Dataset Information

A metagenomic insight into the Yangtze finless porpoise virome.

ABSTRACT: The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.

SUBMITTER: Liu Z

PROVIDER: S-EPMC9478467 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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A metagenomic insight into the Yangtze finless porpoise virome.

Liu Zhigang Z Ding Xin X Haider Muhammad Shahan MS Ali Farah F Yu Han H Chen Xin X Tan Shuaishuai S Zu Yuan Y Liu Wenlong W Ding Bangzhi B Zheng Aifang A Zheng Jinsong J Qian Zhengyi Z Ashfaq Hassan H Yu Daoping D Li Kun K

Frontiers in veterinary science 20220902

The Yangtze finless porpoise (<i>Neophocaena phocaenoides asiaeorientalis</i>) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze ...[more]

PMID: 36118360

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Project description:The Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) living in different environments display significant differences in behavior and physiology. To compare and analyze gene expression differences between an ex situ population and a controlled environment population of the Yangtze finless porpoise, we sequenced the transcriptome of blood tissues living in a semi-natural reserve and an artificial facility, respectively. We identified 6860 differentially expressed genes (DEGs), of which 6603 were up-regulated and 257 were down-regulated in the controlled environment vs ex situ comparison. GO and KEGG enrichment analysis showed that the up-regulated genes in the controlled environment population were significantly associated with glucose metabolism, amino acid metabolism, and the nervous system, while those up-regulated in the ex situ population were significantly associated with energy supply and biosynthesis. Further analysis showed that metabolic and hearing-related genes were significantly affected by changes in the environment, and key metabolic genes such as HK, PFK, IDH, and GLS and key hearing-related genes such as OTOA, OTOF, SLC38A1, and GABBR2 were identified. These results suggest that the controlled environment population may have enhanced glucose metabolic ability via activation of glycolysis/gluconeogenesis, the TCA cycle, and inositol phosphate metabolism, while the ex situ population may meet higher energy requirements via enhancement of the amino acid metabolism of the liver and muscle and oxidative phosphorylation. Additionally, the acoustic behavior and auditory-related genes of Yangtze finless porpoise may show responsive changes and differential expression under different environment conditions, and thus the auditory sensitivity may also show corresponding adaptive characteristics. This study provides a new perspective for further exploration of the responsive changes of the two populations to various environments and provides a theoretical reference for further improvements in conservation practices for the Yangtze finless porpoise.

Project description:BackgroundThe gut microbiota is a complex ecosystem, which is essential for the metabolism, health and immunity of host. Many diseases have been shown to be closely related to the alteration of intestinal flora. Aeromonas veronii as a conditioned pathogen can cause disease in Yangtze finless porpoise through intestinal infections. However, it is not clear whether the disease caused by Aeromonas veronii is related to changes of intestinal flora. In the current study, the diversity and composition of gut microbiota in the healthy and Aeromonas veronii-infected Yangtze finless porpoise were evaluated by high-throughput sequencing to further investigate the potential association between intestinal flora alteration and pathogen invasion.ResultsA total of 127,3276 high-quality sequences were achieved and 2465 operational taxonomic units (OTUs) were in common among all samples. The results of alpha diversity showed that there was no obvious difference in richness and diversity between healthy and Aeromonas veronii-infected Yangtze finless porpoise. Firmicutes, Bacteroidetes and Proteobacteria were the most dominant phyla in all samples. In addition, the healthy Yangtze finless porpoise exhibited higher abundance of Firmicutes and Fusobacteria than Aeromonas veronii-infected Yangtze finless porpoise, while, the level of Proteobacteria was decreased. At the genus level, Paeniclostridium and Paraclostridium were the predominant bacteria genera in the CK (healthy Yangtze finless porpoise) group. In the DIS (Aeromonas veronii-infected Yangtze finless porpoise) group, Lactobacillus and unidentified_Enterobacteriaceae were the dominant bacteria genera and the proportion of Paeniclostridium, Paraclostridium, Terrisporobacter, Cetobacterium, Candidatus Arthromitus, Terrabacter and Dechloromonas were reduced.ConclusionsIn conclusion, our results showed that Aeromonas veronii infection can alter the gut microbiota of the Yangtze finless porpoise by affecting the number of harmful bacteria and beneficial bacteria.

Project description:Under increasing anthropogenic pressure, species with a previously contiguous distribution across their ranges have been reduced to small fragmented populations. The critically endangered Yangtze finless porpoise ( Neophocaena asiaeorientalis asiaeorientalis), once commonly observed in the Yangtze River-Poyang Lake junction, is now rarely seen in the river-lake corridor. In this study, static passive acoustic monitoring techniques were used to detect the biosonar activities of the Yangtze finless porpoise in this unique corridor. Generalized linear models were used to examine the correlation between these activities and anthropogenic impacts from the COVID-19 pandemic lockdown and boat navigation, as well as environmental variables, including hydrological conditions and light levels. Over approximately three consecutive years of monitoring (2020-2022), porpoise biosonar was detected during 93% of logged days, indicating the key role of the corridor for finless porpoise conservation. In addition, porpoise clicks were recorded in 3.80% of minutes, while feeding correlated buzzes were detected in 1.23% of minutes, suggesting the potential existence of localized, small-scale migration. Furthermore, both anthropogenic and environmental variables were significantly correlated with the diel, lunar, monthly, seasonal, and annual variations in porpoise biosonar activities. During the pandemic lockdown period, porpoise sonar detection showed a significant increase. Furthermore, a significant negative correlation was identified between the detection of porpoise click trains and buzzes and boat traffic intensity. In addition to water level and flux, daylight and moonlight exhibited significant correlations with porpoise biosonar activities, with markedly higher detections at night and quarter moon periods. Ensuring the spatiotemporal reduction of anthropogenic activities, implementing vessel speed restrictions (e.g., during porpoise migration and feeding), and maintaining local natural hydrological regimes are critical factors for sustaining porpoise population viability.

Dataset Information

A metagenomic insight into the Yangtze finless porpoise virome.

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A metagenomic insight into the Yangtze finless porpoise virome.

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