bioRxiv - Genomics最新文献

{"title":"Pre and Post antibiotic epoch: insights into the historical spread of antimicrobial resistance","authors":"Adrian Cazares, Wendy Figueroa, Daniel Cazares, Leandro Lima, Jake D. Turnbull, Hannah McGregor, Jo Dicks, Sarah Alexander, Zamin Iqbal, Nicholas Thomson","doi":"10.1101/2024.09.03.610986","DOIUrl":"https://doi.org/10.1101/2024.09.03.610986","url":null,"abstract":"Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced this is limited by a paucity of data predating the antibiotic era (PAE). By investigating plasmids from clinically relevant bacteria isolated between 1917 and 1954 and comparing them to modern plasmids, we captured over 100 years of evolution. We show that while all PAE plasmids were devoid of resistance genes and most never acquired them, a small minority evolved to drive the global spread of resistance to first-line and last-resort antibiotics in Gram-negative bacteria. They have evolved through complex microevolution and fusion events into a distinct group of highly recombinogenic, multi-replicon, self-transmissible plasmids that now pose the highest risk to resistance dissemination, and therefore human health.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"282 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A workflow for practical training in ecological genomics using Oxford Nanopore long-read sequencing","authors":"Robert Foster, Heleen De Weerd, Nathan C Medd, Tim Booth, Caitlin Newman, Helen Ritch, Javier Santoyo-Lopez, Urmi Trivedi, Alex D Twyford","doi":"10.1101/2024.09.03.610948","DOIUrl":"https://doi.org/10.1101/2024.09.03.610948","url":null,"abstract":"Long-read single molecule sequencing technologies continue to grow in popularity for genome assembly and provide an effective way to resolve large and complex genomic variants. However, uptake of these technologies for teaching and training is hampered by the complexity of high molecular weight DNA extraction protocols, the time required for library preparation and the costs for sequencing, as well as challenges with downstream data analyses. Here, we present a full long-read workflow optimised for teaching, that covers each stage from DNA extraction, to library preparation and sequencing, to data QC and genome assembly and characterisation, that can be completed in under two weeks. We use a specific case study of plant identification, where students identify an anonymous plant sample by sequencing and assembling the genome and comparing it to other samples and to reference databases. In testing, long-read genome skimming of nine wild-collected plant species extracted with a modified kit-based approach produced an average of 8Gb of Oxford Nanopore data, enabling the complete assembly of plastid genomes, and partial assembly of nuclear genomes. In the classroom, all students were able to complete the protocols, and to correctly identify their plant samples based on BOLD searches of barcoding loci extracted from the plastid genome, coupled with phylogenetic analyses of whole plastid genomes. We supply all the learning material and raw data allowing this to be adapted to a range of teaching settings.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"113 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic ancestry in Puerto Rican Afro-descendants illustrates diverse histories of African diasporic populations","authors":"Maria A Nieves-Colón, Emma C Ulrich, Lijuan Chen, Gabriel A. Torres Colón, Maricruz Rivera Clemente, La Corporación Piñones Se Integra (COPI), Jada Benn Torres","doi":"10.1101/2024.09.02.610898","DOIUrl":"https://doi.org/10.1101/2024.09.02.610898","url":null,"abstract":"Objectives: Genetic studies of contemporary Puerto Ricans reflect a demographic history characterized by admixture between Indigenous American, African, and European peoples. While previous studies provide genetic perspectives on the general Puerto Rican population, less is known about the islands sub-populations, specifically Afro-Puerto Ricans. Materials and Methods: In this study, the genetic ancestry of Afro-Puerto Ricans is characterized and compared to other Caribbean populations. Thirty DNA samples collected among self-identified Puerto Ricans of African descent in Loíza (n=2), Piñones (n=13), San Juan (n=2), Mayag&uumlez (n=9), and Ponce (n=4), were genotyped at 750,000 loci on the National Geographic Genochip. We then applied unsupervised clustering and dimensionality-reduction methods to detect continental and subcontinental African and European genetic ancestry patterns. Results: Admixture analyses reveal that on average, the largest genetic ancestry component for Afro-Puerto Ricans is African in origin, followed by European and Indigenous American genetic ancestry components. African biogeographic origins of Afro-Puerto Ricans align most closely with contemporary peoples of Lower Guinea and the Bight of Biafra, while the European genetic ancestry component is most similar to contemporary Iberian, Italian, and Basque populations. These findings contrast with the biogeographic origins of comparative Barbadian and Puerto Rican populations. Discussion: Our results suggest that while there are similarities in general patterns of genetic ancestry among African descendants in the Caribbean, there is previously unrecognized regional heterogeneity, including among Puerto Rican sub-populations. These results are also consistent with available historical sources, while providing depth absent from the documentary record, particularly with regard to African ancestry.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring adaptive introgression in modern human circadian rhythm genes","authors":"Christopher Kendall, Amin Nooranikhojasteh, Guilherme Debortoli, Vinicius Cauê Furlan Roberto, Marla Mendes, David Samson, Esteban Parra, Bence Viola, Michael Schillaci","doi":"10.1101/2024.08.12.607550","DOIUrl":"https://doi.org/10.1101/2024.08.12.607550","url":null,"abstract":"Interbreeding between modern humans and archaic hominins, including Neanderthals and Denisovans, occurred as modern humans migrated outside of Africa. Here, we report on evidence of introgression from archaic hominins within genomic regions associated with circadian rhythm and chronotype using 76 worldwide modern human populations from the Human Genome Diversity Project and 1000 Genomes Project. We calculated the extent of regions indicative of adaptive introgression across the autosomes and identified regions that are suggested to be under positive selection. We tested for evidence of a latitudinal cline within 36 core haplotypes along with presenting the likely archaic donor for each of these haplotypes. We identified 265 independent segments that overlap genes described as having a circadian rhythm component or contain variants and segments previously identified as being associated with circadian rhythm or chronotype. Within these segments we found 1,729 archaically derived variants with allele frequencies of at least 40% intersecting 303 genes and intergenic segments. Seventeen of these segments show evidence of positive selection, three of which are found within our core haplotypes. We found that many of our genes are associated with the immune system or gastrointestinal function. Additionally, variants associated with complex traits such as schizophrenia and bipolar disorder are present within our adaptively introgressed regions. Lastly, genes and markers associated with sleep and chronotype phenotypes and serotonin pathways were also found in our adaptive introgression results, potentially signalling selection on genes related to seasonal light variation as modern humans migrated into new environments after leaving Africa.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a novel resistance gene which provides insight into Vip3Aa mode of action in Helicoverpa armigera","authors":"Andreas Bachler, Amanda Padovan, Craig J. Anderson, Yiyun Wei, Yidong Wu, Stephen Pearce, Sharon Downes, Bill James, Ashley Tessnow, Gregory A. Sword, Michelle Williams, Wee Tek Tay, Karl H. J. Gordon, Tom K. Walsh","doi":"10.1101/2024.08.11.607516","DOIUrl":"https://doi.org/10.1101/2024.08.11.607516","url":null,"abstract":"The global reliance on Bacillus thuringiensis (Bt) proteins for controlling lepidopteran pests in cotton, corn, and soybean crops underscores the critical need to understand resistance mechanisms. Vip3Aa, one of the most widely deployed and currently effective Bt proteins in genetically modified crops, plays a pivotal role in pest management. This study identifies the molecular basis of Vip3Aa resistance in Australian Helicoverpa armigera through genetic crosses, and integrated genomic and transcriptomic analyses. We identified a previously uncharacterized gene, LOC110373801 (designated HaVipR1), as a crucial determinant of Vip3Aa resistance in two field-derived resistant lines. Functional validation using CRISPR-Cas9 knockout in susceptible lines confirmed the gene's role in conferring resistance. Despite extensive laboratory selection of Vip3Aa-resistant colonies in Lepidoptera, the biochemical mechanisms underlying resistance have remained elusive. Our research demonstrates that HaVipR1-mediated resistance operates independently of known resistance genes, including midgut-specific chitin synthase and the transcription factor SfMyb. The identification of HaVipR1 offers further insights into the Vip3Aa mechanism of action. This discovery is vital for devising strategies to counteract resistance and sustain the efficacy of Bt crops. Future research should focus on elucidating the biochemical pathways involving HaVipR1 and investigating its interactions with other resistance mechanisms. Our findings underscore the utility of analysing field-derived resistant lines in providing biologically relevant insights and stress the necessity for comprehensive management strategies to maintain agricultural productivity.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Examining NFκB Genomic Interactions by ChIP-seq and CUT&Tag","authors":"Allison E Daly, Allison Schiffman, Alexander Hoffmann, Stephen Smale","doi":"10.1101/2024.08.11.607521","DOIUrl":"https://doi.org/10.1101/2024.08.11.607521","url":null,"abstract":"An understanding of the mechanisms and logic by which transcription factors coordinate gene regulation requires delineation of their genomic interactions at a genome-wide scale. Chromatin immunoprecipitation-sequencing (ChIP-seq) and more recent techniques, including CUT&Tag, typically reveal thousands of genomic interactions by transcription factors, but without insight into their functional roles. Due to cost and time considerations, optimization of ChIP experimental conditions is typically carried out only with representative interaction sites rather than through genome-wide analyses. Here, we describe insights gained from the titration of two chemical crosslinking reagents in genome-wide ChIP-seq experiments examining two members of the NF-κB family of transcription factors: RelA and c-Rel. We also describe a comparison of ChIP-seq and CUT&Tag. Our results highlight the large impact of ChIP-seq experimental conditions on the number of interactions detected, on the enrichment of consensus and non-consensus DNA motifs for the factor, and on the frequency with which the genomic interactions detected are located near potential target genes. We also found considerable consistency between ChIP-seq and CUT&Tag results, but with a substantial fraction of genomic interactions detected with only one of the two techniques. Together, the results demonstrate the dramatic impact of experimental conditions on the results obtained in a genome-wide analysis of transcription factor binding, highlighting the need for further scrutiny of the functional significance of these condition-dependent differences.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OzWheat: a genome-to-phenome platform to resolve complex traits for wheat pre-breeding and research.","authors":"Jessica E Hyles, Howard A Eagles, Kerrie Ramm, Bjorg Sherman, Andrew Gock, Sandra Stops, Tanya Phongkham, Emmett Leyne, Tina Rathjen, Radoslaw Suchecki, Lauren E Stevens, Louise Ord, Nick S Fradgley, Meredith D McNeil, Annelie Marquardt, Samuel C Andrew, Kerrie Forrest, Russell F Eastwood, Adam Norman, Annette Tredrea, Richard Trethowan, Ben Trevaskis, Shannon K Dillon","doi":"10.1101/2024.08.11.603522","DOIUrl":"https://doi.org/10.1101/2024.08.11.603522","url":null,"abstract":"For over a century, Australian wheat breeders have successfully adapted wheat to a broad range of climatic conditions and crop management practices. The OzWheat genome-to-phenome (G2P) platform was established to capture this breeding history and explore traits, genes, and their interactions with the environment to enable ongoing research and deliver targets for wheat improvement. A panel of 285 cultivars and landraces were chosen through knowledge of breeding pedigrees to represent both global diversity and the historic flow of genetic variation over more than 100 years of selective breeding in Australia. Genetic characterisation of the panel included identification of genome-wide sequence variants and gene expression profiling across environments. Important traits for adaptation (flowering time and plant height) were assayed in controlled environments and at multiple field sites and years, with genome-wide association analyses using linear mixed models detecting both known and novel loci. Here, we report establishment of the OzWheat G2P platform as a powerful tool to integrate wheat genomes and phenomes and demonstrate its use to identify candidate genes and understand gene by environment interactions. This provides the wheat research and breeding community a new resource to support future cultivar development.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploiting functional regions in the viral RNA genome as druggable entities","authors":"Dengguo Wei, Dehua Luo, Yingge Zheng, Zhiyuan Huang, Zi Wen, Lijun Guo, Yingxiang Deng, Qingling Li, Yuqing Bai, Shozeb Haider, Gary N Parkinson","doi":"10.1101/2024.08.11.607475","DOIUrl":"https://doi.org/10.1101/2024.08.11.607475","url":null,"abstract":"The design of RNA-targeting antivirals offers a potent means in controlling viral infections. An essential prerequisite to this design depends on identifying functional RNA structures in the viral genome, as well as those that are readily accessible to drugs in cells. Techniques that probe RNA structures in situ have been developed recently including SHAPE-MaP. In this study, we report on the application of SHAPE-MaP to the Porcine Epidemic Diarrhea Virus (PEDV) RNA genome to categorize RNAs that are well folded, dynamic, or in the single strands by the combination of two parameters, SHAPE reactivity and Shannon entropy. Dynamic RNAs have the potential to fold into specific structures, and stabilizing their structures with compounds could be a new idea for drug design, which is demonstrated by the example of the G-quadruplex forming sequence. siRNAs targeting stable single-stranded RNA regions presented higher antiviral success rates. Our results show that the RNAs in the single strands could be efficient antiviral targets, and that SHAPE-MaP is an effective method to identify targetable structures in the viral RNA genomes through analysis of folding features.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-resolution global diversity copy number variation maps and association with ctyper","authors":"Mark Chaisson, Walfred Ma","doi":"10.1101/2024.08.11.607269","DOIUrl":"https://doi.org/10.1101/2024.08.11.607269","url":null,"abstract":"Genetic analysis of copy number variations (CNVs), especially in complex regions, is challenging due to reference bias and ambiguous alignment of Next-Generation Sequencing (NGS) reads to repetitive DNA. Consequently, aggregate copy numbers are typically analyzed, overlooking variation between gene copies. Pangenomes contain diverse sequences of gene copies and enable the study of sequence-resolved CNVs. We developed a method, ctyper, to discover sequence-resolved CNVs in NGS data by leveraging CNV genes from pangenomes. From 118 public assemblies, we constructed a database of 3,351 CNV genes, distinguishing each gene copy as a resolved allele. We used phylogenetic trees to organize alleles into highly similar allele-types that revealed events of linked small variants due to stratification, structural variation, conversion, and duplication. Saturation analysis showed that new samples share an average of 97.8% CNV alleles with the database. The ctyper method traces individual gene copies in NGS data to their nearest alleles in the database and identifies allele-specific copy numbers using multivariate linear regression on k-mer counts and phylogenetic clustering. Applying ctyper to 1000 Genomes Project (1kgp) samples showed Hardy-Weinberg Equilibrium on 99.3% of alleles and a 97.6% F1 score on genotypes based on 641 1kgp trios. Leave-one-out analysis on 39 assemblies matched to 1kgp samples showed that 96.5% of variants in query sequences match the genotyped allele. Genotyping 1kgp data revealed 226 population-specific CNVs, including a conversion on SMN2 to SMN1, potentially impacting Spinal Muscular Atrophy diagnosis in Africans. Our results revealed two models of CNV: recent CNVs due to ongoing duplications and polymorphic CNVs from ancient paralogs missing from the reference. To measure the functional impact of CNVs, after merging allele-types, we conducted genome-wide Quantitative Trait Locus analysis on 451 1kgp samples with Geuvadis rRNA-seqs. Using a linear mixed model, our genotyping enables the inference of relative expression levels of paralogs within a gene family. In a global evolutionary context, 150 out of 1,890 paralogs (7.94%) and 546 out of 16,628 orthologs (3.28%) had significantly different expression levels, suggesting divergent expression from original genes. Specific examples include lower expression on the converted SMN and increased expression on translocated AMY2B (GTEx pancreas data). Our method enables large cohort studies on complex CNVs to uncover hidden health impacts and overcome reference bias.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis of somatic non-coding mutation patterns and mitochondrial heteroplasmy in type B1 and B2 thymomas","authors":"Kohei Fujikura, Isabel Correa, Susanne Heck, Juliet King, Emma McLean, Andrea Bille, Daisuke Nonaka","doi":"10.1101/2024.08.09.607250","DOIUrl":"https://doi.org/10.1101/2024.08.09.607250","url":null,"abstract":"Introduction: Type B1 and B2 thymomas are lymphocyte-rich malignant tumors with few somatic mutations in protein-coding regions of the nuclear genome; nonetheless, non-coding regions remain uncharacterized. Here, we developed a rigorous tumor isolation method from lymphocyte-rich thymoma tissues and identified somatic mutations in non-coding and mitochondrial DNA. Methods: CD205+CD45- pure tumor cells were isolated from fresh-frozen tissues using DEPArray system. Deep whole-genome sequencing was performed, and recurrent somatic alterations in coding, non-coding, and mitochondria regions were systemically identified by computational framework. The mutations were classified according to gene function, cis-regulatory element, and mutational signature. Results: The total number of somatic mutations was approximately 80 times higher in non-coding regions than in coding regions in type B1-2 thymomas (1,671.3 vs. 21.1 per case). Coding mutations were identified in epigenetic regulators, DNA repair genes, and some other genes. Nevertheless, 40% of cases exhibited fewer than four mutations in coding regions. A systematic non-coding analysis identified a total of 405.0 mutations per case on cis-regulatory elements, and detected six recurrent mutations: one interferon regulatory factor (IRF8), two E3 ubiquitin ligases (UBR2 and RNF213), and three intergenic regions. Mitochondrial heteroplasmy was observed in 90% of cases, with a significant proportion of mutations located in D-loop region. The single-base substitution pattern was signature 12. Conclusions: Numerous non-coding mutations and mitochondrial heteroplasmy were detected in type B1 and B2 thymomas. Given the paucity of coding mutations observed in this disease entity, disruption of the non-coding landscape and mitochondrial heteroplasmic shift may be the primary cause of thymoma.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}