Identification and Expression Profiling of miRNAome in Goat <i>longissimus dorsi</i> Muscle from Prenatal Stages to a Neonatal Stage

<div><p>Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, such as microRNAs (miRNAs). In the current study, we made use of the deep sequencing data from Jianzhou Da’er goat <i>longissimus dorsi</i> sampled on days 45, 60, and 105 of gestation, as well as day three after birth to identify miRNAs that regulate goat skeletal myogenesis, and examine their temporal expression profiles. A total of 410 known goat miRNAs, 752 miRNA homologs and 88 novel miRNAs were identified across four stages. Besides three myomiRs, the abundance of 17 miRNAs, including chi-miR-424, chi-miR-542-3p and chi-miR-136-5p was more than 10,000 reads per million mapped reads (RPM), on average. Furthermore, 50 miRNAs with more than 100 RPM clustered at the imprinted <i>DLK1–DIO3</i> locus on chromosome 21 and showed similar expression patterns, indicating that these miRNAs played important roles in skeletal myogenesis of goats. Based on pairwise comparisons, 221 differentially expressed (DE), known miRNAs were identified across four stages. GO and KEGG analyses of the genes targeted by the DE miRNAs revealed the significantly enriched processes and pathways to be consistent with temporal changes of skeletal muscle development across all sampled stages. However, follow-up experimental studies were required to explore functions of these miRNAs and targets underlying skeletal myogenesis.</p></div

Additional file 4: Table S3. of Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

List of differentially expressed lncRNAs from four skeletal muscle developmental stages. (XLSX 122 kb

Most abundant 19 known miRNAs across all four stages (RPM>10000).

<p>Most abundant 19 known miRNAs across all four stages (RPM>10000).</p

qPCR validation of miRNA expression in skeletal muscle samples.

<p>The r value represents the Pearson Correlation Coefficient between two methods. The abundance of the miRNAs is normalized to abundance of U6 snRNA.</p

Basic analysis of the sequencing data.

<p>(A) Sequence length distribution of clean reads; (B) Sequence length distribution of known miRNAs.</p

STEM analysis of the DE known miRNAs expression profiles.

<p>(A) Each box corresponds to a type expression profile and only colored profiles are statistically significant. The upper-left and bottom-left numbers in each box indicate the order of profiles and P-values, respectively. (B) Four significant clusters of miRNA profiles across all four stages.</p

Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development

The rumen is an important digestive organ in ruminants. Numerous regulatory factors including microRNAs (miRNAs) are involved in embryonic organ development. In the present study, miRNAs expressed in the rumens of goats (Capra hircus) and their potential roles in the pathways involved in rumen development were identified using high-throughput sequencing. Histological morphology revealed a distinct difference in each layer of rumen during the period from embryonic day 60 (E60) to embryonic day 135 (E135). We determined the expression profiles of miRNAs in the goat rumen, and identified 423 known miRNAs and 559 potentially novel miRNAs in the E60 and E135 embryonic rumen, respectively. Bioinformatics analysis annotated the 42 differentially expressed miRNAs and the top 10 most highly expressed miRNAs of the two libraries to 48 and 38 gene ontology categories, as well as to 168 and 71 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. The expression patterns of eight randomly selected miRNAs were validated by stem-loop quantitative reverse transcription PCR, suggesting that the sequencing data were reliable. We profiled the genome-wide expression of rumen-expressed miRNAs at different prenatal stages of rumen tissues, revealing that a subset of miRNAs might play important roles in the formation of the rumen layers. Taken together, these findings will aid the investigation of dominant rumen-related miRNA sets and help understand the genetic control of rumen development in goats

Polymorphisms, differentiation, and phylogeny of 10 Tibetan goat populations inferred from mitochondrial D-loop sequences

<p>China has abundant population of Tibetan goats, but available information regarding genetic structure and phylogenetic status remains limited. Here, 130 mitochondrial D-loop sequences of individuals from 10 Tibetan goat populations located in distinct plateau areas were analyzed. Eighty-six haplotypes were defined, among which 97.7% were group-specific haplotypes. Haplotype and nucleotide diversity indices were 0.990 ± 0.003 and 0.0145 ± 0.0013, respectively. The pairwise Wright’s <i>F</i>-statistics ranged from −0.028 to 0.385, and over half of them were greater than 0.05, indicating apparent genetic differentiation among the populations. AMOVA analysis (<i>F_ST </i>= 0.0858) manifested that the genetic structure has become weak. Phylogenetic trees revealed four haplogroups (A, B, C, and D), suggesting that Tibetan goats had four origins. Mismatch distribution analyses and neutrality tests indicated that at least one population expansion event occurred during the demographic history of Tibetan goat. These results will provide a more complete understanding of Tibetan goat genetic resources.</p

Number of commonly and uniquely DE miRNAs between the different stages of pairwise comparisons.

<p>Number of up-regulated (A) and down-regulated (B) miRNAs among prenatal stages (E45 vs E60, E45 vs E105 and E60 vs E105). Number of down-regulated (C) and up- regulated (D) miRNAs between the neonatal stage and prenatal stages (E45 vs B3, E60 vs B3, and E105 and B3). Differentially expressed miRNAs were detected using the cutoff values of |log2 (Fold change)| > 1 and FDR < 0.05. Here the fold changes were calculated from the pseudo-counts based on the UQ normalizations which was different from the fold changes based on RPM values of the miRNAs.</p

Genomic distribution of the known miRNAs across goat chromosomes.

<p>The numbers at the bottom of the chromosome schematic bars represent amounts of miRNAs detected on each chromosome. Red circles at the right of the chromosomes represent the known miRNAs located on the chromosomes. The blue bar on chromosome 21 represents the miRNA cluster at 62.0 Mb—63.0 Mb region. It is noteworthy that many miRNAs on the same chromosome (i.e. the miRNA cluster on chromosome 21) are compactly arrayed and may not be distinguishable in this figure due to their close proximity.</p