Genotyping-by-sequencing reveals the impact of restocking on wild common carp populations of the southern Caspian basin

publishedVersio

Reference genome of wild goat (<i>capra aegagrus</i>) and sequencing of goat breeds provide insight into genic basis of goat domestication

BACKGROUND: Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS: We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION: Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users

In silico prediction of long intergenic non-coding RNAs in sheep

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep including brain, heart, kidney, liver, lung, ovary, skin and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability and tissue-specific scores. 64 putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development and multicellular organismal development. The findings reported here have important implications for the study of sheep genome.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Genomic information obtained on the brood stocks of <i>S</i>. <i>caspius</i>.

Genomic information obtained on the brood stocks of S. caspius.</p

The UPGMA phylogenetic tree using the nei-based genetic distances between different brood stocks of <i>s</i>. <i>caspius</i>.

The UPGMA phylogenetic tree using the nei-based genetic distances between different brood stocks of s. caspius.</p

DAPC scatter plot of investigated brood stocks of <i>S</i>. <i>caspius</i>.

DAPC scatter plot of investigated brood stocks of S. caspius.</p

FineSTRUCTURE classification based on the obtained SNP markers on <i>S</i>. <i>caspius</i> in the Kelardasht breeding Center.

Individuals classified along the heatmap’s diagonal have common shared coancestry histories and pairwise comparisons outside the diagonal illustrates level of shared coancestry between groups of S. caspius.</p

Pair-wise Fst (upper diagonal) and AFD (lower diagonal) indices between different brood stocks of <i>S</i>. <i>caspius</i>.

Pair-wise Fst (upper diagonal) and AFD (lower diagonal) indices between different brood stocks of S. caspius.</p

Restocking center of Caspian salmon at Kalardasht, Iran.

Restocking center of Caspian salmon at Kalardasht, Iran.</p