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Identification and differential expression analysis of microRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle

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TROPICAL ANIMAL HEALTH AND PRODUCTION 2025年第2期57卷 1-14页

作者： Liu, Rong Liu, Hesong Li, Rong Li, Chunqing Xiao, Heng chen, shanyuan Yunnan Univ Sch Ecol & Environm Sci Kunming 650500 Peoples R China Yunnan Univ Sch Life Sci Kunming 650500 Peoples R China Yunnan Normal Univ Coll Life Sci Kunming 650500 Peoples R China

Extensive research has shown that miRNAs play a crucial role in regulating biological processes within organisms. This study analyzed miRNAs differentially expressed and potentially associated with immune function and tissue-specific expression in Yunnan Zebu and Holstein cattle. To achieve this, 20 liver and spleen tissue samples from the two cattle breeds were collected for high-throughput miRNA sequencing, with the liver tissue as a reference. The findings revealed that bta-miR-122 and bta-miR-143 are the most abundantly expressed known miRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle, respectively. Additionally, AC_000181.1_27195 and AC_000168.1_14386 emerged as the most highly expressed novel miRNAs in these tissues, exhibiting significant homology with human hsa-miR-3591-3p and hsa-miR-126-3p, respectively. Six differentially expressed miRNAs were selected for validation using stem-loop RT-qPCR, and the results were largely consistent with the high-throughput sequencing data. Functional enrichment analysis of the target genes of these known miRNAs revealed their association with critical metabolic and immune-related pathways in cattle, such as the insulin pathway, mTOR signaling, IFN-gamma pathway, and signaling mechanisms mediated by IL5 and IL3. These results enriched the miRNA database for liver and spleen tissues of Yunnan Zebu and Holstein cattle.

关键词： Yunnan Zebu Holstein cattle MicroRNAs Immune function Differential expression High-throughput sequencing

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Structural characterization and catalytic sterilization performance of a TiO2 nano-photocatalyst

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FOOD SCIENCE & NUTRITION 2020年第7期8卷 3638-3646页

作者： Yang, Yue Guan, chengli chen, shanyuan Yangjiang Polytech Yangjiang 529566 Peoples R China South China Univ Technol Guangdong Prov Key Lab Atmospher Environm & Pollu Guangzhou Peoples R China

In view of the food safety and hygiene issues caused by pathogenic microorganisms, tetrabutyl titanate was used as a precursor for the preparation of a TiO2 nano-semiconductor photocatalyst via the sol-gel process. The plate count method was then adopted to investigate the photocatalytic sterilization performance of the synthesized TiO2 nanoparticles toward Escherichia coli, Staphylococcus aureus, and Candida albicans. Subsequently, a backpropagation (BP) neural network model was developed to predict the photocatalytic sterilization performance. The photocatalyst was structurally characterized by the Brunauer-Emmett-Teller method for specific surface area determination, transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The results indicated that the prepared TiO2 nano-photocatalyst was of high purity with a specific surface area of 76.5 m(2)/g and the particle size range 15-18 nm. The nanoparticles exhibited characteristic peaks corresponding to the oxide component Ti-O, hydroxyl group (OH)-O-center dot and oxygen chemisorbed and presented an anatase-dominated multiphase structure that enhanced the photocatalytic performance. UV irradiation at 254 nm produced better sterilization effects on E. coli, S. aureus, and C. albicans, with elimination rates after 30 min of reaction of 97.8%, 99.4%, and 93.6%, respectively. These results indicated that the TiO2 nano-photocatalyst is a promising environmentally friendly catalyst with good sterilization performance. The constructed BP neural network also exhibited high training accuracy and good generalization ability, with correlation coefficients between the network-predicted and experimental target values of 0.9789. These results support research on the intelligent processing of photocatalytic sterilization with TiO2 nanoparticles.

关键词： backpropagation neural network Candida albicans Escherichia coli Staphylococcus aureus sterilization performance TiO2 nano-photocatalyst

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Molecular evidence for fat-tailed sheep domestication

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TROPICAL ANIMAL HEALTH AND PRODUCTION 2011年第7期43卷 1237-1243页

作者： Rocha, Joana chen, shanyuan Beja-Pereira, Albano Univ Porto CIBIO UP Ctr Invest Biodiversidade & Recursos Genet P-4485661 Vairao Portugal

The sheep is one of the most successful and widely spread domestic animals. Archaeological evidence traces the first domestic sheep back to the Near East region around 9,000 years ago. It is also known that soon after, the domesticated sheep started to flow out of the centre of origin and spread all over the ancient world following the expansion of agriculture. Throughout time, herders, nature elements and eventually some hybridization with different wild relatives produced a multitude of breeds. However, until the advent of the molecular genetics field, very little was known about the origins of most of those breeds. Two decades after the first genetic studies, we have gathered considerable information on the origins, phylogenetic relationships and patterns of genetic diversity of the sheep across the world. Indeed, the genetic studies confirmed the Near East region as the main centre of origin and also revealed other contributions from other regions. Specifically about the fat-tailed sheep, molecular genetics was also able to link their maternal origin to a specific group. So far, modern sheep have originated from five different maternal origins. Nonetheless, the technological advances of the DNA sequencing techniques are bringing more data that is showing the complexity of the domestication process.

关键词： Ovis aries Fat tailed Domestication Sheep Genetics

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A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species

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MICROBIAL ECOLOGY 2020年第2期79卷 299-311页

作者： chen, Hongyu Li, Chunqing Liu, Tao chen, shanyuan Xiao, Heng Yunnan Univ Sch Life Sci Kunming 650500 Yunnan Peoples R China Yunnan Univ Natl Demonstrat Ctr Expt Life Sci Educ Kunming Yunnan Peoples R China

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the alpha-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous;however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.

关键词： Intestinal microbes Sinocyclocheilus Cavefish Food habit

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Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes

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ECOLOGY AND EVOLUTION 2020年第24期10卷 14256-14271页

作者： Li, Chunqing chen, Hongyu Zhao, Yinchen chen, shanyuan Xiao, Heng Yunnan Univ Sch Ecol & Environm Sci Yunnan Key Lab Plateau Mt Ecol & Restorat Degrade Kunming Yunnan Peoples R China Yunnan Univ Sch Life Sci Kunming Yunnan Peoples R China

Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight Sinocyclocheilus species (Cypriniformes: Cyprinidae) that included surface- and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatic comparisons revealed 10,629 and 6,442 significantly differentially expressed unigenes between four different surface-cave fish groups. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including GNAQ, PKA, NRAS, and p38) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.

关键词： cavefish comparative transcriptomics pigmentation Sinocyclocheilus troglomorphic trait

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Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan

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JOURNAL OF ANIMAL BREEDING AND GENETICS 2021年第1期138卷 108-121页

作者： Li, Rong Sun, Jianshu Zhao, Yincheng Xiao, Heng chen, shanyuan Yunnan Univ Sch Ecol & Environm Sci Kunming 650500 Yunnan Peoples R China Yunnan Univ Sch Life Sci Kunming Yunnan Peoples R China

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 +/- 0.079 to 0.982 +/- 0.015 and from 0.028 +/- 0.003 to 0.043 +/- 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

关键词： domestic goats domestication history maternal lineages mtDNA phylogeographic structure

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The complete mitochondrial genome sequence of Buceros bicornis (Bucerotiformes: Bucerotidae)

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CONSERVATION GENETICS RESOURCES 2018年第3期10卷 287-290页

作者： chen, Yanyan Li, Chunqing Yan, Haiya Xiao, Heng chen, shanyuan Yunnan Univ Sch Life Sci 2 North Cuihu Rd Kunming 650091 Yunnan Peoples R China Yunnan Univ Key Lab Anim Genet Divers & Evolut High Educ Yunn Kunming 650091 Yunnan Peoples R China

Buceros bicornis (Bucerotiformes: Bucerotidae) has been listed as a near threatened species by the International Union for Conservation of Nature and Natural Resources (IUCN) due to over-hunting and habitat loss. Thus, it is a great challenge for us to efficiently protect the Buceros bicornis resource from extinct. Molecular biology research can provide the scientific basis for the conservation of key endangered species. In this work, we first reported the complete mitochondrial genome (mitogenome) sequence of Buceros bicornis by next-generation sequencing (NGS). The total length of the complete mitogenome was 17,117 bp and its overall base composition was estimated to be 30.2% for A, 23.5% for T, 32.3% for C and 14.0% for G, indicating an A + T (53.7%)-rich feature in the Buceros bicornis complete mitogenome. In addition, it contained the typical structure of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs) and a non-coding control region (D-loop region). The newly obtained mitogenome sequence seems to be useful for conservation biology and evolutionary studies on hornbill bird species, which would contribute to enrich the Buceros bicornis mitogenome resource and promote its biological research.

关键词： Buceros bicornis Mitochondrial genome Next generation sequencing

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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Rhyticeros undulatus (Bucerotiformes: Bucerotidae)

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CONSERVATION GENETICS RESOURCES 2019年第1期11卷 27-30页

作者： chen, Yanyan Yan, Haiya Sun, Jianshu Li, Chunqing Xiao, Heng chen, shanyuan Yunnan Univ Sch Life Sci 2 North Cuihu Rd Kunming 650091 Yunnan Peoples R China Yunnan Univ Key Lab Anim Genet Divers & Evolut High Educ Yunn 2 North Cuihu Rd Kunming 650091 Yunnan Peoples R China

The wreathed hornbill (Rhyticeros undulatus) has been listed in the IUCN Red List of Threatened Species, because of decreasing population trend. There is a lack of genomic information on this species, which can provide valuable resource for conservation biology and phylogenetic studies on hornbill birds. Here we first characterized the complete mitochondrial genome (mitogenome) sequence of R. undulatus by next-generation sequencing and conducted phylogenomic analysis of hornbill species with mitogenome sequences available. The complete mitogenome of R. undulatus was 17,842bp in length and incorporated 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA genes, and 1 control region (D-loop). The overall nucleotide composition of this mitogenome was 30.3% A, 22.4% T, 32.6% C, and 14.7% G, with AT content of 52.7%. Phylogenomic analysis using mitogenomes of eight hornbill birds showed that R. undulatus was more closely related to Penelopides panini and two Aceros species.

关键词： Rhyticeros undulatus Mitochondrial genome Next-generation sequencing

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The complete mitochondrial genome sequence of Anthracoceros coronatus (Bucerotiformes: Bucerotidae)

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CONSERVATION GENETICS RESOURCES 2018年第3期10卷 401-404页

作者： Li, Rong chen, Yanyan Yan, Haiya Li, Chunqing Xiao, Heng chen, shanyuan Yunnan Univ Sch Life Sci 2 North Cuihu Rd Kunming 650091 Yunnan Peoples R China Yunnan Univ Key Lab Anim Genet Divers & Evolut High Educ Yunn Kunming 650091 Yunnan Peoples R China

Anthracoceros coronatus (Bucerotiformes: Bucerotidae) has been listed in near threatened category in the IUCN Red List of Threatened Species, due to population decline. Mitochondrial genome (mitogenome) sequence is informative and very useful for systematics and conservation biology studies. In this study, we first determined and characterized the complete mitogenome of A. coronatus using next-generation sequencing platform. The complete mitogenome of A. coronatus was 17,214 bp in length, with an AT ratio of 52.8%. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region or D-loop region, with an identical gene order to that of most other vertebrates. The complete mitogenome sequence of A. coronatus would not only provide additional molecular markers of choice for detecting illegal poaching and trafficking of this bird species, but also would contribute to phylogenomic study of hornbill birds.

关键词： Anthracoceros coronatus Mitochondrial genome Next generation sequencing

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The complete mitochondrial genome of Sinocyclocheilus tingi (Cypriniformes: Cyprinidae): characterization and phylogenetic position

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CONSERVATION GENETICS RESOURCES 2019年第2期11卷 125-128页

作者： Li, Chunqing chen, Yanyan Ning, Tiao Zhang, Sichun chen, shanyuan Xiao, Heng Yunnan Univ Sch Life Sci Kunming 650091 Yunnan Peoples R China Kunming Univ Coll Agr Sci Kunming 650214 Yunnan Peoples R China Fishery Technol Promot Stn Jiangchuan Cty Jiangchuan 652600 Yunnan Peoples R China Yunnan Univ Key Lab Anim Genet Div & Evolut High Educ Yunnan Kunming 650091 Yunnan Peoples R China

Sinocyclocheilus tingi is a cyprinid fish species endemic to China and has been listed as endangered species in the IUCN Red List of Threatened Species, due to over-fishing, introduced species competition, and loss of spawning grounds. In this study, we first sequenced and characterized the complete mitochondrial genome (mitogenome) of S. tingi by next-generation sequencing. The complete mitogenome is 16,584bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and control region. Its gene arrangement pattern was identical to that of Sinocyclocheilus fishes available in GenBank database. The overall base composition is 30.42% A, 25.34% T, 26.98% C and 17.26% G, showing AT-rich feature (55.76%). Phylogenetic analyses showed that S. tingi from Fuxian Lake was closely related to Sinocyclocheilus grahami from Dianchi Lake. This work would provide molecular information fundamental to conservation and resource restoration studies on this endangered fish species.

关键词： Sinocyclocheilus tingi Mitochondrial genome Next-generation sequencing

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