Republic Of China ◽  
Red Panda ◽  
Open Land ◽  
Selection Of

The giant panda (Ailuropoda melanoleuca (David, 1869)), red panda (Ailurus fulgens F.G. Cuvier, 1825), and tufted deer (Elaphodus cephalophus Milne-Edwards, 1872) are endemic to the Himalayan Hengduan Mountains; the red panda extends into India, Burma, Bhutan, and Nepal, and the tufted deer extends marginally into Burma, while the giant panda is endemic to China. In Sichuan Province, uniquely, all three species occur sympatrically. We investigated microhabitat characteristics at 150 fecal-group sites from November 2002 to March 2003 to improve understanding of microhabitat separation among the three species at the Fengtongzhai Nature Reserve, Baoxing County, Sichuan Province, People's Republic of China. Density and height of bamboo were greater in the giant and red pandas' micro habitats than in those of the tufted deer. The red panda preferred microhabitats with greater tree-stump density, smaller trees, and shorter fallen log dispersion distance than the other two species. Tufted deer often occurred at sites with greater shrub density and herb cover and more open land with poorer concealment conditions than sites where the two panda species occurred. Both pandas' microhabitats were mostly concentrated on the upper hillside, unlike those of the tufted deer. The giant panda preferred microhabitats with a gentler slope and lower density of fallen logs. Selection of specific microhabitats by each species is an ecological adaptation dependent on behavior linked to its diet, body size, energy metabolism, and other factors. Microhabitat separation among these species reflects the integrated effects of their differences in diet, body size, and energy metabolism, which could facilitate their successful coexistence.

scholarly journals Isolation and Characterization of Uropathogenic Escherichia coli (UPEC) from Red Panda (Ailurus fulgens)

2020 ◽  
Author(s):  
Songrui Liu ◽  
Yunli Li ◽  
Chanjuan Yue ◽  
Dongsheng Zhang ◽  
Xiaoyan Su ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Infection ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Uropathogenic Escherichia Coli ◽  
Ex Situ ◽  
Whole Genome ◽  
Red Panda ◽  
Ailurus Fulgens

Abstract Background Disease prevention and control is a significant part in the ex-situ conservation of the endangered red panda (Ailurus fulgens), being bacterial infection is one of the most important health threats to the captive population. To date, studies about the infection caused by Escherichia coli in the red panda are scarce. This study was conducted to determine the cause of death of a captive red panda through clinical symptoms, complete blood count, biochemical analysis, pathological diagnosis and bacterial whole genome sequencing. Case presentation The following report describes a case of a 1.5 year old captive red panda (Ailurus fulgens) that was found lethargic and anorectic. She was moved to the quarantine area for daily treatment with 50mg of Cefpodoxime Proxetil. During the three-day treatment, she did not eat or defecate, and then died. Clinical hematology revealed the values of neutrophils, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and blood urea nitrogen (BUN) were significantly higher. Histological analysis demonstrated major pathological damage in the kidneys, liver and lungs, characterized by hyperemia, parenchymal cell degeneration and necrosis and inflammatory cell infiltration which were predominantly neutrophilic. A bacterial strain confirmed as Escherichia coli was isolated post mortem. Whole genome sequencing of the E. coli showed the complete genome size was 4.99 Mbp. PapA, PapC, OmpA, OmpU and other virulence factors which specific to Uropathogenic Escherichia coli (UPEC) were found in the isolate. Among the virulence factors, P pili, type I pili and related factors of the iron uptake system were associated with nephrotoxicity. Conclusion The red panda died of bacterial infection caused by an uropathogenic strain of Escherichia coli. The pathogenic mechanisms of the strain are closely related to the expression of specific virulence genes.

Thirty-three microsatellite loci for noninvasive genetic studies of the giant panda (Ailuropoda melanoleuca)

2008 ◽  
Vol 10 (3) ◽  
pp. 649-652 ◽  
Author(s):  
Hua Wu ◽  
Xiang-Jiang Zhan ◽  
Ze-Jun Zhang ◽  
Li-Feng Zhu ◽  
Li Yan ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Giant Panda ◽  
Ailuropoda Melanoleuca ◽  
Genetic Studies
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