Genome BiologyPub Date : 2025-06-01DOI: 10.1186/s13059-025-03621-7
Davide Francioli, Ioannis D. Kampouris, Theresa Kuhl-Nagel, Doreen Babin, Loreen Sommermann, Jan H. Behr, Soumitra Paul Chowdhury, Rita Zrenner, Narges Moradtalab, Michael Schloter, Joerg Geistlinger, Uwe Ludewig, Günter Neumann, Kornelia Smalla, Rita Grosch
{"title":"Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale","authors":"Davide Francioli, Ioannis D. Kampouris, Theresa Kuhl-Nagel, Doreen Babin, Loreen Sommermann, Jan H. Behr, Soumitra Paul Chowdhury, Rita Zrenner, Narges Moradtalab, Michael Schloter, Joerg Geistlinger, Uwe Ludewig, Günter Neumann, Kornelia Smalla, Rita Grosch","doi":"10.1186/s13059-025-03621-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03621-7","url":null,"abstract":"Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits. Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores. Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"5 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144193325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-28DOI: 10.1186/s13059-025-03597-4
Udita Chandola, Marinna Gaudin, Camille Trottier, Louis-Josselin Lavier-Aydat, Eric Manirakiza, Samuel Menicot, Erik Jörg Fischer, Isabelle Louvet, Thomas Lacour, Timothée Chaumier, Atsuko Tanaka, Georg Pohnert, Samuel Chaffron, Leïla Tirichine
{"title":"Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment","authors":"Udita Chandola, Marinna Gaudin, Camille Trottier, Louis-Josselin Lavier-Aydat, Eric Manirakiza, Samuel Menicot, Erik Jörg Fischer, Isabelle Louvet, Thomas Lacour, Timothée Chaumier, Atsuko Tanaka, Georg Pohnert, Samuel Chaffron, Leïla Tirichine","doi":"10.1186/s13059-025-03597-4","DOIUrl":"https://doi.org/10.1186/s13059-025-03597-4","url":null,"abstract":"Non-cyanobacteria diazotrophs (NCDs) are shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance. This raises fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. The absence of laboratory cultures of these bacteria significantly limits our ability to understand their behavior in natural environments and, consequently, their contribution to the marine nitrogen cycle. Here, via a multidisciplinary approach, we identify the presence of NCDs within the phycosphere of the model diatom Phaeodactylum tricornutum (Pt), which sustain the survival of Pt in nitrogen-depleted conditions. Through bacterial metacommunity sequencing and genome assembly, we identify multiple NCDs belonging to the Rhizobiales order, including Bradyrhizobium, Mesorhizobium, Georhizobium, and Methylobacterium. We demonstrate the nitrogen-fixing ability of PtNCDs through in silico identification of nitrogen fixation genes and by other experimental assays. We show the wide occurrence of this type of interactions with the isolation of NCDs from other microalgae, their identification in the environment, and their predicted associations with photosynthetic microalgae. Our study underscores the importance of microalgae interactions with NCDs to support nitrogen fixation. This work provides a unique model Pt-NCDs to study the ecology of this interaction, advancing our understanding of the key drivers of global marine nitrogen fixation.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"25 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-28DOI: 10.1186/s13059-025-03613-7
Natalia Zajac, Ioannis S. Vlachos, Sija Sajibu, Lennart Opitz, Shuoshuo Wang, Sridar V. Chittur, Christopher E. Mason, Kevin L. Knudtson, John M. Ashton, Hubert Rehrauer, Catharine Aquino
{"title":"The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers","authors":"Natalia Zajac, Ioannis S. Vlachos, Sija Sajibu, Lennart Opitz, Shuoshuo Wang, Sridar V. Chittur, Christopher E. Mason, Kevin L. Knudtson, John M. Ashton, Hubert Rehrauer, Catharine Aquino","doi":"10.1186/s13059-025-03613-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03613-7","url":null,"abstract":"Transcriptome sequencing (RNA-seq) is a powerful technology for gene expression profiling. Selection of optimal parameters for cDNA library generation is crucial for acquisition of high-quality data. In this study, we investigate the impact of the amount of RNA and the number of PCR cycles used for sample amplification on the rate of PCR duplication and, in consequence, on the RNA-seq data quality. For broader applicability, we sequenced the data on four short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. The native Illumina libraries were converted for sequencing on AVITI and G4 to assess the effect of library conversion, containing additional PCR cycles. We find that the rate of PCR duplicates depends on the combined effect of RNA input material and the number of PCR cycles used for amplification. For input amounts lower than 125 ng, 34–96% of reads were discarded via deduplication with the percentage increasing with lower input amount and decreasing with increasing PCR cycles. The reduced read diversity for low input amounts leads to fewer genes detected and increased noise in expression counts. Data generated with each of the four sequencing platforms presents similar associations between starting material amount and the number of PCR cycles on PCR duplicates, a similar number of detected genes, and comparable gene expression profiles.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"172 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-28DOI: 10.1186/s13059-025-03598-3
Marek Glombik, Ramesh Arunkumar, Samuel Burrows, Sophie Louise Mogg, Xiaoming Wang, Philippa Borrill
{"title":"Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations","authors":"Marek Glombik, Ramesh Arunkumar, Samuel Burrows, Sophie Louise Mogg, Xiaoming Wang, Philippa Borrill","doi":"10.1186/s13059-025-03598-3","DOIUrl":"https://doi.org/10.1186/s13059-025-03598-3","url":null,"abstract":"Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization has been characterized, on shorter timescales such as those found in crop breeding programs, the extent to which homoeolog expression bias is preserved or altered between generations remains elusive. Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common “Paragon” parent to explore the inheritance of homoeolog expression bias in the F5 generation. We found that homoeolog expression bias is inherited for 26–27% of triads in both populations. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace × elite cross, than in the population with two elite parents. These results demonstrate that there is significant reprogramming and stabilization of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"12 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-27DOI: 10.1186/s13059-025-03629-z
Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng, Xiao-Bing Zhang
{"title":"Author Correction: Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage","authors":"Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng, Xiao-Bing Zhang","doi":"10.1186/s13059-025-03629-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03629-z","url":null,"abstract":"<p><b>Author Correction</b><b>: </b><b>Genome Biol 18, 35 (2017)</b></p><p><b>https://doi.org/10.1186/s13059-017-1164-8</b></p><br/><p>Following publication of the original article [1], the authors identified an error in Figure 2: the last two flowcharts in Figure 2b were inadvertently duplicated. This error does not affect the main results and conclusions of the paper.</p><p>The incorrect Fig. 2 is given below</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03629-z/MediaObjects/13059_2025_3629_Figa_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure a\" aria-describedby=\"Figa\" height=\"1033\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03629-z/MediaObjects/13059_2025_3629_Figa_HTML.png\" width=\"685\"/></picture></figure><p>The correct Fig. 2 is given below</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03629-z/MediaObjects/13059_2025_3629_Figb_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure b\" aria-describedby=\"Figb\" height=\"1037\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03629-z/MediaObjects/13059_2025_3629_Figb_HTML.png\" width=\"685\"/></picture></figure><ol data-track-component=\"outbound reference\" data-track-context=\"references section\"><li data-counter=\"1.\"><p>Zhang JP, Li XL, Li GH, et al. Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage. Genome Biol. 2017;18:35. https://doi.org/10.1186/s13059-017-1164-8.</p><p>Article CAS PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><span>Author notes</span><ol><li><p>Jian-Ping Zhang and Xiao-Lan Li equal contributors.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>State Key Laboratory of Experimental Hematology, Tianjin, China</p><p>Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Weiping Yuan, Tao Cheng & Xiao-Bing Zhang</p></li><li><p>Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China</p><p>Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Weiping Yuan, Tao Cheng & Xiao-Bing Zhang</p></li><li><p>Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China</p><p>Tao Cheng & Xiao-Bing Zhang</p></li><li><p>Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China</p><p>Tao Cheng & Xiao-Bing Zhang</p></li><li><p>Collaborative Innovation Center for Cancer Medicine, Tianjin, China</p><p>Tao Cheng</p></li><li><p>Tianjin Key Laboratory of Blood Cell Therapy ","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"152 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144145565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-27DOI: 10.1186/s13059-025-03546-1
Linda Shearwin-Whyatt, Jane Fenelon, Hongshi Yu, Andrew Major, Zhipeng Qu, Yang Zhou, Keith Shearwin, James Galbraith, Alexander Stuart, David Adelson, Guojie Zhang, Michael Pyne, Stephen Johnston, Craig Smith, Marilyn Renfree, Frank Grützner
{"title":"AMHY and sex determination in egg-laying mammals","authors":"Linda Shearwin-Whyatt, Jane Fenelon, Hongshi Yu, Andrew Major, Zhipeng Qu, Yang Zhou, Keith Shearwin, James Galbraith, Alexander Stuart, David Adelson, Guojie Zhang, Michael Pyne, Stephen Johnston, Craig Smith, Marilyn Renfree, Frank Grützner","doi":"10.1186/s13059-025-03546-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03546-1","url":null,"abstract":"Egg-laying mammals (monotremes) evolved multiple sex chromosomes independently of therian mammals and lack the sex-determining gene SRY. The Y-localized anti-Müllerian hormone gene (AMHY) is the candidate sex-determination gene in monotremes. Here, we describe the evolution of monotreme AMHX and AMHY gametologues and for the first time, investigate their expression during gonad sexual differentiation in a monotreme. Monotreme AMHX and AMHY have significant sequence divergence at the promoter, gene, and protein level, likely following an original allele inversion in the early stages of monotreme sex chromosome differentiation but retaining the conserved features of TGF-β molecules. We show that the expression of sexual differentiation genes in the echidna fetal gonad, including DMRT1 and SOX9, is significantly different from that of therian mammals. Importantly, AMHY is expressed exclusively in the male gonad during sexual differentiation consistent with a role as the primary sex-determination gene whereas AMHX is expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinize the female urogenital system, as does chicken AMH, a possible result of mammalian-specific changes to AMH proteins preventing function in the chicken. Our results provide insight into the early steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex-determination gene of platypus and echidna.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"239 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144145561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-25DOI: 10.1186/s13059-025-03610-w
Joseph H. Lobel, Nicholas T. Ingolia
{"title":"Precise measurement of molecular phenotypes with barcode-based CRISPRi systems","authors":"Joseph H. Lobel, Nicholas T. Ingolia","doi":"10.1186/s13059-025-03610-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03610-w","url":null,"abstract":"Genome-wide CRISPR-Cas9 screens have untangled regulatory networks driving diverse biological processes. Their success relies on interrogating specific molecular phenotypes and distinguishing key regulators from background effects. Here, we realize these goals by optimizing CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) to dramatically improve the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely matched promoters. We use our improved CiBER-seq to accurately capture known components of well-studied RNA and protein quality control systems. These results demonstrate the precision and versatility of CiBER-seq for dissecting cellular pathways.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"57 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144133442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-23DOI: 10.1186/s13059-025-03607-5
Haichao Wang, Paulius D. Mennea, Yu Kiu Elkie Chan, Zhao Cheng, Maria C. Neofytou, Arif Anwer Surani, Aadhitthya Vijayaraghavan, Emma-Jane Ditter, Richard Bowers, Matthew D. Eldridge, Dmitry S. Shcherbo, Christopher G. Smith, Florian Markowetz, Wendy N. Cooper, Tommy Kaplan, Nitzan Rosenfeld, Hui Zhao
{"title":"A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data","authors":"Haichao Wang, Paulius D. Mennea, Yu Kiu Elkie Chan, Zhao Cheng, Maria C. Neofytou, Arif Anwer Surani, Aadhitthya Vijayaraghavan, Emma-Jane Ditter, Richard Bowers, Matthew D. Eldridge, Dmitry S. Shcherbo, Christopher G. Smith, Florian Markowetz, Wendy N. Cooper, Tommy Kaplan, Nitzan Rosenfeld, Hui Zhao","doi":"10.1186/s13059-025-03607-5","DOIUrl":"https://doi.org/10.1186/s13059-025-03607-5","url":null,"abstract":"Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes and validated in 1182 plasma samples from published studies. Our results clarify the variations from library preparation and feature quantification methods. We design the Trim Align Pipeline and cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualization to standardize multi-modal feature engineering and integration for machine learning.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"145 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A survey of sequence-to-graph mapping algorithms in the pangenome era","authors":"Yingbo Cui, Chenchen Peng, Zeyu Xia, Canqun Yang, Yifei Guo","doi":"10.1186/s13059-025-03606-6","DOIUrl":"https://doi.org/10.1186/s13059-025-03606-6","url":null,"abstract":"A pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias. Pangenomes are often represented as genome graphs, making sequence-to-graph mapping a fundamental task for pangenome construction and analysis. Numerous sequence-to-graph mapping algorithms have been developed over the past few years. Here, we provide a review of the advancements in sequence-to-graph mapping algorithms in the pangenome era. We also discuss the challenges and opportunities that arise in the context of pangenome graphs.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"136 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-22DOI: 10.1186/s13059-025-03617-3
Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch, Stephanie D. McKay
{"title":"Analyzing the relationship of RNA and DNA methylation with gene expression","authors":"Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch, Stephanie D. McKay","doi":"10.1186/s13059-025-03617-3","DOIUrl":"https://doi.org/10.1186/s13059-025-03617-3","url":null,"abstract":"DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m6A) methylation are prevalent modifications in eukaryotes, both playing crucial roles in gene regulation. Recent studies have explored their crosstalk and impact on transcription. However, the intricate relationships among 5mC, m6A, and gene expression remain incompletely elucidated. We collect data on 5mC, m6A, and gene expression from samples from three tissues from each of four pregnant cattle and sheep. We construct a comprehensive genome-wide self-interaction (same gene) and across-interaction (across genes) network of 5mC and m6A within gene-bodies or promoters and gene expression in both species. Qualitative analysis identifies uniquely expressed genes with specific m6A methylation in each tissue from both species. A quantitative comparison of gene expression ratio between methylated and unmethylated genes for m6A within gene body and promoter, and 5mC within gene body and promoter confirms the positive effect of RNA methylation on gene expression. Importantly, the influence of RNA methylation on gene expression is stronger than that of DNA methylation. The predominant self- and across-interactions are between RNA methylation within gene bodies and gene expression, as well as between RNA methylation within promoters and gene expression in both species. RNA methylation has a stronger effect on gene expression than does DNA methylation within gene bodies and promoters. DNA and RNA methylation in gene-bodies has a greater impact on gene expression than those in promoters. These findings deepen comprehension of the dynamics and complex relationships among the epigenome, epitranscriptome, and transcriptome, offering fresh insights for advancing epigenetics research.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"1 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}