Dataset Information

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys.

ABSTRACT: Background:Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500-4,500 m) temperate forests in southern and central China. Methods:We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results:We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions:Our results indicate that ERV sequences are widely distributed in snub-nosed monkeys, and their phylogenetic history can mirror that of their hosts over long evolutionary time scales. In addition, ERV sequences appear to have an important influence on the evolution of host pathology.

SUBMITTER: Wang X

PROVIDER: S-EPMC6428148 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys.

Wang Xiao X Wang Boshi B Liu Zhijin Z Garber Paul A PA Pan Huijuan H

PeerJ 20190318

<h4>Background</h4>Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate ta ...[more]

PMID: 30918756

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Project description:Many threatened species have undergone range retraction, and are confined to small fragmented populations. To increase their survival prospects, it is necessary to find suitable habitat outside their current range, to increase and interconnect populations. Species distribution models may be used to this purpose and can be an important part of the conservation strategies. One pitfall is that such mapping will typically assume that the current distribution represents the optimal habitat, which may not be the case for threatened species. Here, we use maximum entropy modelling (Maxent) and rectilinear bioclimatic envelope modelling with current and historical distribution data, together with the location of protected areas, and environmental and anthropogenic variables, to answer three key questions for the conservation of Rhinopithecus, a highly endangered genus of primates consisting of five species of which three are endemic to China, one is endemic to China and Myanmar and one is endemic to Vietnam; Which environmental variables best predict the distribution? To what extent is Rhinopithecus living in an anthropogenically truncated niche space? What is the genus' potential distribution in the region? Mean temperature of coldest and warmest quarter together with annual precipitation and precipitation during the driest quarter were the variables that best explained Rhinopithecus' distribution. The historical records were generally in warmer and wetter areas and in lower elevation than the current distribution, strongly suggesting that Rhinopithecus today survives in an anthropogenic truncated niche space. There is 305,800-319,325 km2 of climatic suitable area within protected areas in China, of which 96,525-100,275 km2 and 17,175-17,550 km2 have tree cover above 50 and 75%, respectively. The models also show that the area predicted as climatic suitable using Maxent was 72-89% larger when historical records were included. Our results emphasise the importance of considering historical records when assessing restoration potential and show that there is high potential for restoring Rhinopithecus to parts of its former range.

Dataset Information

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys.

Publications

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys.

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