Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq
| Autor: | Huilin Zhang, Liyan Ge, Junting Cao, Xiaolin Liu, Zhigang Hu, Jianqin Zhang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Male
0301 basic medicine Untranslated region Databases Factual lcsh:QR1-502 RNA-Seq Biology Polymerase Chain Reaction Polymorphism Single Nucleotide Biochemistry Article lcsh:Microbiology 03 medical and health sciences Exon 0302 clinical medicine medicine Animals DEG KEGG pathway RNA Messenger Phosphorylation skeletal muscle Muscle Skeletal Molecular Biology Cytoskeleton Gene Library Genetics Genome Gene Expression Profiling Alternative splicing Intron Computational Biology Genetic Variation High-Throughput Nucleotide Sequencing Skeletal muscle Genomics Actin cytoskeleton Actins Ducks 030104 developmental biology medicine.anatomical_structure Hanzhong Ma duck RNA splicing Female Soybeans transcriptome 030217 neurology & neurosurgery |
| Zdroj: | Biomolecules, Vol 11, Iss 315, p 315 (2021) Biomolecules Volume 11 Issue 2 |
| Popis: | As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteristics of transcripts. A total of 632,172,628 (average 52,681,052) and 637,213,938 (average 53,101,162) reads were obtained from the sequencing data of breast and leg muscles, respectively. Over 71.63% and 77.36% of the reads could be mapped to the Anas platyrhynchos genome. In the skeletal muscle of Hanzhong duck, intron variant (INTRON), synonymous variant (SYNONYMOUS_CODING), and prime 3′ UTR variant (UTR_3_PRIME) were the main single nucleotide polymorphisms (SNP) annotation information, and “INTRON”, “UTR_3_PRIME”, and downstream-gene variant (DOWNSTREAM) were the main insertion-deletion (InDel) annotation information. The predicted number of alternative splicing (AS) in all samples were mainly alternative 5′ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)-the last exon splicing (TTS). Besides, there were 292 to 2801 annotated differentially expressed genes (DEGs) in breast muscle and 304 to 1950 annotated DEGs in leg muscle from different databases. It is worth noting that 75 DEGs in breast muscle and 49 DEGs in leg muscle were co-expressed at all developmental points of comparison, respectively. The RNA-Seq data were confirmed to be reliable by qPCR. The identified DEGs, such as CREBL2, RHEB, GDF6, SHISA2, MYLK2, ACTN3, RYR3, and STMN1, were specially highlighted, indicating their strong associations with muscle development in the Hanzhong Ma duck. KEGG pathway analysis suggested that regulation of actin cytoskeleton, oxidative phosphorylation, and focal adhesion were involved in the development of skeletal muscle. The findings from this study can contribute to future investigations of the growth and development mechanism in duck skeletal muscle. |
| Databáze: | OpenAIRE |
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