Genomics最新文献

{"title":"Rapid sequencing and identification for 18-STRs long amplicon panel using portable devices and nanopore sequencer","authors":"Jiarong Zhang ,&nbsp;Tingting Yang ,&nbsp;Zihan Xie ,&nbsp;Zilin Ren ,&nbsp;Linyu Shi ,&nbsp;Jiang-wei Yan ,&nbsp;Ming Ni","doi":"10.1016/j.ygeno.2024.110970","DOIUrl":"10.1016/j.ygeno.2024.110970","url":null,"abstract":"<div><div>STRs are the most commonly used forensic genetic markers for human identification. Nanopore sequencing has shown the advantages of high portability and large data throughput. Previous studies indicate it has great potential for profiling STRs based on the ligation library preparation method. However, this method, which requires more library preparation time and operations, is unsuitable for rapid STR profiling, particularly for field forensic applications. The transposase-based rapid library preparation method offers the possibility to perform human identification using portable instruments. However, the amplicons of conventional STR panels are too small and would be cut into scraps with rapid methods, making them impractical for genotyping. In this study, we developed an 18-STRs multiplex amplification panel with amplicons of ∼1.4 Kbp. The PCR conditions were optimized to be finished within 2 h and 12 min, and the PCR products could undergo rapid methods that involved random fragmentation. We found that, on average, 29.16 % of reads from the long-amplicon panel and rapid library kit covered the whole STR region, sufficient for downstream STR profiling analysis. We conducted a small validation experiment on 24 samples using portable instruments powered by a 1.5 kW‧h portable power source. The entire process took 10.5 h and we obtained enough data from 24 samples to perform trustworthy pairwise identification analysis using the STR profiles. The overall accuracy of the analysis was 95.36 %. In sum, the study evaluated and demonstrated the viability and potential of nanopore sequencing for forensic application in the field.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110970"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750463","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":"Transcriptome and metabolome revealed the effects of hypoxic environment on ovarian development of Tibetan sheep","authors":"Dan Zhang ,&nbsp;Chao Yuan ,&nbsp;Xuejiao An ,&nbsp;Tingting Guo ,&nbsp;Zengkui Lu ,&nbsp;Jianbin Liu","doi":"10.1016/j.ygeno.2024.110973","DOIUrl":"10.1016/j.ygeno.2024.110973","url":null,"abstract":"<div><div>Many studies on the adaptability of Tibetan sheep to hypoxia have been reported, but little attention has been paid to the reproduction of Tibetan sheep living at an altitude of more than 4000 m. In this study, the ovaries of Alpine Merino sheep (AM) living in middle-high altitude areas (2500 m) and the ovaries of Gangba Tibetan sheep (GB) and Huoba Tibetan sheep (HB) living in ultra-high altitude areas (4400 m or more) were collected. Through morphological, transcriptomics and metabolomics, the effects of ultra-high altitude areas on Tibetan sheep ovarian development and the molecular mechanism of sheep's adaptability to ultra-high altitude environment were explored. The results showed that the number of granulosa cells in AM was significantly higher than that in GB and HB. The transcriptome revealed several genes related to follicular development, such as <em>DAPL1</em>, <em>IGFBP1</em>, <em>C5</em>, <em>GPR12</em>, <em>STRA6</em>, <em>BMPER</em>, etc., which were mainly enriched in related pathways such as cell growth and development. Through metabolomics analysis, it was found that the differential metabolites between the three groups of sheep were mainly lipids and lipid-like small molecules, such as Glycerol 3-Phosphate, PC (16: 0 / 18: 3 (9Z, 12Z, 15Z)), mainly enriched in lipid metabolism and other related pathways. The results of combined analysis showed that Tryptophan metabolism and Steroid hormone biosynthesis may have a significant effect on Tibetan sheep follicular development. Some genes (including <em>HSD17B7</em>, <em>CYP11A1</em>, <em>CYP19</em>, <em>HSD3B1</em>, <em>CYP17</em>, etc.) and some metabolites (including Cortisone, 2-Methoxyestrone, etc.) are enriched in these pathways, regulating ovarian and follicular development by affecting estrogen, progesterone, etc.. The results further revealed the molecular mechanism of Tibetan sheep to adapt to the ultra-high altitude environment and maintain normal ovarian and follicular development through the regulation of genes and metabolites.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110973"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779877","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":"SlAN2 overexpression improves cold resistance in tomato (Solanum lycopersicum L.) by regulating glycolysis and ascorbic acid metabolism","authors":"Minghui Ye ,&nbsp;Deying Wang ,&nbsp;Ruixin Li ,&nbsp;Kunyang Zhuang ,&nbsp;Hongjiao Wang ,&nbsp;Xinyin Cao ,&nbsp;Tengfei Qin ,&nbsp;Hengjia Zhang ,&nbsp;Shangjing Guo ,&nbsp;Bingjie Wu","doi":"10.1016/j.ygeno.2024.110978","DOIUrl":"10.1016/j.ygeno.2024.110978","url":null,"abstract":"<div><div>Chilling stress seriously affects the growth and yield of tomato. Anthocyanin is a typical chilling-induced metabolite with strong antioxidant activity and photoprotective capacity. Here, we found that anthocyanin was also involved in ascorbic acid biosynthesis and glycolysis under chilling stress. <em>SlAN2</em> is an important positive gene in anthocyanin biosynthesis. The results of physiological indicators showed that <em>SlAN2</em> overexpression lines (A189) had a greater ability to tolerate cold stress than wild-type (WT) plants. Conjoint analysis of transcriptomics and metabonomics of A189 lines and WT plants was used to analyze the metabolic difference and the cold resistance mechanisms caused by anthocyanin under chilling stress. The anthocyanin accumulated more in A189 than that in WT under chilling stress at 4 °C for 24 h, which led to hexoses and ascorbic acid increased significantly. Results indicate that <em>SlAN2</em> overexpression reduces the expression of key enzyme genes in glycolytic pathway such as phosphofructokinase (PFK) and pyruvate kinase (PK) genes, weakens glycolysis ability, and promotes accumulation of hexoses in A189 lines at 4 °C for 24 h compared with wild lines. Additionally, ascorbic acid content is increased by up-regulated the genes of ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR). The increased hexose content can reduce cell osmotic potential, freezing point and synthesize more ascorbic acid, while the increased ascorbic acid content can enhance the ability to scavenge reactive oxygen species, so improves the cold resistance of tomato. The glycolysis and ascorbic acid metabolism pathway mediated by <em>SlAN2</em> provides a new insight for the molecular mechanism of anthocyanins in improving the cold resistance of tomato and provides a new theoretical basis for cultivating new cold-tolerant tomato varieties.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110978"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823539","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":"Single-cell RNA sequencing reveals the heterogeneity of myofibroblasts in wound repair","authors":"Miaonan Liu ,&nbsp;Xiaoxuan Liu ,&nbsp;Jingchi Zhang ,&nbsp;Shaocong Liang ,&nbsp;Yan Gong ,&nbsp;Shengjun Shi ,&nbsp;Xiaopeng Yuan","doi":"10.1016/j.ygeno.2024.110982","DOIUrl":"10.1016/j.ygeno.2024.110982","url":null,"abstract":"<div><div>Skin wound repair involves myofibroblasts crucial for tissue integrity. This study utilized single-cell RNA sequencing to explore myofibroblast diversity in various wound healing scenarios. Analysis of 89,148 cells from skin ulcers, keloids, and normal scars identified 13 cell clusters. Myofibroblast subcluster analysis unveiled 11 subsets, with subclusters 1 and 9 predominant in ulcers. Subcluster 1 exhibited heightened matrix metalloproteinase expression and involvement in bacterial response and angiogenesis, crucial in inflammation. Tissue validation confirmed subcluster 1 significance., while animal models supported upregulated <em>CA12</em>, <em>TDO2</em>, and <em>IL-7R</em> in chronic ulcers. These findings illuminate myofibroblast heterogeneity and their impact on wound healing, offering insights into potential therapeutic targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110982"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871887","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":"Genomic regions associated with Holstein heifer times bred to artificial insemination and embryo transfer services","authors":"Victoria Kelson ,&nbsp;Jennifer Kiser ,&nbsp;Kimberly Davenport ,&nbsp;Emaly Suarez ,&nbsp;Brenda Murdoch ,&nbsp;Holly Neibergs","doi":"10.1016/j.ygeno.2024.110972","DOIUrl":"10.1016/j.ygeno.2024.110972","url":null,"abstract":"<div><div>This study aimed to identify loci (<em>p</em> &lt; 1 × 10⁻⁵) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, <em>n</em> = 2754) or that were embryo transfer (ET, <em>n</em> = 1566) recipients. Eight loci were associated (p &lt; 1 × 10⁻⁵) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients. The gene set enrichment analysis with SNP data identified one gene set enriched (NES ≥ 3.0) with TBRD in AI bred heifers and two gene sets that were enriched with TBRD in ET recipients. The estimated pseudo-heritability for times bred to AI was 0.063 and 0.043 for ET. The identification of loci associated with embryonic loss aids in the selection of Holstein heifers with higher reproductive efficiencies that are AI bred or that are ET recipients.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110972"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779876","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":"A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis","authors":"Na Zhang ,&nbsp;Puguang Zhao ,&nbsp;Wenda Zhang ,&nbsp;Huiying Wang ,&nbsp;Kaixuan Wang ,&nbsp;Xiangyu Wang ,&nbsp;Zhanjiang Zhang ,&nbsp;Ninghua Tan ,&nbsp;Lingyun Chen","doi":"10.1016/j.ygeno.2024.110979","DOIUrl":"10.1016/j.ygeno.2024.110979","url":null,"abstract":"<div><div><em>Lobelia seguinii</em> is a plant with great ecological and medicinal value and belongs to Campanulaceae. <em>Lobelia</em> contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of <em>L</em>. <em>seguinii</em> with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of <em>Campanula</em> and <em>Adenophora</em>, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of <em>Platycodon grandiflorus</em> represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of <em>L</em>. <em>seguinii</em>. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110979"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828056","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":"Single-cell RNA sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation","authors":"Yadan Jin,&nbsp;Fangdi Zhang,&nbsp;Ruixue Ma,&nbsp;Jingya Xing,&nbsp;Min Wang,&nbsp;Yujiang Sun,&nbsp;Guoliang Zhang","doi":"10.1016/j.ygeno.2024.110974","DOIUrl":"10.1016/j.ygeno.2024.110974","url":null,"abstract":"<div><h3>Introduction</h3><div>With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.</div></div><div><h3>Objectives</h3><div>This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.</div></div><div><h3>Methods</h3><div>In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.</div></div><div><h3>Results</h3><div>The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.</div></div><div><h3>Conclusions</h3><div>We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110974"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853480","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":"Retraction notice to “LncRNA HOTAIR regulates the expression of E-cadherin to affect nasopharyngeal carcinoma progression by recruiting histone methylase EZH2 to mediate H3K27 trimethylation” [Genomics Volume 113, Issue 4, July 2021, Pages 2276–2289]","authors":"Feng-lian Yang ,&nbsp;Yu-xia Wei ,&nbsp;Bi-yun Liao ,&nbsp;Gui-jiang Wei ,&nbsp;Hai-mei Qin ,&nbsp;Xiao-xia Pang ,&nbsp;Jun-li Wang","doi":"10.1016/j.ygeno.2024.110939","DOIUrl":"10.1016/j.ygeno.2024.110939","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110939"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692859","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 CCR7 as a potential biomarker in polycystic ovary syndrome through transcriptome sequencing and integrated bioinformatics","authors":"Zuwei Yang ,&nbsp;Chengliang Zhou ,&nbsp;Li Jin ,&nbsp;Jiexue Pan","doi":"10.1016/j.ygeno.2024.110968","DOIUrl":"10.1016/j.ygeno.2024.110968","url":null,"abstract":"<div><div>Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, yet its mechanisms remain elusive. This study employed transcriptome sequencing on granulosa cells from 5 PCOS women and 5 controls, followed by bioinformatic analyses. We identified 684 mRNAs and 167 lncRNAs with significant differential expression. Gene Ontology and KEGG analyses highlighted enrichment in immune and inflammatory responses among these genes. Through CytoHubba plug-in and three machine learning algorithms, CCR7 was identified as the hub gene of PCOS, further validated through analysis of GSE65746, GSE34526 and a cohort of eighty subjects (40 PCOS and 40 controls). Furthermore, a competing endogenous RNA network targeting CCR7 was constructed. Immune infiltration analysis unveiled a significant decrease in monocyte infiltration in PCOS women, with CCR7 expression positively correlated to naïve B cells. Our findings suggest CCR7 and related molecules play a crucial role in the pathogenesis of PCOS, potentially serving as biomarkers for the disorder.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110968"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750457","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":"Purslane (Portulaca oleracea L.) polysaccharide attenuates carbon tetrachloride-induced acute liver injury by modulating the gut microbiota in mice","authors":"Jiahui Li,&nbsp;Yuyang Chen,&nbsp;Shuang Zhang,&nbsp;Yuehan Zhao,&nbsp;Demeng Gao,&nbsp;Jiaying Xing,&nbsp;YuYan Cao,&nbsp;Guangyu Xu","doi":"10.1016/j.ygeno.2024.110983","DOIUrl":"10.1016/j.ygeno.2024.110983","url":null,"abstract":"<div><div>This study investigated the preventive and protective effects of <em>Portulaca oleracea</em> polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of <em>Bacteroides</em>, reduced the number of <em>Proteobacteria</em>, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110983"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142902875","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}