Pig H3K4me3,H3K27ac,and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.

Histone H3K27me3 methylation regulates the expression of secreted proteins distributed at fast-evolving regions through transcriptional repression of transposable elements

The fine-tuned expression dynamics of the effector genes are pivotal for the transition from vegetative growth to host colonization of pathogenic filamentous fungi.However,mechanisms underlying the dynamic regulation of these genes remain largely unknown.Here,through comparative transcriptome and chromatin immunoprecipitation sequencing(ChIP-seq)analyses of the methyltransferase PoKmt6 in rice blast fungus Pyricularia oryzae(syn.Magnaporthe oryzae),we found that PoKmt6-mediated H3K27me3 deposition was enriched mainly at fast-evolving regions and contributed to the silencing of a subset of secreted proteins(SP)and transposable element(TE)families during the vegetative growth of P.oryzae.Intriguingly,we observed that a group of SP genes,which were depleted of H3K27me3 modification,could also be silenced via the H3K27me3-mediated repression of the nearby TEs.In conclusion,our results indicate that H3K27me3 modification mediated by PoKmt6 regulates the expression of some SP genes in fast-evolving regions through the suppression of nearby TEs.

Dynamic evolution of transposable elements,demographic history,and gene content of paleognathous birds

Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.

High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus'

Two miniature inverted-repeat transposable elements（MITEs）, MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus＇ known to be associated with citrus Huanglongbing（HLB, yellow shoot disease）. MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus＇ isolates from China, the United States and Brazil. Out of the 12 sequence types, three（T4, T5-2, T6） were reported for the first time. Recombination events were found in the two unique sequence types（T5-2 and T6） which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, S？o Paulo isolates and a few Florida isolates.

Isolating the Mutator Transposable Element Insertional Mutant Gene mio16 of Maize Using Double SelectedAmplification of Insertion Flanking Fragments (DSAIFF)

Mutator transposable element （Mu） has been used as an effective tool to clone maize （Zea mays L.） genes. One opaque endosperm mutant （miol6） was identified in a pool of Mu inserted mutants. A modified method, termed the double selected amplification of insertion flanking fragments （DSAIFF）, was employed to isolate the Mu flanking fragments （MFFs） of miol6. The target site duplications （TSDs） isolated from the Msp I and Mse I digested MFFs had a same 9-bp sequence and were confirmed to be the flanking sequence of one identically inserted gene. Co-segregation analysis suggested that the MFFs were associated with the mutant opaque endosperm, and miol6 was mapped in silico onto the physical position ranged from 229 965 021 to 229 965 409 bp of the maize chromosome 4.09 bin. The full-length cDNA of the wild-type gene was obtained by an RT-PCR primer-scanning technique, and Mio16 was found to putatively encode a homolog of the Arabidopsis MAP3K delta-1 protein kinase. RT-PCR result the mRNA expression of miol6 region anchored by primers Mu20 and af276 was not interrupted by Mu insertion. Further researches will be done to elucidate how the expression of miol6 is alternated by Mu insertion.

Diversity and association analysis of important agricultural trait based on miniature inverted-repeat transposable element specific marker in Brassica napus L.

Miniature inverted-repeat transposable elements(MITEs)are a group of DNA transposable element(TE)which preferentially distributed with gene associated regions.Tens of MITEs families have been revealed in Brassica napus genome,they scatter across the genome with tens of thousands copies and produce polymorphisms both intra-and inter-species.Our previous studies revealed a Tourist-like MITE,Monkey King,associated with vernalization requirement of B.napus,however there are still few studies reveal MITE association with agricultural traits in B.napus.In the present study,80 polymorphic markers were developed from 55 MITEs,and used to evaluate genetic diversity in a panel of B.napus accessions consisting of 101 natural and 25 synthetic genotypes.Five agricultural traits,oil content,glucosinolate content,erucic acid content,weight of thousand seeds(WTS)and plant height,were investigated across 3-years field experiments,in addition,two traits,hypocotyl length and root length,were evaluated at the 4-leaf stage in the laboratory.Correlations between the MITE-based markers and seven traits were analyzed,finally,10 polymorphic markers produced by 6 pairs of MITE specific primers were revealed relatively high correlation with 5 traits.Two polymorphic markers were anchored with two candidate genes,BnaA02g13530D and BnaA08g20010D,respectively,which may contribute to glucosinolate content and WTS.This research may contribute to genetic improvement through utilization of MITE-induced polymorphisms in Brassica species.

Genomic imbalance modulates transposable element expression in maize

Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.

Differentiation of a Miniature Inverted Transposable Element （MITE） System in Asian Rice Cultivars and Its Inference for a Diphyletic Origin of Two Subspecies of Asian Cultivated Rice

In the present study, we report a survey on a Miniature Inverted Transposable Element （MITE） system known as mPing in 102 varieties of Asian cultivated rice （Oryza sativa L.）. We found that mPing populations could be generalized Into two families, mPing-1 and mPing-2, according to their sequence structures. Further analysis showed that these two families of mPing had significant bias in their distribution pattern in two subspecies of rice, namely O. sativa ssp. japonica and indica. 0. sativa japonica has a higher proportion of mPing-1 as a general trait, whereas 0. sativa indica has a higher proportion of roPing-2. We also examined the mPing system In a doubled haploid （DH） cross-breeding population of jingxi 17 （japonica） and zhaiyeqing 8 （indica） varieties and observed that the mPing system was not tightly linked to major subspecies-determining genes. Furthermore, we checked the mPing system in 28 accessions of Asian common wild rice O. rufipogon and found the roPing system in 0. rufipogon. The distribution pattern of the roPing system in O. rufipogon indicated a diphyletlc origin of the Asian cultivated rice O. sativa species. We did not find the mPing system in another 20 Oryza species. These results substantiated a previous hypothesis that O. ruflpogon and O. nivara species were the closest relatives of O. sativa and that the two extant subspecies of O. sativa were evolved independently from corresponding ecotypes of O. ruflpogon.

Codon Usage Biases of Transposable Elements and Host Nuclear Genes in Arabidopsis thaliana and Oryza sativa

Transposable elements （TEs） are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa （r=0.944 and 0.839, respectively, P〈0.0001） but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.

PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae

Dear Editor ：The sustainable cultivation of rice, which serves as staple food crop for more than half of the world＇s population, is under serious threat due to the huge yield losses inflicted by rice blast disease caused by the globally destructive fungus Magnaporthe oryzae （Pyricularia oryzae） （Dean et al., 2012; Nalley et al., 2016; Deng et al., 2017）. This filamentous ascomycete fungus is also capable of causing blast infection on other economically important cereal crops, including wheat, millet, and barley, making it the world＇s most important plant pathogenic fungus （Zhong et al., 2016）.

DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent

Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs （IncRNAs）, many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and IncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild- type （WT） and ataxia telangiectasia mutated （atm） mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is 〉 2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cy- cle is largely lost. In contrast, only less than 0.6% of TEs and IncRNAs respond to DNA damage in WT plants, and the regulation of 〉95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and IncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and IncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and IncRNAs located close to genes commonly function as controlling elements.

Silencing of Transposable Elements by piRNAs in Drosophila:An Evolutionary Perspective

Transposable elements （TEs） are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated bio- logical processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established ＂transposition-selection＂ population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis （PIW1）- interacting RNAs （piRNAs） were demonstrated to be master repressors of TE activities in Droso- phila, The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The inter- action between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysge- nesis for the IoR and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their complexity.We have developed a TE genotyping pipeline(TEmarker)and applied it to whole-genome genome-wide association study(GWAS)data from 176 Oryza sativa subsp.japonica accessions to identify genetic elements associated with specific agronomic traits.TE markers recovered a large proportion(69%)of single-nucleotide polymorphism(SNP)-based GWAS peaks,and these TE peaks retained ca.25%of the SNPs.The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium(LD)among SNP markers.A genome scan revealed positive selection on TEs associated with agronomic traits.We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs,including an allele of LOC_Os11g08410 associated with plant height and panicle length traits.Together,these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.

Gene capture by transposable elements leads to epigenetic conflict in maize

Transposable elements(TEs)regularly capture fragments of genes.When the host silences these TEs,siRNAs homologous to the captured regions may also target the genes.This epigenetic crosstalk establishes an intragenomic conflict:silencing the TEs has the cost of silencing the genes.If genes are important,however,natural selection may maintain function by moderating the silencing response,which may also advantage the TEs.In this study,we examined this model by focusing on Helitrons,Pack-MULEs,and Sirevirus LTR retrotransposons in the maize genome.We documented 1263 TEs containing exon fragments from 1629 donor genes.Consistent with epigenetic conflict,donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture.However,these patterns differed between syntelog versus translocated donor genes.Syntelogs appeared to maintain function,as measured by gene expression,consistent with moderation of silencing for functionally important genes.Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation.Translocated genes,in contrast,bore the signature of silencing.They were highly methylated and less expressed,but also overrepresented among donor genes and located away from chromosomal arms,which suggests a link between capture and gene movement.Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings.TE families captured genes in different ways,but the evidence for their advantage was generally less obvious;nevertheless,TEs with captured fragments were older,mapped fewer siRNAs,and were slightly less methylated than TEs without captured fragments.Collectively,our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.

Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis

Nitrogen(N)availability is a major limiting factor for plant growth and agricultural productivity.Although the gene regulation network in response to N starvation has been extensively studied,it remains unknown whether N starvation has an impact on the activity of transposable elements(TEs).Here,we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions.Through genetic screening of idm1-14 suppressors,we cloned GLU1,which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway.We found that glutamate synthase 1(GLU1)and its functional homologs GLU2 and glutamate transport 1(GLT1)are redundantly required for TE silencing,suggesting that N metabolism can regulate TE activity.Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation.Genetic analysis indicated that N starvationinduced TE activation is also independent of other well-established epigenetic mechanisms,including histone methylation and heterochromatin decondensation.Our results provide new insights into the regulation of TE activity under stressful environments in planta.

Characterization of functional transposable element enhancers in acute myeloid leukemia

Transposable elements(TEs)have been shown to have important gene regulatory functions and their alteration could lead to disease phenotypes.Acute myeloid leukemia(AML)develops as a consequence of a series of genetic changes in hematopoietic precursor cells,including mutations in epigenetic factors.Here,we set out to study the gene regulatory role of TEs in AML.We first explored the epigenetic landscape of TEs in AML patients using ATAC-seq data.We show that a large number of TEs in general,and more specifically mammalian-wide interspersed repeats(MIRs),are more enriched in AML cells than in normal blood cells.We obtained a similar finding when analyzing histone modification data in AML patients.Gene Ontology enrichment analysis showed that genes near MIRs in open chromatin regions are involved in leukemogenesis.To functionally validate their regulatory role,we selected 19 MIR regions in AML cells,and tested them for enhancer activity in an AML cell line(Kasumi-1)and a chronic myeloid leukemia(CML)cell line(K562);the results revealed several MIRs to be functional enhancers.Taken together,our results suggest that TEs are potentially involved in myeloid leukemogenesis and highlight these sequences as potential candidates harboring AML-associated variation.

Detection transposable elements in Botrytis cinerea in latent infection stage from symptomless apples

Objective:To detect Botrytis cinerea(B.cinerea)latent infections on apples before storage,which is essential for effective control strategies in the fruit postharvest industry.Methods:In the present study,a polymerase chain reaction detection method,based on primers designed on B.cinerea transposable elements(boty and flipper)and intergenic spacer region as internal control,were utilized to reveal the presence of symptomless infections on apple fruits.This molecular method proved to be highly specific and sensitive in detecting latent infections.It revealed the presence of the pathogen in 83%of the samples from infected apples with 104 conidia/mL,whereas those infected with 106 conidia/mL detected 94%as compared to the traditional method that revealed the pathogen in 40%and 66%of the samples inoculated with 10^(4)and 10^(6)conidia/mL respectively.Furthermore,the method characterized B.cinerea as subpopulation transposa-type by the presence of the transposable elements boty and flipper Results:The results obtained from DNA quantification method were compared with enzyme-linked immunosorbent assay and these studies showed good correlation.Therefore our method has important advantages compared with others detection methods for B.cinerea,because the proposed methodology allowed distinguishes between its two subpopulations(vacuma and transposa)and this would allow establish possible appropriate control strategies.Conclusions:Finally,the method can be an interesting alternative for its possible application in the phytosanitary programs of the fruit industry worldwide.

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

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 ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal 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 prior-itized 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 regula-tory variants of loci associated with complex traits in pigs.