Animals

Research

18 pages, 3042 KiB

Open AccessArticle

The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

by Chuang Tang, Jideng Ma, Fanli Kong, Bo Li, Qinjiao Du, Yali Zhang, Haoming Wang, Qianzi Tang, Silu Hu, Lingyan Liu, Xuewei Li and Mingzhou Li

Animals 2022, 12(21), 2925; https://doi.org/10.3390/ani12212925 - 25 Oct 2022

Cited by 5 | Viewed by 1707

Abstract

The intestine is a tubular organ with multiple functions such as digestion absorption and immunity, but the functions of each intestinal segments are different. Intestinal regionalization is necessary for normal physiological function, but it also means the research results obtained at specific sites [...] Read more.

The intestine is a tubular organ with multiple functions such as digestion absorption and immunity, but the functions of each intestinal segments are different. Intestinal regionalization is necessary for normal physiological function, but it also means the research results obtained at specific sites may not be applicable to other intestinal segments. In order to comprehensively describe the functional changes in the intestine, different intestinal segments and their contents (duodenum, jejunum, ileum, cecum, colon, and rectum) of guinea pigs were collected for RNA seq and 16S rRNA seq, respectively. The results showed differential genes of each intestinal segment mainly involve mucosa, digestion, absorption, and immunity. The gene sets related to fat, bill salts, vitamins, aggregates, amino acids, and water absorption were highly expressed in the small intestine, and the gene sets related to metal ions, nucleotides, and SCFAs were highly expressed in the large intestine. In terms of immunity, the CD8⁺ T, Th1, eosinophils, pDCs, and natural killer (NK) T cells in the small intestine showed higher scores than those in the large intestine, while the pattern-recognition receptor signaling pathway-related genes are highly expressed in the large intestine. In terms of microbial composition, Proteobacteria and Actinobacteria are abundant in the small intestine, while Firmicutes and Spirochaete are abundant in large intestine. The correlation analysis showed a high correlation between intestinal microorganisms and gene modules related to digestion and absorption. In addition, cross-species analysis showed the SCFA metabolism gene expression trends in human and rodent intestine were different. In conclusion, we analyzed the changes in substance transport, immune and microbial composition between different intestinal segments of guinea pigs, and explored the relationship between intestinal transcriptome and microorganisms, our research will provides a reference for subsequent intestinal-related research. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

19 pages, 3595 KiB

Open AccessArticle

Profiling Analysis of N6-Methyladenosine mRNA Methylation Reveals Differential m6A Patterns during the Embryonic Skeletal Muscle Development of Ducks

by Biao Chen, Shuibing Liu, Wentao Zhang, Ting Xiong, Mingfang Zhou, Xiaolong Hu, Huirong Mao and Sanfeng Liu

Animals 2022, 12(19), 2593; https://doi.org/10.3390/ani12192593 - 28 Sep 2022

Cited by 7 | Viewed by 1834

Abstract

N6-Methyladenosine is a reversible epigenetic modification that influences muscle development. However, the m6A modification profile during poultry skeletal muscle development is poorly understood. Here, we utilized m6A-specific methylated RNA immunoprecipitation sequencing to identify m6A sites during two stages of breast muscle development in [...] Read more.

N6-Methyladenosine is a reversible epigenetic modification that influences muscle development. However, the m6A modification profile during poultry skeletal muscle development is poorly understood. Here, we utilized m6A-specific methylated RNA immunoprecipitation sequencing to identify m6A sites during two stages of breast muscle development in ducks: embryonic days 13 (E13) and E19. MeRIP-seq detected 19,024 and 18,081 m6A peaks in the E13 and E19 groups, respectively. Similarly to m6A distribution in mammalian transcripts, our results revealed GGACU as the main m6A motif in duck breast muscle; they also revealed that m6A peaks are mainly enriched near the stop codons. In addition, motif sequence analysis and gene expression analysis demonstrated that m6A modification in duck embryo skeletal muscles may be mediated by the methyltransferase-like 14. GO and KEGG analysis showed that m6A peaks containing genes at E19 were mainly enriched in muscle-differentiation- and muscle-growth-related pathways, whereas m6A peaks containing genes in E13 were mainly enriched in embryonic development and cell proliferation pathways. Combined analysis of MeRIP-seq and RNA-seq showed that the mRNA expression may be affected by m6A modification. Moreover, qRT-PCR analysis of the expression of METTL14 and its cofactors (WTAP, ZC3H13, RBM15 and VIRMA) during duck embryonic skeletal muscle development in breast and leg muscle samples revealed a significant downward trend as the developmental age progressed. Our results demonstrated that m6A mRNA methylation modifications control muscle development in ducks. This is the first study of m6A modification patterns in duck muscle tissue development, and it lays the foundation for the study of the effects of RNA modification on poultry skeletal muscle development. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

15 pages, 6490 KiB

Open AccessArticle

Identification of miRNA–mRNA Networks Associated with Pigeon Skeletal Muscle Development and Growth

by Hao Ding, Can Chen, Tao Zhang, Lan Chen, Weilin Chen, Xuanze Ling, Genxi Zhang, Jinyu Wang, Kaizhou Xie and Guojun Dai

Animals 2022, 12(19), 2509; https://doi.org/10.3390/ani12192509 - 21 Sep 2022

Cited by 1 | Viewed by 1568

Abstract

The growth and development of skeletal muscle determine the productivity of pigeon meat production, and miRNA plays an important role in the growth and development of this type of muscle. However, there are few reports regarding miRNA regulating the growth and development of [...] Read more.

The growth and development of skeletal muscle determine the productivity of pigeon meat production, and miRNA plays an important role in the growth and development of this type of muscle. However, there are few reports regarding miRNA regulating the growth and development of skeletal muscle in pigeons. To explore the function of miRNA in regulating the growth and development of pigeon skeletal muscle, we used RNA sequencing technology to study the transcriptome of pigeons at two embryonic stages (E8 and E13) and two growth stages (D1 and D10). A total of 32,527 mRNAs were identified in pigeon skeletal muscles, including 14,378 novel mRNAs and 18,149 known mRNAs. A total of 2362 miRNAs were identified, including 1758 known miRNAs and 624 novel miRNAs. In total, 839 differentially expressed miRNAs (DEmiRNAs) and 11,311 differentially expressed mRNAs (DEGs) were identified. STEM clustering analysis assigned DEmiRNAs to 20 profiles, of which 7 were significantly enriched (p-value < 0.05). These seven significantly enriched profiles can be classified into two categories. The first category represents DEmiRNAs continuously downregulated from the developmental stage to the growth stage of pigeon skeletal muscle, and the second category represents DEmiRNAs with low expression at the development and early growth stage, and significant upregulation at the high growth stage. We then constructed an miRNA–mRNA network based on target relationships between DEmiRNAs and DEGs belonging to the seven significantly enriched profiles. Based on the connectivity degree, 20 hub miRNAs responsible for pigeon skeletal muscle development and growth were identified, including cli-miR-20b-5p, miR-130-y, cli-miR-106-5p, cli-miR-181b-5p, miR-1-z, cli-miR-1a-3p, miR-23-y, cli-miR-30d-5p, miR-1-y, etc. The hub miRNAs involved in the miRNA–mRNA regulatory networks and their expression patterns during the development and growth of pigeon skeletal muscle were visualized. GO and KEGG enrichment analysis found potential biological processes and pathways related to muscle growth and development. Our findings expand the knowledge of miRNA expression in pigeons and provide a database for further investigation of the miRNA–mRNA regulatory mechanism underlying pigeon skeletal muscle development and growth. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

14 pages, 2686 KiB

Open AccessArticle

Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing

by Pengfei Hu, Zhen Wang, Jiping Li, Dongxu Wang, Yusu Wang, Quanmin Zhao and Chunyi Li

Animals 2022, 12(17), 2203; https://doi.org/10.3390/ani12172203 - 26 Aug 2022

Viewed by 1670

Abstract

The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference [...] Read more.

The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely RNA Binding Motif Protein X-Linked (RBMX) and methyltransferase-like 3 (METTL3), respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

22 pages, 7425 KiB

Open AccessArticle

Transcriptional Characteristics Showed That miR-144-y/FOXO3 Participates in Embryonic Skin and Feather Follicle Development in Zhedong White Goose

by Ichraf Mabrouk, Yuxuan Zhou, Sihui Wang, Yupu Song, Xianou Fu, Xiaohui Xu, Tuoya Liu, Yudong Wang, Ziqiang Feng, Jinhong Fu, Jingyun Ma, Fangming Zhuang, Heng Cao, Honglei Jin, Jingbo Wang and Yongfeng Sun

Animals 2022, 12(16), 2099; https://doi.org/10.3390/ani12162099 - 17 Aug 2022

Cited by 6 | Viewed by 1995

Abstract

Skin and feather follicle development are essential processes for goose embryonic growth. Transcriptome and next-generation sequencing (NGS) network analyses were performed to improve the genome of Zhedong White goose and discover the critical genes, miRNAs, and pathways involved in goose skin and feather [...] Read more.

Skin and feather follicle development are essential processes for goose embryonic growth. Transcriptome and next-generation sequencing (NGS) network analyses were performed to improve the genome of Zhedong White goose and discover the critical genes, miRNAs, and pathways involved in goose skin and feather follicle morphogenesis. Sequencing output generated 6,002,591,668 to 8,675,720,319 clean reads from fifteen libraries. There were 1234, 3024, 4416, and 5326 different genes showing differential expression in four stages, E10 vs. E13, E10 vs. E18, E10 vs. E23, and E10 vs. E28, respectively. The differentially expressed genes (DEGs) were found to be implicated in multiple biological processes and pathways associated with feather growth and development, such as the Wnt signaling pathway, cell adhesion molecules, ECM–receptor interaction signaling pathways, and cell cycle and DNA replication pathways, according to functional analysis. In total, 8276 DEGs were assembled into twenty gene profiles with diverse expression patterns. The reliability of transcriptome results was verified by real-time quantitative PCR by selecting seven DEGs and five miRNAs. The localization of forkhead box O3 (FOXO3), connective tissue growth factor (CTGF), protein parched homolog1 (PTCH1), and miR-144-y by in situ hybridization showed spatial-temporal expression patterns and that FOXO3 and miR-144-y have an antagonistic targeting relationship. The correlation coefficient of FOXO3 and miR-144-y was -0.948, showing a strong negative correlation. Dual-luciferase reporter assay results demonstrated that miR-144-y could bind to the expected location to suppress the expression of FOXO3, which supports that there is a targeting relationship between them. The detections in this report will provide critical insight into the complex molecular mechanisms and breeding practices underlying the developmental characteristics of skin and feather follicles in Zhedong white geese. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

15 pages, 2362 KiB

Open AccessArticle

Transcriptome Comparison Reveals the Difference in Liver Fat Metabolism between Different Sheep Breeds

by Taotao Li, Meilin Jin, Xiaojuan Fei, Zehu Yuan, Yuqin Wang, Kai Quan, Tingpu Wang, Junxiang Yang, Maochang He and Caihong Wei

Animals 2022, 12(13), 1650; https://doi.org/10.3390/ani12131650 - 27 Jun 2022

Cited by 3 | Viewed by 2178

Abstract

Hu sheep and Tibetan sheep are two commonly raised local sheep breeds in China, and they have different morphological characteristics, such as tail type and adaptability to extreme environments. A fat tail in sheep is the main adipose depot in sheep, whereas the [...] Read more.

Hu sheep and Tibetan sheep are two commonly raised local sheep breeds in China, and they have different morphological characteristics, such as tail type and adaptability to extreme environments. A fat tail in sheep is the main adipose depot in sheep, whereas the liver is an important organ for fat metabolism, with the uptake, esterification, oxidation, and secretion of fatty acids (FAs). Meanwhile, adaptations to high-altitude and arid environments also affect liver metabolism. Therefore, in this study, RNA-sequencing (RNA-seq) technology was used to characterize the difference in liver fat metabolism between Hu sheep and Tibetan sheep. We identified 1179 differentially expressed genes (DEGs) (Q-value < 0.05) between the two sheep breeds, including 25 fat-metabolism-related genes. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 16 pathways were significantly enriched (Q-value < 0.05), such as the proteasome, glutamatergic synapse, and oxidative phosphorylation pathways. In particular, one of these pathways was enriched to be associated with fat metabolism, namely the thermogenesis pathway, to which fat-metabolism-related genes such as ACSL1, ACSL4, ACSL5, CPT1A, CPT1C, SLC25A20, and FGF21 were enriched. Then, the expression levels of ACSL1, CPT1A, and FGF21 were verified in mRNA and protein levels via qRT-PCR and Western blot analysis between the two sheep breeds. The results showed that the mRNA and protein expression levels of these three genes were higher in the livers of Tibetan sheep than those of Hu sheep. The above genes are mainly related to FAs oxidation, involved in regulating the oxidation of liver FAs. So, this study suggested that Tibetan sheep liver has a greater FAs oxidation level than Hu sheep liver. In addition, the significant enrichment of fat-metabolism-related genes in the thermogenesis pathway appears to be related to plateau-adaptive thermogenesis in Tibetan sheep, which may indicate that liver- and fat-metabolism-related genes have an impact on adaptive thermogenesis. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

13 pages, 3324 KiB

Open AccessArticle

IGF1R and LOX Modules Are Related to Antler Growth Rate Revealed by Integrated Analyses of Genomics and Transcriptomics

by Pengfei Hu, Zhen Wang, Jiping Li, Dongxu Wang, Yusu Wang, Quanmin Zhao and Chunyi Li

Animals 2022, 12(12), 1522; https://doi.org/10.3390/ani12121522 - 11 Jun 2022

Viewed by 1489

Abstract

Deer antlers are organs of bone and have an extremely rapid growth rate. Thus far, the molecular mechanism underlying rapid antler growth has not been properly elucidated, and key genes driving this growth rate have not been fully identified. In this study, based [...] Read more.

Deer antlers are organs of bone and have an extremely rapid growth rate. Thus far, the molecular mechanism underlying rapid antler growth has not been properly elucidated, and key genes driving this growth rate have not been fully identified. In this study, based on the newly assembled high-quality sika deer genome, we conducted an integrated analysis of genome-wide association analysis (GWAS) and weighted gene co-expression network analysis (WGCNA) using genome resequencing data from our previous GWAS, with weight and transcriptome sequencing data of faster- vs. slower-growing antlers of sika deer. The expressions of key genes were verified using Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) in different tissue zones of the antler growth center, different types of sika deer tissues and antler tissues collected from faster and slower growth rates. The results show that a total of 49 genes related to antler growth rate were identified, and most of those genes were enriched in the IGF1R and LOX modules. The gene regulation network of antler growth rate through the IGF1R pathway was constructed. In conclusion, the integration of GWAS and WGCNA analyses had great advantages in identifying regulatory genes of complex antler growth traits over using singular methods individually, and we believe that our findings in the present study can provide further insight into unveiling the mechanism underlying extraordinary fast antler growth rate in particular, as well as the regulatory mechanism of rapid tissue proliferation in general. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

13 pages, 2508 KiB

Open AccessArticle

Sex Identification of Feather Color in Geese and the Expression of Melanin in Embryonic Dorsal Skin Feather Follicles

by Xiaohui Xu, Sihui Wang, Ziqiang Feng, Yupu Song, Yuxuan Zhou, Ichraf Mabrouk, Heng Cao, Xiangman Hu, Haojia Li and Yongfeng Sun

Animals 2022, 12(11), 1427; https://doi.org/10.3390/ani12111427 - 31 May 2022

Cited by 5 | Viewed by 1922

Abstract

In production practice, we have found that the gray and black down on the backs of the Holdobaggy goslings is usually darker in females than in males. Melanin is the key pigment affecting the color of poultry plumage. Therefore, to determine whether the [...] Read more.

In production practice, we have found that the gray and black down on the backs of the Holdobaggy goslings is usually darker in females than in males. Melanin is the key pigment affecting the color of poultry plumage. Therefore, to determine whether the darkness of the dorsal plumage of the Holdobaggy goslings is related to sex, we study the melanin in the feather follicles of the dorsal skin during the embryonic period. The feather follicle structure and melanin distribution on the dorsal surface of the goose embryo is observed by HE staining and melanin-specific staining. The melanin content in the feather follicles of the dorsal skin of goslings is determined by ELISA. The results showed that the melanin content is higher in female geese than in males (p < 0.05). In addition, we also analyze the mRNA and protein expression levels of melanin-related genes (TYRP1 and ASIP) by quantitative real-time PCR and Western blotting analysis. The results show that the mRNA expression level of TYRP1 is significantly higher in the females’ dorsal skin feather follicles (p < 0.05), while the mRNA expression level of ASIP is significantly higher in the dorsal skin feather follicles of male geese (p < 0.05). In conclusion, the difference between males and females in the color of the black feathers on the dorsal track of the Holdobaggy goslings is verified, and it is feasible to identify the sex by the initial plumage color. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

15 pages, 6717 KiB

Open AccessArticle

MiR-24-3p Conservatively Regulates Muscle Cell Proliferation and Apoptosis by Targeting Common Gene CAMK2B in Rat and Cattle

by Ge Yang, Mingli Wu, Xinqi Liu, Fuwen Wang, Mei Li, Xiaoya An, Fuxia Bai, Chuzhao Lei and Ruihua Dang

Animals 2022, 12(4), 505; https://doi.org/10.3390/ani12040505 - 17 Feb 2022

Cited by 5 | Viewed by 2405

Abstract

Skeletal muscle plays an important role in the growth and development of meat animals. MicroRNAs (miRNAs) can participate in the regulation of muscle development-related functions; however, there have been few reports on whether there are related miRNAs that conservatively regulate muscle development among [...] Read more.

Skeletal muscle plays an important role in the growth and development of meat animals. MicroRNAs (miRNAs) can participate in the regulation of muscle development-related functions; however, there have been few reports on whether there are related miRNAs that conservatively regulate muscle development among different species. In this study, the miRNA transcriptome sequencing data of the muscle tissue of cattle, rat, goat, and pig showed that miR-24-3p may conservatively regulate muscle development in these species. Furthermore, mmu-miR-24-3p can positively regulate C2C12 cell proliferation and apoptosis by regulating key proliferation and apoptosis genes in muscle development, which was verified by CCK-8 and RT-qPCR. Bta-miR-24-3p can also positively regulate the proliferation and apoptosis of bovine muscle primary cells by regulating key proliferation and apoptosis genes in the process of muscle development, as verified by CCK-8 and RT-qPCR. The target genes of miR-24-3p in cattle, rat, goat, and pig, which include a large proportion of target genes shared among the four species, are enriched in multiple cell functions and signal pathways that are closely related to muscle development, as revealed by GO and KEGG enrichment analysis. A double luciferase test showed that the shared target genes WNT4, CAMK2B, and TCF7 were targeted by mmu-miR-24-3p in rat and bta-miR-24-3p in cattle. These three shared target genes WNT4, CAMK2B, and TCF7 are involved in the Wnt signaling pathway, which showed that miR-24-3p plays an important role in rat and cattle. The shared target gene (CAMK2B) in rat and cattle increased significantly after the inhibition of miR-24-3p by RT-qPCR. The findings of this study contribute to a better understanding of the role of miR-24-3p in the regulation of muscle development. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

12 pages, 2188 KiB

Open AccessFeature PaperArticle

Comparison of lncRNA Expression in the Uterus between Periods of Embryo Implantation and Labor in Mice

by Zijiao Zhao, Lu Chen, Maosheng Cao, Tong Chen, Yiqiu Huang, Nan Wang, Boqi Zhang, Fangxia Li, Kaimin Chen, Chenfeng Yuan, Chunjin Li and Xu Zhou

Animals 2022, 12(3), 399; https://doi.org/10.3390/ani12030399 - 08 Feb 2022

Cited by 9 | Viewed by 1984

Abstract

Uterine function during pregnancy is regulated mainly by progesterone (P4) and estrogen (E2). Serum P4 levels are known to fluctuate significantly over the course of pregnancy, especially during embryo implantation and labor. In this study, pregnant mice at E0.5, E4.5, E15.5, and E18.5 [...] Read more.

Uterine function during pregnancy is regulated mainly by progesterone (P4) and estrogen (E2). Serum P4 levels are known to fluctuate significantly over the course of pregnancy, especially during embryo implantation and labor. In this study, pregnant mice at E0.5, E4.5, E15.5, and E18.5 (n = 3/E) were used for an RNA-Seq-based analysis of mRNA and lncRNA expression. In this analysis, 1971 differentially expressed (DE) mRNAs, 493 known DE lncRNAs, and 1041 novel DE lncRNAs were found between E0.5 and E4.5 at the embryo implantation stage, while 1149 DE mRNAs, 192 known DE lncRNAs, and 218 novel DE lncRNAs were found between E15.5 and E18.5 at the labor stage. The expression level of lncRNA-MMP11 was significantly downregulated by P4 treatment on MSM cells, while lncRNA-ANKRD37 was significantly upregulated. Notably, 117 DE mRNAs, 19 known DE lncRNAs, and 31 novel DE lncRNAs were commonly expressed between the two stages, indicating that these mRNAs and lncRNAs may be directly or indirectly regulated by P4. Full article

(This article belongs to the Special Issue RNA-Sequencing Technique in Animals Research)

► Show Figures

Figure 1

Journal Menu

Journal Browser

RNA-Sequencing Technique in Animals Research

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (10 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI