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Background: A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. Results: Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle. Conclusions: Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. [ABSTRACT FROM AUTHOR]

Typical entomopathogenic filamentous fungi such as Beauveria bassiana infect susceptible hosts via penetration of insect cuticle. The pathogenicity of B. bassiana strain to diverse insect hosts is different. While the molecular mechanisms of B. bassiana adapt to different insects are not well clear. B. bassiana GXsk1011 is a hyper-virulent strain from silkworm, which was investigated on the metabolic responses to three cuticle extracts of Bombyx mori , Helicoverpa armigera and Clanis bilineata at 24 h by RNA-seq method. A total of 638 up- and 400 down-regulated differentially expressed genes (DEGs) were identified in B. bassiana grown on H. armigera compared with B. mori , and 910 up- and 401 down-regulated genes for C. bilineata compared with B. mori. Functional categorization showed that DEGs are mainly involved in metabolic processes, localization, catalytic activity and transporter activity. Analysis of 20 highest fold change genes in DEGs showed that when B. bassiana transferred to non-original hosts as H. armigera and C. bilineata , the adhesion (Mad1), protease (Pr2) and cell surface protein (BBA_09174), etc. were down-regulated. While the class III chitinase ChiA2 (BBA_05353, Bbchi-17), major allergen Asp f 2-like protein (BBA_05395, Bb-f2) and nonribosomal peptide synthase, etc. were up-regulated. The secretory lipase that responded to H. armigera and the phosphate permease responded to C. bilineata were also up-regulated in the Top 20 DEGs. These special expressed genes indicate when the B. bassiana transferred to non-original hosts (or called as non-natural hosts), the strain appeared the changes of metabolic response and infection strategies to adapt to new hosts, and implied the key actions of infected adaptation were to break the barrier of different cuticle chitin component and against the immune stress of hosts. This study provided an insight into the B. bassiana that with wide host ranges how to adapt to infect different insect hosts, which will help us to further understand the pathogenesis of B. bassiana infection. • RNA-seq of Beauveria bassiana Gxsk1011 responds to three insect cuticles. • A large number of differentially expressed genes were annotated in different hosts. • Typical virulence genes (Mad1, Pr2 , etc.) were up-regulated in the silkworm. • Allergen Bb-f2 and chitinase Bbchi-17 , etc. were up-regulated in the other insects. • The results showed the changes in fungal metabolic response and infection strategy. [ABSTRACT FROM AUTHOR]

Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome‐wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super‐enhancers from ChIP‐Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence‐based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs. [ABSTRACT FROM AUTHOR]

Structural variations (SVs) are important DNA polymorphisms that contribute to genetic diversity and evolution in humans, animals, and plants. In this study, we present a novel swine SV dataset of 79,919 deletions, 23,638 duplications, and 9333 inversions with average sequence depths of 24.1× from 24 varieties of worldwide pig populations, encompassing 305 individuals. Genotypes of SVs, particularly deletions, can accurately group individuals based on their population identity. We showed that exon‐covering deletions were subject to negative selection. Fixation index and differential allele frequency analysis identified highly differentiated SVs between European and Asian indigenous pigs, including deletions in NR6A1 and PLAG1, which are significantly associated with vertebrate numbers and growth performances, respectively. The growth‐enhancing allele at the deletion in PLAG1 was shared by European commercial pigs and Northern Chinese indigenous pigs including Laiwu and Min pigs, suggesting potential introgression from European commercial breeds into Chinese indigenous breeds. Moreover, we uncovered highly differentiated SVs in 139 genes between domesticated pigs and wild boars in Asia, temperature and altitude adaptation‐associated SVs in 41 genes, and population‐specific SVs in 718 genes. This study provides novel insights into the role of porcine SVs in domestication, environmental adaptation, and breed formation. [ABSTRACT FROM AUTHOR]