Dataset Information

A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis).

ABSTRACT: We obtained the complete mitochondrial genome of U.thibetanus mupinensis by DNA sequencing based on the PCR fragments of 18 primers we designed. The results indicate that the mtDNA is 16,868 bp in size, encodes 13 protein genes, 22 tRNA genes, and 2 rRNA genes, with an overall H-strand base composition of 31.2% A, 25.4% C, 15.5% G and 27.9% T. The sequence of the control region (CR) located between tRNA-Pro and tRNA-Phe is 1422 bp in size, consists of 8.43% of the whole genome, GC content is 51.9% and has a 6bp tandem repeat and two 10bp tandem repeats identified by using the Tandem Repeats Finder. U. thibetanus mupinensis mitochondrial genome shares high similarity with those of three other Ursidae: U. americanus (91.46%), U. arctos (89.25%) and U. maritimus (87.66%).

SUBMITTER: Hou WR

PROVIDER: S-EPMC1752227 | biostudies-literature | 2006 Dec

REPOSITORIES: biostudies-literature

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A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis).

Hou Wan-ru WR Chen Yu Y Wu Xia X Hu Jin-chu JC Peng Zheng-song ZS Yang Jung J Tang Zong-xiang ZX Zhou Cai-Quan CQ Li Yu-ming YM Yang Shi-kui SK Du Yu-jie YJ Kong Ling-lu LL Ren Zheng-long ZL Zhang Huai-yu HY Shuai Su-rong SR

International journal of biological sciences 20061223 2

We obtained the complete mitochondrial genome of U.thibetanus mupinensis by DNA sequencing based on the PCR fragments of 18 primers we designed. The results indicate that the mtDNA is 16,868 bp in size, encodes 13 protein genes, 22 tRNA genes, and 2 rRNA genes, with an overall H-strand base composition of 31.2% A, 25.4% C, 15.5% G and 27.9% T. The sequence of the control region (CR) located between tRNA-Pro and tRNA-Phe is 1422 bp in size, consists of 8.43% of the whole genome, GC content is 51. ...[more]

PMID: 17205108

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Project description:The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear.

Project description:BackgroundThe major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations.ResultsAmong 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected.ConclusionsThe low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.

Project description:In this study, we present first data concerning the morphological observations of the orbital region, eye tunics, upper and lower eyelids, superficial gland of the third eyelid with the third eyelid, and lacrimal gland in captive adult male Asiatic black bear. The following research methods were used in the work: the eyeball morphometry, the orbital region description, macroscopic description, morphometric and histological analysis of the eye tunics and selected the accessory organs of the eye (Fontana-Masson, hematoxylin & eosin (H&E), Methyl-green-pyronin Y (MGP Y), Movat pentachrome, and picro-Mallory trichrome) as well as histochemical examination (PAS, AB pH 1.0, AB pH 2.5, AB pH 2.5/PAS and HDI). The eyeball of the Asiatic black bear was a spherical shape, while the periorbita was funnel/conical-shaped and the eye socket was of the open type. The cornea was absent of the Bowman's membrane similar to all domestic dogs and some wild dogs. There were palisades of Vogt in the corneal limbus epithelium similar to the Canidae. Degenerative choroidal tapetum lucidum similar to ranch mink (Mustelidae) has been found. The pupil was big and round in shape. The ciliary muscle, dilatator and sphincter muscle were well developed, similar to the pinnipeds. The lens was biconvex round, similar to the Canidae. The retina was composed similarly to the diurnal terrestrial carnivores. In both eyelids were observed very well-developed tarsal glands, ciliary glands and sebaceous glands. The orbital zone in the eyelids was characterized by lymphoid follicles, diffuse lymphocytes and specialized high endothelial venules. In the anterior palpebral margin of the upper eyelid, soft and short eyelashes were observed, while in the lower eyelids they were absent. The third eyelid was T-shaped and composed of the hyaline tissue, and it contained CALT, similar to that in Canidae. The superficial gland of the third eyelid was a multilobar alveolar branched complex with seromucous nature, while the lacrimal gland was also a multilobar acinar branched complex gland, but producing a mucous-serous secretion. The results of our research indicate that the features of the anatomy of the eye and orbital region in Asiatic black bear are also typical of the Ursidae family. Moreover, a detailed analysis of the morphological eye region may be useful in comparative studies and veterinary diagnostics in this bear species.

Dataset Information

A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis).

Publications

A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis).

Similar Datasets

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