A chromosome-level genome assembly of the Echiura Urechis unicinctus.

Echiura is a distinctive family of unsegmented sausage-shaped marine worms whose phylogenetic relationship still needs strong evidence from the phylogenomic analysis. In this family, Urechis unicinctus is known for its high nutritional and medicinal value and adaptation to harsh intertidal conditions. Herein, we combined PacBio long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of U. unicinctus. The assembled genome spans ~1,138.6 Mb with a scaffold N50 of 68.3 Mb, of which 1,113.8 Mb (97.82%) were anchored into 17 pseudo-chromosomes. The BUSCO analysis demonstrated the completeness of the genome assembly and gene model prediction are 93.5% and 91.5%, respectively. A total of 482.1 Mb repetitive sequences, 21,524 protein-coding genes, 1,535 miRNAs, 3,431 tRNAs, 124 rRNAs, and 348 snRNAs were annotated. This study significantly improves the quality of U. unicinctus genome assembly, sets the footsteps for molecular breeding and further study in genome evolution, genetic and molecular biology of U. unicinctus.

The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig.

circRNAs, as miRNA sponges, participate in many important biological processes. However, it remains unclear whether circRNAs can regulate lipid metabolism. This study aimed to explore the competing endogenouse RNA (ceRNA) regulatory network that affects the difference between intramuscular fat (IMF) and subcutaneous fat (SCF) deposition, and to screen key circRNAs and their regulatory genes. In this experiment, we identified 265 differentially expressed circRNAs, of which 187 up-regulated circRNA and 78 down-regulated circRNA in IMF. Subsequently, we annotated the function of DEcircRNA's host genes, and found that DEcircRNA's host genes were mainly involved in GO terms (including cellular response to fatty acids, lysophosphatidic acid acyltransferase activity, R-SMAD binding, etc.) and signaling pathways (fatty acid biosynthesis, Citrate cycle, TGF- ß Signal pathway) related to adipogenesis, differentiation and lipid metabolism. By constructing a circRNA-miRNA network, we screened out DEcircRNA that can competitively bind to more miRNAs as key circRNAs (circRNA_06424 and circRNA_08840). Through the functional annotation of indirect target genes and protein network analysis, we found that circRNA_06424 affects the expression of PPARD, MMP9, UBA7 and other indirect target genes by competitively binding to miRNAs such as ssc-miR-339-5p, ssc-miR-744 and ssc-miR-328, and participates in PPAR signaling pathway, Wnt signaling pathway, unsaturated fatty acid and other signaling pathways, resulting in the difference of fat deposition between IMF and SCF. This study provide a theoretical basis for further research investigating the differences of lipid metabolism in different adipose tissues, providing potential therapeutic targets for ectopic fat deposition and lipid metabolism diseases.

Genome-Wide Expression Profiling and Networking Reveals an Imperative Role of IMF-Associated Novel CircRNAs as ceRNA in Pigs.

Intramuscular fat (IMF) deposition is a biological process that has a strong impact on the nutritional and sensorial properties of meat, with relevant consequences on human health. Pork loins determine the effects of marbling on the sensory attributes and meat quality properties, which differ among various pig breeds. This study explores the crosstalk of non-coding RNAs with mRNAs and analyzes the potential pathogenic role of IMF-associated competing endogenous RNA (ceRNA) in IMF tissues, which offer a framework for the functional validation of key/potential genes. A high-throughput whole-genome transcriptome analysis of IMF tissues from longissimus dorsi muscles of Large White (D_JN) and Laiwu (L_JN) pigs resulted in the identification of 283 differentially expressed circRNAs (DECs), including two key circRNAs (circRNA-23437, circRNA-08840) with potential binding sites for multiple miRNAs regulating the whole network. The potential ceRNA mechanism identified the DEC target miRNAs-mRNAs involved in lipid metabolism, fat deposition, meat quality, and metabolic syndrome via the circRNA-miRNA-mRNA network, concluding that ssc-mir-370 is the most important target miRNA shared by both key circRNAs. TGM2, SLC5A6, ECI1, FASN, PER1, SLC25A34, SOD1, and COL5A3 were identified as hub genes through an intensive protein-protein interaction (PPI) network analysis of target genes acquired from the ceRNA regulatory network. Functional enrichments, pathway examinations, and qRT-PCR analyses infer their implications in fat/cholesterol metabolism, insulin secretion, and fatty acid biosynthesis. Here, circRNAs and miRNA sequencing accompanied by computational techniques were performed to analyze their expressions in IMF tissues from the longissimus dorsi muscles of two pig breeds. Their target gene evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations, and structural advances with high-throughput protein modeling, following genomic organizations, will provide new insights into the underlying molecular mechanisms of adipocyte differentiation and IMF deposition and a much-needed qualitative framework for future research to improve meat quality and its role as a biomarker to treat lipid metabolic syndromes.

Comparative genomics of Sarcoptes scabiei provide new insights into adaptation to permanent parasitism and within-host species divergence.

Sarcoptes scabiei is the causative agent of a highly contagious skin disease in humans and more than 100 mammals. Here, we reported the first chromosome-level reference genome of S. scabiei isolated from rabbits, with a contig N50 size of 5.92 Mb, a total assembled length of 57.30 Mb, ∼12.65% repetitive sequences and 9333 predicted protein-coding genes. The phylogenetic tree based on 1338 shared high-confidence single-copy orthologous genes estimated that the mammalian ectoparasite S. scabiei and the plant-feeding mite Tetranychus urticae separated ∼340 million years ago. Both neighbour-joining tree and principal component analysis of 20 mite populations isolated from four hosts (humans, pigs, dogs and rabbits) distributed in three countries (China, Australia and the USA) consistently supported genetic subdivisions according to host species rather than geographical location. The demographic history of S. scabiei reconstructed by multiple sequentially Markovian coalescent analysis suggested that S. scabiei isolated from rabbits, humans, dogs and pigs diverged ∼5000 years ago. Investigation of the homeobox (Hox) genes revealed that S. scabiei contains 8 of 10 canonical Hox genes that are present in the arthropod ancestor, and the absence of the Abd-A gene may correlate with the long gap between their front and back legs. Comparative genomics demonstrated that genes specific to scabies mites were mainly enriched in nutrition digestive systems, whereas genes in the families that involved detoxification (cytochrome P450, carboxyl/cholinesterases and the ATP-binding cassette transporter C group) were extremely contracted compared with that of other mites analysed in this study. Selective sweep analysis of mite populations from various pairs of two out of the four host species revealed that the strongest selective sweep signals were mainly enriched in cysteine-type peptidase activity and apoptosis. The results provided clues for the mechanisms of S. scabiei adaptation to a permanent parasitic lifestyle and knowledge that would enable further control of this highly contagious skin disease.

Identification of potential miRNA-mRNA regulatory network and the key miRNAs in intramuscular and subcutaneous adipose.

Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), severely affecting the meat rate of pigs. Studying the mechanisms of miRNAs related to lipogenesis and lipid metabolism has important implications for pig breeding. We constructed two small RNA libraries from intramuscular and subcutaneous fat to evaluate the patterns of lipogenesis in Laiwu pig, a Chinese breed. A total of 286 differentially expressed miRNAs (DEmiRNAs), including 193 known miRNA and 93 novel miRNAs, were identified from two types of adipose. GO and KEGG enrichment analysis for DEmiRNAs showed that their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as Wnt signaling pathway,MAPK signaling pathway, Hippo signaling pathway, PI3K-Akt signaling pathway, Melanogenesis, Signaling pathways regulating pluripotency of stem cells and so on. Then, we constructed a miRNA-mRNA interaction network to find out which miRNAs were the key miRNAs of regulation in Wnt signaling pathway. In this pathway, miR-331-3p, miR-339-5p, miR-874 and novel346_mature target PPARD, WNT10B, RSPO3, WNT2B. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation and predicting and treating diseases caused by ectopic fat.

Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens.

BACKGROUND: Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS: Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS: Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.

Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving "living fossil".

The nautilus, commonly known as a "living fossil," is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.

Integrative Analysis of miRNAs Involved in Fat Deposition in Different Pig Breeds.

BACKGROUND: miRNAs are a set of small, noncoding RNAs that bind to partially complementary sequences on target mRNAs. This leads to the post-transcriptional regulation of gene expression. Many studies have shown that microRNAs play critical roles in adipose cell differentiation and fat metabolism. The aim of this study was to explore the regulatory functions of miRNAs in fat deposition for the prevention and therapy of lipid metabolism-related diseases. METHODS: The significant differences in the fat deposition of Laiwu (LW) pigs and Large White (LY) pigs were studied. To investigate the genetic relationships of miRNAs that regulate fat deposition, we performed a genome-wide analysis of miRNAs derived from subcutaneous adipose tissue of LW and LY pigs using RNA-seq. RESULTS: There were 39 known miRNAs and 56 novel miRNAs significantly differential expressed between the two breeds of pigs. In the analysis of the Gene Ontology and KEGG pathways, predicted targets of these differentially expressed miRNAs were involved in several fat-associated pathways, such as the peroxisome proliferator-activated receptor (PPAR), mitogen-activated protein kinases (MAPK) and Wnt signaling pathways. In addition, ssc-miR-133a-3p, ssc-miR-486 and ssc-miR-1 each had a great impact on the development of porcine subcutaneous fat through the PPAR signaling pathway. CONCLUSIONS: We explored the role of differentially expressed miRNAs and studied the mechanisms of adipogenesis and fat deposition between two different pig breeds. In addition, these results also contribute to research relevant to human obesity.

Identification and analysis of lncRNA, miRNA and mRNA related to subcutaneous and intramuscular fat in Laiwu pigs.

Background: Long non-coding RNAs (lncRNAs) regulate adipocyte differentiation and metabolism, However, their function on subcutaneous and intramuscular adipose tissues in pigs is unclear. Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), which severely affects the meat rate of pigs. It is of great significance for porcine breeding to study the mechanism of lncRNA related to adipogenesis and lipid metabolism. Methods: We identified differentially expressed lncRNAs, miRNAs and mRNAs in subcutaneous and intramuscular adipose tissues in three female Laiwu pigs by deep RNA-sequencing(|log2foldchange|≥1, P_value ≤ 0.05). The gene expression profiles of IMF and SCF in Laiwu pigs were comparatively analyzed by Bioinformatics methods to identify key lncRNAs, miRNAs, and mRNAs associated with lipid metabolism and adipogenesis. Results: A total of 1209 lncRNAs (DElncRNAs), 286 miRNAs (DEmiRNAs), and 1597 mRNAs (DEgenes) were differentially expressed between two types of adipose. Among them, 17 DElncRNAs and 103 target genes play a role in the co-expression network, as well as 59 DElncRNAs, 44 DEmiRNAs, and 88 DEgenes involved in ceRNA network. In GO(Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DElncRNAs their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as PPAR signaling pathway, Wnt signaling pathway, MAPK signaling pathway. Conclusions: By constructing co-expression and ceRNAs network we found that Wnt signaling pathway play a critical regulatory role in intramuscular adipogenesis and lipid accumulation in Laiwu pigs. TCONS_00006525, TCONS_00046551 and TCONS_00000528 may target WNT5A, WNT10B and FDZ3 in co-expression network, TCONS_00026517 and other lncRNAs regulate the expression of PPARG, RXRG and SCD in ceRNA network, and were involved in Wnt signaling pathway. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation, predicting and treating diseases caused by ectopic fat.

The genome of the thin-necked bladder worm Taenia hydatigena reveals evolutionary strategies for helminth survival.

Taenia hydatigena is a widespread gastrointestinal helminth that causes significant health problems in livestock industry. This parasite can survive in a remarkably wide range of intermediate hosts and affects the transmission dynamics of zoonotic parasites. T. hydatigena is therefore of particular interest to researchers interested in studying zoonotic diseases and the evolutionary strategies of parasites. Herein we report a high-quality draft genome for this tapeworm, characterized by some hallmarks (e.g., expanded genome size, wide integrations of viral-like sequences and extensive alternative splicing during development), and specialized adaptations related to its parasitic fitness (e.g., adaptive evolutions for teguments and lipid metabolism). Importantly, in contrast with the evolutionarily close trematodes, which achieve gene diversification associated with immunosuppression by gene family expansions, in T. hydatigena and other cestodes, this is accomplished by alternative splicing and gene loss. This indicates that these two classes have evolved different mechanisms for survival. In addition, molecular targets for diagnosis and intervention were identified to facilitate the development of control interventions. Overall, this work uncovers new strategies by which helminths evolved to interact with their hosts.

De Novo Sequencing and High-Contiguity Genome Assembly of Moniezia expansa Reveals Its Specific Fatty Acid Metabolism and Reproductive Stem Cell Regulatory Network.

Moniezia expansa (M. expansa) parasitizes the small intestine of sheep and causes inhibited growth and development or even death. Being globally distributed, it causes considerable economic losses to the animal husbandry industry. Here, using Illumina, PacBio and BioNano techniques, we obtain a high-quality genome assembly of M. expansa, which has a total length of 142 Mb, a scaffold N50 length of 7.27 Mb and 8,104 coding genes. M. expansa has a very high body fat content and a specific type of fatty acid metabolism. It cannot synthesize any lipids due to the loss of some key genes involved in fatty acid synthesis, and it may can metabolize most lipids via the relatively complete fatty acid ß-oxidation pathway. The M. expansa genome encodes multiple lipid transporters and lipid binding proteins that enable the utilization of lipids in the host intestinal fluid. Although many of its systems are degraded (with the loss of homeobox genes), its reproductive system is well developed. PL10, AGO, Nanos and Pumilio compose a reproductive stem cell regulatory network. The results suggest that the high body lipid content of M. expansa provides an energy source supporting the high fecundity of this parasite. Our study provides insight into host interaction, adaptation, nutrient acquisition, strobilization, and reproduction in this parasite and this is also the first genome published in Anoplocephalidae.

Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818).

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high-quality chromosome-level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and Hi-C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single-Copy Orthologs were determined in this genome assembly. And Hi-C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein-coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.

The sequence and de novo assembly of hog deer genome.

Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds.

BACKGROUND/AIMS: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. METHODS: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. RESULTS: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. CONCLUSION: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

Identification and Characterization of CircRNAs of Two Pig Breeds as a New Biomarker in Metabolism-Related Diseases.

BACKGROUND/AIMS: CircRNAs, as miRNA sponges, participate in many important biological processes. However, it remains unclear whether circRNAs can regulate lipid metabolism. This paper aims to study the molecular mechanism of fat deposition and provide useful information for the prevention and therapy of lipid metabolism-related diseases. METHODS: CircRNA sequencing was performed to investigate the expression of circRNAs in the subcutaneous adipose tissues of Large White pig and Laiwu pig. The expression of circRNAs was further validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, circRNA-microRNAs (miRNA)-mRNA interaction networks were constructed using bioinformatics tools. In addition, GO and KEGG enrichment analyses were performed for the target genes of circRNAs. RESULTS: In the subcutaneous adipose tissue of Laiwu pig, 70 up-regulated circRNAs and 205 down-regulated circRNAs were identified. Two circRNAs (up-regulated circRNA_26852 and down-regulated circRNA_11897), the expressions of which were confirmed by qRT-PCR, were selected for subsequent analysis. CircRNA-miRNA-mRNA interaction networks were constructed for circRNA_26852 and its target genes as well as circRNA_11897 and its target genes. GO and KEGG enrichment analyses reveal that the target genes of circRNA_26852 and circRNA_11897 are enriched in pathways related to adipocyte differentiation and lipid metabolism, as well as in disease-related pathways. CONCLUSIONS: In this study, circRNA sequencing and bioinformatics technique were used to analyze, for the first time, the expression of circRNAs in the subcutaneous adipose tissues of Large White pig and Laiwu pig. It is inferred that circRNAs might regulate adipogenic differentiation and lipid metabolism. The results provide a theoretical basis for further study on fat deposition mechanism and provide potential therapy targets for metabolism-related diseases.

Differential regulation of mRNAs and lncRNAs related to lipid metabolism in two pig breeds.

Long non-coding RNAs (lncRNAs) can regulate lipid metabolism and adipogenesis. However, there is little research on the role of lncRNAs in fat deposition in pig. In this study, RNA-seq technology was used to analyze the gene expression profiles of subcutaneous adipose tissue in Laiwu (LW) and Large White (LY) pigs. Then, key lncRNAs and genes associated with lipid metabolism and adipogenic differentiation were identified. Fifty four lncRNAs and 482 known mRNAs were differentially expressed in the two pig breeds. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that differentially expressed genes and the target genes of differentially expressed lncRNAs were significantly enriched in PPAR signaling pathway and biological processes including fat cell differentiation and fatty acid metabolism. Key lncRNAs might regulate adipogenic differentiation and fatty acid metabolism by regulating genes involved in above signaling pathway and biological processes. Specifically, XLOC_014379, XLOC_011279, XLOC_064871, XLOC_019518 and XLOC_013639 might target SCD, LPIN1, TRIB3, EGR2 and FABP3, respectively, and then play critical regulatory role. These results are useful for understanding fat deposition in pig, breeding livestock with high quality meat, and preventing and treating lipid metabolic disease.

Identification of differentially expressed genes between subcutaneous and intramuscular adipose tissue of Large White pig using RNA-seq.

To explore the molecular mechanisms of lipid accumulation in different types of adipose tissue, the transcriptomes of the subcutaneous and intramuscular adipose tissues from the Large White pig were determined using RNA-seq technology and bioinformatics methods. The differential gene expression profiles were identified and analyzed with the Gene Ontology, KEGG pathway and protein-protein interaction network strategies. There were 180 differentially expressed genes between the two adipose tissues. The genes up-regulated in the subcutaneous, as compared to intramuscular, adipose tissues were mainly involved in the biological processes related to lipid metabolism. The down-regulated genes were significantly enriched in MAPK signaling pathway, suggesting that this signaling pathway could have an important regulatory role(s) in adipocyte differentiation. In summary, differentially expressed genes between the subcutaneous and intramuscular adipose tissues were predominantly involved in lipid metabolism/accumulation and regulation of adipogenesis in the Large White pig.

Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle.

Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified. Gene Ontology and KEGG pathway analysis revealed that many differentially expressed genes were enriched in several biological processes and pathways relevant to adipogenesis and lipid metabolism, in which PPAR and fatty acid metabolism signaling pathways with related genes such as PPARγ, PLIN2 and ELOVL6 et al. play a critical role. Protein-protein interaction network analysis showed EGR1, FOS, SERPINE1, AGT, MMP2 may have great impact on adipocyte differentiation and adipogenesis. Moreover, potential alternative splicing events and single nucleotide polymorphisms (SNPs) were also identified. In summary, we comprehensively analyzed and discussed the transcriptome of subcutaneous adipose tissue of Wagyu and Holstein cattle, which might provide a theoretical basis for better understanding molecular mechanism of fat metabolism and deposition in beef cattle.

Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle.

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.

[Recent advances of miRNAs in adipose tissues].

microRNAs (miRNAs), a class of endogenous non-coding RNA about 22 nucleotide long, regulate gene expression at the post-transcription level by inhibiting the translation or inducing the degradation of their target mRNAs in organisms. A lot of studies reveal that miRNAs in adipose tissues are involved in adipocyte differentiation and lipid metabolism and modulated by multiple transcription factors, adipocytokines and environmental factors, which form a complex regulatory network maintaining the homeostasis of adipose tissues. The discovery of circulating miRNAs adds new elements to the regulatory network. To study the metabolic diseases such as obesity, we should keep a new insight into the complex dynamic network. In this review, we summarize the latest studies of miRNAs in adipose tissues, which might provide new strategies for the treatment of obesity and other related diseases.