Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal

Changsha, China

Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal

Changsha, China
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Weng B.,Hunan University | Ran M.,Hunan University | Chen B.,Hunan University | He C.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 2 more authors.
Genomics | Year: 2017

A comprehensive and systematic understanding of the roles of lncRNAs in the postnatal development of the pig testis has still not been achieved. In the present study, we obtained more than one billion clean reads and identified 15,528 lncRNA transcripts; these transcripts included 5032 known and 10,496 novel porcine lncRNA transcripts and corresponded to 10,041 lncRNA genes. Pairwise comparisons identified 449 known and 324 novel lncRNAs that showed differential expression patterns. GO and KEGG pathway enrichment analyses revealed that the targeted genes were involved in metabolic pathways regulating testis development and spermatogenesis, such as the TGF-beta pathway, the PI3K-Akt pathway, the Wnt/β-catenin pathway, and the AMPK pathway. Using this information, we predicted some lncRNAs and coding gene pairs were predicted that may function in testis development and spermatogenesis; these are listed in detail. This study has provided the most comprehensive catalog to date of lncRNAs in the postnatal pig testis and will aid our understanding of their functional roles in testis development and spermatogenesis. © 2017.


Weng B.,Hunan University | Weng B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 11 more authors.
Genes and Genomics | Year: 2017

microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) execute important regulatory roles in testis development and spermatogenesis, while previous studies mainly focus on the expression profiles in immature and mature porcine testes, which may cause a bottleneck for further understanding their complex physiological processes in porcine testes development and spermatogenesis. Thus, we presented the expression and characterization of miRNAs and piRNAs in DS (60-day-old), DN (90-day-old), DT (120-day-old) and DF (150-day-old) pig testes. In total, 12,834,628, 13,359,726, 12,851,249 and 12,938,601 clean reads were generated from these libraries, respectively. 293 mature and 36 novel miRNAs as well as 4923 piRNA clusters were identified from pig testes, and they showed an age-dependent manner. GO enrichment analysis of miRNA target genes and piRNA generated genes showed that they participated widely in regulating the pig spermatogenesis process. In addition, 12 differentially expressed miRNAs were randomly selected to validate using qRT-PCR. Our results provided novel comprehensive expression profiles of miRNAs and piRNAs in pig testes at different stages of sexual maturity, which will promote our knowledge of them in regulating the pig testes development and spermatogenesis process. © 2017 The Genetics Society of Korea and Springer Science+Business Media B.V.


Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Weng B.,Hunan University | Weng B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 6 more authors.
Genes and Genomics | Year: 2017

Testicular development and spermatogenesis are strictly regulated with the complex interactions between several cell types in testis. However, the limited availability of genomic and molecular information limits our understanding of this complex physiological process. In this study, we characterized the transcriptome between immature (30-day-old) and mature (180-day-old) pig testes using RNA-seq technology. 24,469 known coding gene transcripts corresponding to 20,566 genes were mapped in these two developmental stages, 3,328 genes were differentially expressed, and numerous novel transcripts and alternative splicing events were also identified. Ten differentially expressed genes were validated by measuring the relative expression using real-time quantitative polymerase chain reaction (PCR). 125 Gene Ontology (GO) terms were significantly enriched, and most of them involved in GO terms related to male reproduction, testicular development, and spermatogenesis. In addition, this study also represented the prediction of 10,000 circRNAs, as well as the validation of six pig circRNAs using Find_cric algorithm. Our study substantially expanded our knowledge about the transcriptomic profile of immature and mature pig testes, and provided a useful resource to study the mechanisms of pig testis development and spermatogenesis at the molecular level. © 2017 The Genetics Society of Korea and Springer Science+Business Media B.V.


Dong L.,Hunan University | Dong L.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Maoliang R.,Hunan University | Maoliang R.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 4 more authors.
Mitochondrial DNA Part B: Resources | Year: 2016

In this study, we cloned and sequenced the complete mitochondrial genome DNA of Chinese pig, the Meishan pig. The sample was taken from Yencheng City, Jiangsu province in China. The complete genome DNA is 16 708 bp in length. We also performed a comparative analysis of the Meishan pig mitochondrial to the mitogenome sequences of 21 pig breeds which have been deposited in GenBank. Phylogenetic analysis using neighbour-joining computational algorithms showed that the analyzed species are divided into four major clades; the results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes. © 2016 The Author(s). Published by Taylor & Francis.


Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Chen B.,Hunan University | Chen B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 9 more authors.
Biology of Reproduction | Year: 2016

Thousands of long noncoding RNAs (lncRNAs) have been identified in mouse, rat, and human testes, some of which play important roles in testis development and spermatogenesis. However, systematic analysis of lncRNAs expressed in postnatal pig testes has not been reported. Thus, in this study, we present the expression and characterization of lncRNAs in immature (30-day-old [D30]) and mature (180-day-old [D180]) pig testes. A total of 90 440 168 (85.75%) and 97 001 700 (95.35%) 150-base-pair paired-end clean reads were generated in D30 and D180 cDNA libraries, respectively, using the Illumina HiSeq 4000 platform; 36 727 transcripts were assembled in those two libraries, 777 lncRNA transcripts from 752 lncRNA gene loci were identified using the highly stringent pipeline, and 101 of those lncRNA transcripts were significantly differentially expressed. Those lncRNAs shared some characteristics with other mammals, including fewer exons, shorter length and exon length, and lower expression level compared with those of protein-coding genes; 402 protein-coding genes (<10 kb) were found as nearest neighbors of 294 out of 752 lncRNA genes, and gene ontology enrichment showed that they were enriched in transcription- and development-related processes. Fifteen differentially expressed and 10 novel lncRNAs were randomly selected and validated by quantitative polymerase chain reaction (PCR) and reverse transcriptase PCR. In addition, one of the 10 novel lncRNAs was further confirmed using RACE clone technology. This study provides a catalog of porcine testes lncRNAs for further understanding their regulation roles in pig testis development and spermatogenesis. © 2016 by the Society for the Study of Reproduction, Inc.


Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Chen B.,Hunan University | Chen B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 12 more authors.
RSC Advances | Year: 2015

To understand the complex physiological process underlying pig testis development and spermatogenesis, this study aims to characterize the change in miRNA and mRNA profiles at four developmental stages of embryonic and postnatal testes, including 60 dpc (days post coitus, E60), 90 dpc (E90), 30-day-old (D30) and 180-day-old (D180). A total of 304 mature, 50 novel miRNAs, and 8343 differentially-expressed genes were identified. 93 (48 up and 45 down), 104 (49 up and 55 down), 122 (49 up and 73 down) differentially-expressed miRNAs, as well as 1007 (646 up and 361 down), 1929 (911 up and 1018 down), 7420 (3998 up and 3422 down) differentially-expressed genes were identified in E90 vs. E60, D30 vs. E90 and D180 vs. D30, respectively. Integrating analysis of miRNA and mRNA expression profiles predicted more than 5000 miRNA-mRNA interaction sites. GO and KEGG pathway analysis of the predicted target genes illustrated the likely roles of differentially expressed miRNAs in testis development and spermatogenesis. For example, PI3K-Akt signaling pathway and Hippo signaling pathway related development, and carbon metabolism, fatty acid metabolism, protein digestion and absorption, were involved in metabolite synthesis. These integrated high-throughput expression data show that miRNA is a critical factor in porcine testis development, providing a useful resource to understand global genome expression change in porcine testis development and spermatogenesis. © 2015 The Royal Society of Chemistry.

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