Identification and characterization of miRNA expression profiles across five tissues in giant panda

Wang, Chengdong; Feng, Liang; Deng, Lei; Li, Mingzhou; Wei, Ming; Zeng, Bo; Wu, Kai; Xu, Zhongxian; Wei, Rongping; Wei, Limin; Liu, Weiping; Zhang, Siyuan; Xu, Lin; Huang, Yan; Li, Desheng; Li, Ying; Zhang, Hemin

doi:10.1016/j.gene.2020.145206

Cited by 6 publications

(4 citation statements)

References 65 publications

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“…The giant panda is regarded as the “living fossil” and “China's national treasure,” the image ambassador of the Worldwide Fund for Nature, and the flagship species of the world's biodiversity conservation ( 27 , 28 ). A great deal of effort has been put into preserving this iconic species; increasing evidence emphasizes the close interaction between the gut microflora and animal health ( 29 , 30 ).…”

Section: Discussionmentioning

confidence: 99%

Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

Ning

Zhao

et al. 2021

Front. Vet. Sci.

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The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals in the world; anthropogenic habitat loss and poaching still threaten the survival of wild pandas. Viral infection has become one of the potential threats to the health of these animals, but the available information related to these infections is still limited. In order to detect possible vertebrate viruses, the virome in the fecal samples of seven wild giant pandas from Qinling Mountains was investigated by using the method of viral metagenomics. From the fecal virome of wild giant pandas, we determined six nearly complete genomes belonging to the order Picornavirales, two of which may be qualified as a novel virus family or genus. In addition, four complete genomes belonging to the Genomoviridae family were also fully characterized. This virological investigation has increased our understanding of the gut viral community in giant pandas. Whether these viruses detected in fecal samples can really infect giant panda needs further research.

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Section: Discussionmentioning

confidence: 99%

Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

Ning

Zhao

et al. 2021

Front. Vet. Sci.

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“…Recent advances in RNA sequencing (RNA-seq) have also provided new opportunities to integrate changes in protein-coding mRNAs with regulatory signals, such as those driven by ncRNAs and alternative RNA splicing events ( Ackerman 4th et al, 2018 ). RNA-seq has been widely used to study miRNA expression in humans, other animals and plants ( Chiba et al, 2021 ; Hao et al, 2021 ; Wang et al, 2021 ; Yang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

RNA sequencing-based identification of microRNAs in the antler cartilage of Gansu red deer (Cervus elaphus kansuensis)

Chen

Zhang

et al. 2022

PeerJ

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Background The velvet antler is a complex mammalian bone organ with unique biological characteristics, such as regeneration. The rapid growth stage (RGS) is a special period in the regeneration process of velvet antler. Methods To elucidate the functions of microRNAs (miRNAs) at the RGS of antler development in Gansu red deer (Cervus elaphus kansuensis), we used RNA sequencing (RNA-seq) to analyze miRNA expression profiles in cartilage tissues of deer antler tips at three different growth stages. Results The RNA-seq results revealed 1,073 known and 204 novel miRNAs, including 1,207, 1,242, and 1,204 from 30-, 60-, and 90-d antler cartilage tissues, respectively. To identify key miRNAs controlling rapid antler growth, we predicted target genes of screened 25 differentially expressed miRNAs (DEMs) and specifically expressed miRNAs (SEMs) in 60 d and annotated their functions. The KEGG results revealed that target genes of 25 DEMs and 30 SEMs were highly classified in the “Metabolic pathways”, “Pathways in cancer”, “Proteoglycans in cancer” and “PI3K-Akt signaling pathway”. In addition, a novel miRNA (CM008039.1_315920), highly enriched in “NF-kappa B signaling pathway”, may need further study. Conclusions The miRNAs identified in our study are potentially important in rapid antler growth. Our findings provide new insights to help elucidate the miRNA-mediated regulatory mechanisms involved during velvet antler development in C. elaphus kansuensis.

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“…MiRNAome studies on other species have shown great organ- and age-dependent variations in miRNA expression. Isakova et al identified ~400 organ-dependent miRNAs in mice ( 13 ); Wang et al identified 740 organ-dependent miRNAs in giant panda ( 14 ); Jie et al identified 275 organ-dependent miRNAs in Chinese forest musk deer ( 15 ); Liu et al identified 312 age-dependent miRNAs in the citrus red mite ( 16 ). In particular, the highly ordered distribution of immune cells in the spleen makes it the largest peripheral immune organ to resist pathogens ( 17 ).…”

Section: Introductionmentioning

confidence: 99%

The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer

Jia

Wang

et al. 2022

Front. Vet. Sci.

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Due to the lack of high-quality Sika Deer (Cervus nippon) transcriptome and sRNAome across multiple organs or development stages, it is impossible to comprehensively analyze the mRNA and miRNA regulatory networks related to growth, development and immunity response. In this study, we used single molecule-real time sequencing (SMRT-seq) and Illumina sequencing methods to generate transcriptome and sRNAome from ten tissues and four age groups of Sika Deer to help us understand molecular characteristics and global miRNA expression profiles. The results showed that a total of 240,846 consensus transcripts were generated with an average length of 2,784 bp. 4,329 Transcription factors (TFs), 109,000 Simple Sequence Repeats (SSRs) and 18,987 Long non-coding RNAs (LncRNAs) were identified. Meanwhile, 306 known miRNAs and 143 novel miRNAs were obtained. A large number of miRNAs showed organ-specific and age-specific differential expression patterns. In particular, we found that the organ-specific miRNAs were enriched in the brain, some of which shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. By constructing miRNA96mRNA interaction networks associated with Sika Deer immunity, we found that miRNAs (miR-148a, miR-26a, miR-214, let-7b, etc.) and mRNAs (CD6, TRIM38, C3, CD163, etc.) might play an important role in the immune response of Sika Deer spleen. Together, our study generated an improved transcript annotation for Sika Deer by SMRT-seq and revealed the role of miRNA in regulating the growth, development and immunity response of Sika Deer.

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Identification and characterization of miRNA expression profiles across five tissues in giant panda

Cited by 6 publications

References 65 publications

Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

RNA sequencing-based identification of microRNAs in the antler cartilage of Gansu red deer (Cervus elaphus kansuensis)

The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer

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