Genomics最新文献

{"title":"MicroRNA expression profiles reveal wool development and fineness regulation in Gansu alpine fine-wool sheep","authors":"Zhaohua He,&nbsp;Hongxian Sun,&nbsp;Fangfang Zhao,&nbsp;Longxia Ma,&nbsp;Jiqing Wang,&nbsp;Xiu Liu,&nbsp;Mingna Li,&nbsp;Zhiyun Hao,&nbsp;Shaobin Li","doi":"10.1016/j.ygeno.2024.110922","DOIUrl":"10.1016/j.ygeno.2024.110922","url":null,"abstract":"<div><p>The development of wool has a complex regulatory mechanism both influenced by genetic and environmental factors. MicroRNAs (miRNA) were involved in various biological processes of animals, and may play an important role in the regulation of wool development. In this study, we comprehensively analyzed and identified the histological parameters of hair follicles, as well as the miRNAs, target genes, pathways, and Gene Ontology terms related to wool fineness regulation and wool growth and development using HE staining and RNA-Seqs methods. Both coarse (group C, mean fiber diameter (MFD) = 22.26 ± 0.69 μm, <em>n</em> = 6) and fine (group F, MFD = 16.91 ± 0.29 μm, n = 6) of Gansu alpine fine-wool sheep with different wool fineness were used in this study. The results showed that the primary follicle diameter and secondary wool fiber diameter in group C were significantly higher than those in group F (<em>P</em> &lt; 0.05). And the number of primary and secondary hair follicles in group C was significantly lower than that in group F (<em>P</em> &lt; 0.05). Furthermore, a total of 67 DE miRNAs and 290 potential DE miRNAs target genes were screened in the skin tissues of sheep from groups F and C, and some potential target genes related to wool fineness regulation were screened, such as <em>CDH2</em>, <em>KRT82</em>, <em>FOXN1</em>, <em>LOC101106296</em>, <em>KRT20</em>, <em>MCOLN3</em>, <em>KRT71</em>, and <em>TERT</em>. These genes were closely related to Glutathione metabolism, epidermal cell differentiation, keratinization, and regulation of hair cycle. Moreover, the regulatory network of miRNAs-mRNAs suggested that miRNAs (miR-129-x, novel m0079-3p, miR-2484-z, novel m0025-5P, etc.) may play a key role in the wool development and wool fineness regulation of Gansu alpine fine-wool sheep. In summary, this study expands the existing miRNAs database and provides new information for studying the regulation of wool development in Gansu alpine fine wool sheep.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001435/pdfft?md5=d52c6cc00e316e7e84cd854f3ce2867a&pid=1-s2.0-S0888754324001435-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiological and transcriptomic profiles reveal key regulatory pathways involved in cold resistance in sunflower seedlings","authors":"Huifang Song ,&nbsp;Mingyang Wang ,&nbsp;Jie Shen ,&nbsp;Xi Wang ,&nbsp;Cheng Qin ,&nbsp;Peipei Wei ,&nbsp;Yaojun Niu ,&nbsp;Jiahong Ren ,&nbsp;Xiaoxue Pan ,&nbsp;Ake Liu","doi":"10.1016/j.ygeno.2024.110926","DOIUrl":"10.1016/j.ygeno.2024.110926","url":null,"abstract":"<div><p>During sunflower growth, cold waves often occur and impede plant growth. Therefore, it is crucial to study the underlying mechanism of cold resistance in sunflowers. In this study, physiological analysis revealed that as cold stress increased, the levels of ROS, malondialdehyde, ascorbic acid, and dehydroascorbic acid and the activities of antioxidant enzymes increased. Transcriptomics further identified 10,903 DEGs between any two treatments. Clustering analysis demonstrated that the expression of <em>MYB44a</em>, <em>MYB44b</em>, <em>MYB12</em>, <em>bZIP2</em> and <em>bZIP4</em> continuously upregulated under cold stress. Cold stress can induce ROS accumulation, which interacts with hormone signals to activate cold-responsive transcription factors regulating target genes involved in antioxidant defense, secondary metabolite biosynthesis, starch and sucrose metabolism enhancement for improved cold resistance in sunflowers. Additionally, the response of sunflowers to cold stress may be independent of the CBF pathway. These findings enhance our understanding of cold stress resistance in sunflowers and provide a foundation for genetic breeding.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001472/pdfft?md5=fd87e3f397e18adf773f34575064b96b&pid=1-s2.0-S0888754324001472-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibitor of Myom3 inhibits proliferation and promotes differentiation of sheep myoblasts","authors":"Lingying Kong ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Lixia Sun ,&nbsp;Jianbin Liu ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110921","DOIUrl":"10.1016/j.ygeno.2024.110921","url":null,"abstract":"<div><p>Skeletal muscle quality and yield are important production traits in livestock, and improving skeletal muscle quality while increasing its yield is an important goal of economic breeding. The proliferation and differentiation process of sheep myoblasts directly affects the growth and development of their muscles, thereby affecting the yield of mutton. Myomesin 3 (<em>Myom3</em>), as a functional gene related to muscle growth, currently lacks research on its function in myoblasts. This study aims to investigate the effect of the <em>Myom3</em> gene on the proliferation and differentiation of sheep myoblasts and its potential molecular mechanisms. The results showed that inhibitor of <em>Myom3</em> in the proliferation phase of myoblasts resulted in significant downregulation of the proliferation marker gene paired box 7 (<em>Pax7)</em> and myogenic regulatory factors (<em>MRFs</em>; <em>Myf5</em>, <em>Myod1</em>, <em>Myog</em>, <em>P</em> &lt; 0.01), a significant decrease in the EdU-positive cell rate (<em>P</em> &lt; 0.05), and a significant increase in the cell apoptosis rate (<em>P</em> &lt; 0.01), which inhibited the proliferation of myoblasts and promoted their apoptosis. During the differentiation phase of myoblasts, the inhibitor of <em>Myom3</em> resulted in significant downregulation of the <em>Pax7</em> gene, upregulation of <em>MRFs</em> (<em>Myod1</em>, <em>Myog</em>, <em>P</em> &lt; 0.05), and a significant increase in fusion index (<em>P</em> &lt; 0.05), promoting the differentiation of myoblasts. Further transcriptome sequencing revealed that differentially expressed genes in the <em>Myom3</em> interference group were mainly enriched in the MAPK signaling pathway, TNF signaling pathway, and IL-17 signaling pathway. In summary, the inhibitor of <em>Myom3</em> inhibits myoblast proliferation and promotes myoblast differentiation. Therefore, <em>Myom3</em> has a potential regulatory effect on the growth and development of sheep muscles, and in-depth functional research can be used for molecular breeding practices in sheep.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001423/pdfft?md5=a14a915a5259ef50bb5e524868d3e749&pid=1-s2.0-S0888754324001423-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics reveals ample evidence to Ganoderma sinense cultivars for molecular identification and new FIP exploration","authors":"Ti-Qiang Chen ,&nbsp;Xiao-Lan Xu ,&nbsp;Chi Yang ,&nbsp;Lin Yang ,&nbsp;Zheng-He Ying ,&nbsp;Xiao-Kun Shi ,&nbsp;Meng-Guang Ding","doi":"10.1016/j.ygeno.2024.110924","DOIUrl":"10.1016/j.ygeno.2024.110924","url":null,"abstract":"<div><p>The first dikaryotic genome of <em>Ganoderma</em> cultivar Zizhi S2 (56.76 Mb, 16,681 genes) has been sequenced recently. 98.15% of complete BUSCOs were recovered in this genome assembly and high-confidence annotation rate improved to 91.41%. Collinearity analysis displayed the nuclear genome were 80.2% and 93.84% similar to reference genome of <em>G. sinense</em> at nucleotide and amino acid levels, which presented 8,521 core genes and 880 unique orthologous gene groups. Among that, at least six functional genes (tef1-α, β-tubulin, rpb2, CaM, Mn-SOD and VeA) and a newly discovered <em>fip</em> gene were highly similar 99.27% ∼100% to those in reference genome. And the mt-LSU, mt-SSU and 13 PCGs in their mitogenome were also highly conserved with 99.27%–99.87% and 99.08%–100% identity, respectively. So that, this cultivar Zizhi S2 is confirmed conspecific with <em>Ganoderma sinense</em> (NCBI: txid1077348). The new <em>fip</em> gene (MN635280.1_336bp) existing a novel mutation which can be reflected on the phylogenetic tree and 3-dimensional model topology structure.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001459/pdfft?md5=7c44cefc6e4e824d8aaca73a7fbf9b3d&pid=1-s2.0-S0888754324001459-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global analysis of gene expression in response to double trisomy loquat (Eriobotrya japonica)","authors":"Peng Wang ,&nbsp;Miao Ma ,&nbsp;Haichun Chen ,&nbsp;Haiyan Sun ,&nbsp;Di Wu ,&nbsp;Qiao He ,&nbsp;Danlong Jing ,&nbsp;Qigao Guo ,&nbsp;Jiangbo Dang ,&nbsp;Guolu Liang","doi":"10.1016/j.ygeno.2024.110913","DOIUrl":"10.1016/j.ygeno.2024.110913","url":null,"abstract":"<div><p>Aneuploidy generally has severe phenotypic consequences. However, the molecular basis for this has been focused on single chromosomal dosage changes. It is not clear how the karyotype of complex aneuploidies affects gene expression. Here, we identified six different double-trisomy loquat strains from Q24 progenies of triploid loquat. The differences and similarities of the transcriptional responses of different double trisomy loquat strains were studied systematically via RNA-seq. The global modulation of gene expression indicated that both cis and trans-effects coordinately regulated gene expression in aneuploid loquat to some extent, and this coordinated regulation was determined by different gene functional groups. Aneuploidy can induce specific transcriptional responses on loquat chromosomes. The differentially expressed genes exhibited regional gene expression dysregulation domains along chromosomes. Furthermore, Aneuploidy could also promote the expression of genes with moderate and high in loquats. Our results provide new insights into the genome-wide transcriptional effects of karyotypes with complex aneuploidies.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001344/pdfft?md5=96cd8ebf46daab6eac738de4659d7127&pid=1-s2.0-S0888754324001344-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary construction of non-coding RNAs and ceRNA regulatory networks mediated by exosomes in porcine follicular fluid","authors":"Yangguang Liu ,&nbsp;Fan Xie ,&nbsp;Huibin Zhang ,&nbsp;Haibo Ye ,&nbsp;Haoyu Wen ,&nbsp;Mengyao Qiu ,&nbsp;Yueyun Ding ,&nbsp;Xianrui Zheng ,&nbsp;Zongjun Yin ,&nbsp;Xiaodong Zhang","doi":"10.1016/j.ygeno.2024.110920","DOIUrl":"10.1016/j.ygeno.2024.110920","url":null,"abstract":"<div><h3>Background</h3><p>Follicles are fundamental units of the ovary, regulated intricately during development. Exosomes and ovarian granulosa cells (OGCs) play pivotal roles in follicular development, yet the regulatory mechanisms governing exosomes remain elusive.</p></div><div><h3>Results</h3><p>High-throughput sequencing was employed to evaluate the complete transcript expression profiles of six samples (three porcine ovarian granulosa cells-exosome co-culture samples (GCE) and three porcine ovarian granulosa cells (POGCs) samples). Differential expression analysis revealed 924 lncRNAs, 35 circRNAs, 49 miRNAs, and 9823 mRNAs in the GCE group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated enrichment of differentially expressed transcripts in pathways related to cell proliferation and apoptosis. Furthermore, a ceRNA regulatory network comprising 43 lncRNAs, 6 circRNAs, 11 miRNAs, and 126 mRNAs was constructed based on intergene co-expression correlations. Seven miRNAs associated with cell proliferation and apoptosis regulation were identified within this network, encompassing 92 subnet pairs as candidate genes for further exploration of exosome regulatory mechanisms. Additionally, preliminary verification at the cellular level demonstrated that exosomal miR-200b enhances the viability of POGCs.</p></div><div><h3>Conclusions</h3><p>Transcriptome analysis unveiled a pivotal candidate ceRNA network potentially implicated in exosome-mediated regulation of granulosa cell proliferation and apoptosis, thereby influencing porcine follicular development. These findings offer insights into the molecular mechanisms of follicular fluid exosome regulation, encompassing both coding and non-coding RNA perspectives.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001411/pdfft?md5=29d06600427a7c2aae64234a3b062d59&pid=1-s2.0-S0888754324001411-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma","authors":"Lei Yin ,&nbsp;Anqi Duan ,&nbsp;Wei Zhang ,&nbsp;Bin Li ,&nbsp;Teng Zhao ,&nbsp;Xiaoya Xu ,&nbsp;Lixue Yang ,&nbsp;Baoning Nian ,&nbsp;Kai Lu ,&nbsp;Sheng Chen ,&nbsp;Zhikuan Li ,&nbsp;Jian Liu ,&nbsp;Qiaonan Duan ,&nbsp;Dongyu Liu ,&nbsp;Hao Chen ,&nbsp;Longjiu Cui ,&nbsp;Yanxin Chang ,&nbsp;Yue Kuang ,&nbsp;Dadong Zhang ,&nbsp;Xiang Wang ,&nbsp;Yongjie Zhang","doi":"10.1016/j.ygeno.2024.110916","DOIUrl":"10.1016/j.ygeno.2024.110916","url":null,"abstract":"<div><p>Bile cell-free DNA (cfDNA) has been reported as a promising liquid biopsy tool for cholangiocarcinoma (CCA), however, the whole-genome mutation landscape and structural variants (SVs) of bile cfDNA remains unknown. Here we performed whole-genome sequencing on bile cfDNA and analyzed the correlation between mutation characteristics of bile cfDNA and clinical prognosis. <em>TP53</em> and <em>KRAS</em> were the most frequently mutated genes, and the RTK/RAS, homologous recombination (HR), and HIPPO were top three pathways containing most gene mutations. Ten overlapping putative driver genes were found in bile cfDNA and tumor tissue. SVs such as chromothripsis and kataegis were identified. Moreover, the hazard ratio of HR pathway mutations were 15.77 (95% CI: 1.571–158.4), patients with HR pathway mutations in bile cfDNA exhibited poorer overall survival (<em>P</em> = 0.0049). Our study suggests that bile cfDNA contains genome mutations and SVs, and HR pathway mutations in bile cfDNA can predict poor outcomes of CCA patients.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400137X/pdfft?md5=229260e36fdd2202b35c964b18bebb16&pid=1-s2.0-S088875432400137X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of pan-cancer common and cancer-specific alternative splicing events in 9 types of cancer","authors":"Kun Li ,&nbsp;Chao Cheng ,&nbsp;Qianling Piao ,&nbsp;Qi Zhao ,&nbsp;Jingwen Yi ,&nbsp;Yongli Bao ,&nbsp;Lei Liu ,&nbsp;Luguo Sun","doi":"10.1016/j.ygeno.2024.110917","DOIUrl":"10.1016/j.ygeno.2024.110917","url":null,"abstract":"<div><p>Alternative splicing (AS) has significant clinical relevance with cancers and is a potential source of neoepitopes. In this study, RNA-seq data of 94 solid tumor and matched adjacent normal tissues from 47 clinical patients covering nine cancer types were comprehensively analyzed using SUVA developed by ourselves. The results identified highly conserved pan-cancer differential alternative splicing (DAS) events and cancer-specific DAS events in a series of tumor samples, which in turn revealed the heterogeneity of AS post-transcriptional regulation across different cancers. The co-disturbed network between spliceosome factors (SFs) and common cancer-associated DAS was further constructed, suggesting the potential possibility of the regulation of differentially expressed SFs on DAS. Finally, the common cancer-associated DAS events were fully validated using the TCGA dataset, confirming the significant correlation between cancer-associated DAS and prognosis. Briefly, our study elucidates new insights into conservatived and specific DAS in cancer, providing valuable resources for cancer therapeutic targets.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001381/pdfft?md5=ef713c3e0d2ecb36b06f8191fc82b98a&pid=1-s2.0-S0888754324001381-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and validation of ferroptosis-related hub genes and immune infiltration in liver ischemia-reperfusion injury","authors":"Xinglong Li ,&nbsp;Zhanzhi Meng ,&nbsp;Yongliang Hua ,&nbsp;Zihao Li ,&nbsp;Bing Yin ,&nbsp;Baolin Qian ,&nbsp;Hongjun Yu ,&nbsp;Zhongyu Li ,&nbsp;Yongzhi Zhou ,&nbsp;Zhigang Feng ,&nbsp;Shounan Lu ,&nbsp;Shanjia Ke ,&nbsp;Miaoyu Bai ,&nbsp;Yao Fu ,&nbsp;Yong Ma","doi":"10.1016/j.ygeno.2024.110918","DOIUrl":"10.1016/j.ygeno.2024.110918","url":null,"abstract":"<div><p>Ischemia–reperfusion injury (IRI) is a cumulation of pathophysiological processes that involves cell and organelle damage upon blood flow constraint and subsequent restoration. However, studies on overall immune infiltration and ferroptosis in liver ischemia-reperfusion injury (LIRI) are limited. This study explored immune cell infiltration and ferroptosis in LIRI using bioinformatics and experimental validation. The GSE151648 dataset, including 40 matched pairs of pre- and post- transplant liver samples was downloaded for bioinformatic analysis. Eleven hub genes were identified by overlapping differentially expressed genes (DEGs), iron genes, and genes identified through weighted gene co-expression network analysis (WGCNA). Subsequently, the pathway enrichment, transcription factor-target, microRNA-mRNA and protein-protein interaction networks were investigated. The diagnostic model was established by logistic regression, which was validated in the GSE23649 and GSE100155 datasets and verified using cytological experiments. Moreover, several drugs targeting these genes were found in DrugBank, providing a more effective treatment for LIRI. In addition, the expression of 11 hub genes was validated using quantitative real-time polymerase chain reaction (qRT-PCR) in liver transplantation samples and animal models. The expression of the 11 hub genes increased in LIRI compared with the control. Five genes were significantly enriched in six biological process terms, six genes showed high enrichment for LIRI-related signaling pathways. There were 56 relevant transcriptional factors and two central modules in the protein-protein interaction network. Further immune infiltration analysis indicated that immune cells including neutrophils and natural killer cells were differentially accumulated in the pre- and post-transplant groups, and this was accompanied by changes in immune-related factors. Finally, 10 targeted drugs were screened. Through bioinformatics and further experimental verification, we identified hub genes related to ferroptosis that could be used as potential targets to alleviate LIRI.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001393/pdfft?md5=78e7a6a885ea9102e57edd237814faf6&pid=1-s2.0-S0888754324001393-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated analyses of the intestinal microbiome and transcriptome in Ningxiang piglets","authors":"Zhenguo Hu ,&nbsp;Yuezhou Yao ,&nbsp;Feiyue Chen ,&nbsp;Luya Feng ,&nbsp;Zian Yuan ,&nbsp;Junhao Deng ,&nbsp;Lang Huang ,&nbsp;Yulong Yin ,&nbsp;Xiongzhuo Tang","doi":"10.1016/j.ygeno.2024.110919","DOIUrl":"10.1016/j.ygeno.2024.110919","url":null,"abstract":"<div><p>Ningxiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in stress resistance. However, intestinal microbial feature and gene profiling in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic <em>Bacteroides, Prevotella</em> and <em>Clostridium</em> species in NX piglets. Further functional analyses revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two breeds. In particular, we showed that the improved intestinal function in NX piglets may be determined by enhanced intestinal barrier gene expression and varied immune gene expression through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400140X/pdfft?md5=be1beffbbdce18b142bfbd52060e2e76&pid=1-s2.0-S088875432400140X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}