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in category genomics

6,710 results found. For more information, click each entry to expand.

6541: Aquatic insects are dramatically underrepresented in genomic research
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Posted 21 Aug 2020

Aquatic insects are dramatically underrepresented in genomic research
103 downloads bioRxiv genomics

Scott Hotaling, Joanna L. Kelley, Paul B. Frandsen

Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ~9 terrestrial insect genomes. Instead, ~24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if the quality of genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes) yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group. ### Competing Interest Statement The authors have declared no competing interest.

6542: Transcriptome Analysis in Yeast Reveals the Externality of Position Effect
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Posted 02 Apr 2020

Transcriptome Analysis in Yeast Reveals the Externality of Position Effect
103 downloads bioRxiv genomics

Qian Gui, Shuyun Deng, Wenjun Shi, Xiujuan Cai, Zhen-Zhen Zhou, Jian-Rong Yang, Xiaoshu Chen

When a gene is integrated into the chromosome, its activity depends on the genomic context. Although this phenomenon of "position effect" was widely reported, how the integration event affects the local environment, or the "externality" of position effect, remained largely unexplored, let alone the mechanism or phenotypic consequence of such externality. Here, we examined the transcriptome profiles of ~250 Saccharomyces cerevisiae strains, each with GFP inserted into a different locus of the wild-type strain. We found that the GFP expression level and the change of expression of genes near the integration site decreases in genomic regions with high density of essential genes. This observation was found associated with H3K4me2 by further joint-analysis with public genome-wide histone modification profiles. More importantly, we found that the expression changes of neighboring genes, but not the GFP expression, exerted a significant impact on cellular growth rate. As a result, genomic loci that grant higher GFP expression immediately after the integration will have lower total yield of GFP in the long run. Our results, which were consistent with the competition for transcriptional resources among neighboring genes, revealed a previously unappreciated facet of the position effect, and highlighted its impact on the fate of genomic integration of exogenous genes, which has profound implications for biological engineering and pathology of virus integrative to host genome.

6543: Identification of regulatory microRNAs for hypoxia induced coagulation mechanism by In-silico analysis
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Posted 26 Jun 2020

Identification of regulatory microRNAs for hypoxia induced coagulation mechanism by In-silico analysis
103 downloads bioRxiv genomics

Anju A. Hembrom, Swati Srivastava, Iti Garg, Bhuvnesh Kumar

Background: Hypoxia (oxygen deprivation) is known to induce a prothrombotic state by activating the process of coagulation. Hypoxia inducible factor (HIF), is a major transcription factor involved in cellular response to low oxygen tension. MicroRNAs (miRNAs) are non-coding regulatory sequences capable of post-translational modification of multiple genes. Present study aimed to identify common regulatory miRNAs of HIF gene family and coagulation pathway by In-silico approach in order to understand the molecular mechanism underlying the process of hypoxia induced coagulation.Methods: HIF family and Coagulation pathway genes along with their receptors and mediators were enlisted after comprehensive literature review. Thorough search of three highly cited database was done to identify the miRNAs targeting these genes. The extracted miRNA list was then prioritized on the basis of number and functional relevance of genes targeted. The target genes of all prioritized miRNAs were listed and subjected to followed by gene ontology (GO) study and pathway analysis.Result: Present In-silico analysis identified five candidate miRNAs, viz., hsa-mir-4433a-3p, hsa-mir-4667-5p, hsa-mir-6735-5p, hsa-mir-6777-3p and hsa-mir-6815-3p that co-regulate genes of HIF family and coagulation pathway. GO and pathway analysis revealed that genes regulated by these five microRNAs, predominantly modulate genes facilitating coagulation and hypoxic response.Conclusion: We identified five key microRNAs involved in body’s response to hypoxia and potentially involved in the blood coagulation cascade as well. These five candidate miRNAs may serve as putative epigenetic biomarkers and therapeutic targets to modulate the process of hypoxia induced coagulation.

6544: Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin
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Posted 06 Aug 2020

Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin
103 downloads bioRxiv genomics

Elliot W. Jackson, Roland C. Wilhelm, Mitchell R Johnson, Holly Lutz, Isabelle Danforth, Joseph K. Gaydos, Michael W. Hart, Ian Hewson

A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while >30 complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD. ### Competing Interest Statement The authors have declared no competing interest.

6545: Vaginal Microbiome Topic Modelling of Laboring Ugandan Women With and Without Fever
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Posted 02 Dec 2020

Vaginal Microbiome Topic Modelling of Laboring Ugandan Women With and Without Fever
103 downloads bioRxiv genomics

Mercedeh Movassagh, Lisa M. Bebell, Kathy L Burgoine, Christine Hehnly, Lijun Zhang, Kim Moran, Kathryn Sheldon, Shamim A Sinnar, Edith Kabachelor, Joel Bazira, Elias Kumbakumba, Moses Ochora, Ronnie Mulondo, Brian K Nsubuga, Andrew D. Weeks, Melissa J Gladstone, Peter Olupot-Olupot, Joseph Ngonzi, Drucilla Roberts, Frederick A Meier, Rafael A. Irizarry, James R Broach, Steven J. Schiff, Joseph N. Paulson

The composition of the maternal vaginal microbiome may influence the duration of pregnancy, onset of labor and even neonatal outcomes. Maternal microbiome research in sub Saharan-Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. We examined the vaginal microbiome composition of 99 laboring Ugandan women using routine microbiology and 16S ribosomal DNA sequencing from two hypervariable regions (V1-V2 and V3-V4), using standard hierarchical methods. We then introduce Grades of Membership (GoM) modeling for the vaginal microbiome, a method often used in the text mining machine learning literature. Leveraging GoM models, we create a basis composed of a small number of microbial 'topic's whose linear combination optimally represents each patient yielding more accurate associations. We identified relationships between defined communities and the presentation or absence of intrapartum fever. Using a random forest model we showed that by including novel microbial topic models we improved upon clinical variables to predict maternal fever. We also show by integrating clinical variables with a microbial topic model into this model found young maternal age, fever report earlier in the current pregnancy, and longer labors, as well as a more diverse, less Lactobacillus dominated microbiome were features of labor associated with intrapartum fever. These results better define relationships between presentation or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial communities, and improve our understanding of the impact of the microbiome on maternal and neonatal infection risk.

6546: Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil
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Posted 09 Jan 2021

Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil
102 downloads bioRxiv genomics

Joilson Xavier, Vagner Fonseca, Joao Felipe Bezerra, Manoella do Monte Alves, Maria Angélica Mares-Guia, Ingra Morales Claro, Ronaldo de Jesus, Talita Adelino, Emerson Araújo, Karina Ribeiro Leite Jardim Cavalcante, Stephane Tosta, Themis Rocha de Souza, Flavia Emanuelle Moreira da Cruz, Allison de Araújo Fabri, Elaine Cristina de Oliveira, Noely Fabiana Oliveira de Moura, Rodrigo Fabiano do Carmo Said, Carlos Frederico Campelo de Albuquerque, Vasco Azevedo, Tulio de Oliveira, Ana Maria Bispo de Filippis, Rivaldo Venâncio da Cunha, Kleber Giovanni Luz, Marta Giovanetti, Luiz Carlos Junior Alcantara

The Northeast region of Brazil registered the second highest incidence proportion of chikungunya fever in 2019. In that year an outbreak consisting of patients presented with febrile disease associated with joint pain were reported by the public primary health care service in the city of Natal, Rio Grande do Norte state, in March 2019. At first, the aetiological agent of the disease was undetermined. Since much is still unknown about chikungunya virus (CHIKV) genomic diversity and evolutionary history in this northeasternmost state, we used a combination of portable whole genome sequencing, molecular clock, and epidemiological analyses that revealed the re-introduction of the CHIKV East-Central-South-African (ECSA) lineage into Rio Grande do Norte. We estimated CHIKV ECSA lineage was first introduced into Rio Grande do Norte in early June 2014, while the 2019 outbreak clade diverged around April 2018 during a period of increased chikungunya incidence in the Southeast region, which might have acted as a source of virus dispersion towards the Northeast region. Together, these results confirm the ECSA lineage continues to spread across the country through interregional importation events likely mediated by human mobility. HIGHLIGHTSCHIKV ECSA lineage introduction into Rio Grande do Norte state, Northeast Brazil, was estimated to early June 2014 At least two CHIKV importation events occurred in Rio Grande do Norte state, Brazil The 2019 chikungunya outbreak in Rio Grande do Norte was likely caused by a second event of CHIKV introduction imported from Rio de Janeiro state.

6547: Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks
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Posted 29 Jan 2021

Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks
102 downloads bioRxiv genomics

Chunming Yang, Jun Yan, Shuqin Jiang, Xia Li, Haowei Min, Xiangfeng Wang, Dongyun Hao

Limited knowledge on genomic diversity and the functional genes associated with soybean variety traits has resulted in slow breeding progress. We sequenced the genome of 250 soybean landraces and cultivars from China, America and Europe, and investigated their population structure, genetic diversity and architecture and selective sweep regions of accessions. We identified five novel agronomically important genes and studied the effects of functional mutations in respective genes. We found candidate genes GSTT1, GL3 and GSTL3 associated with isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits. Our phenotype-gene network analysis revealed that hub nodes play a role in complex phenotypic associations. In this work, we describe novel agronomic trait associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

6548: Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin
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Posted 24 Nov 2020

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin
102 downloads bioRxiv genomics

Artem Nedoluzhko, Fedor Sharko, Svetlana Tsygankova, Eugenia Boulygina, Amina Ibragimova, Anton Teslyuk, Jorge Galindo-Villegas, Sergey Rastorguev

Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.

6549: Methylation Quantitative Trait Loci are Largely Consistent across Disease States in Crohns disease
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Posted 17 Nov 2020

Methylation Quantitative Trait Loci are Largely Consistent across Disease States in Crohns disease
101 downloads bioRxiv genomics

Suresh Venkateswaran, Hari K Somineni, Varun Kilaru, Seyma Kartrinli, Jarod Prince, David Okou, Jeffery S Hyams, Denson A Lee, Richard Kellermayer, Greg Gibson, David Cutler, Alicia K Smith, Subra Kugathasan, Karen Conneely

Background: In a recent study, we identified 1189 CpG sites whose DNA methylation (DNAm) level in blood distinguished Crohns disease (CD) cases from controls. We also demonstrated that the vast majority of these differences were a consequence of disease, rather than a cause of CD. Since methylation can be influenced by both genetic and environmental factors, here we focus on CpGs under demonstrable genetic control (methylation quantitative trait loci, or mQTLs). By comparing mQTL patterns across disease states and tissue (blood vs. ileum), we may distinguish patterns unique to CD. Such DNAm patterns may be relevant for the developmental origins of CD. Methods: We investigated three datasets: (i) 402 blood samples from 164 newly diagnosed pediatric CD patients taken at two time points, and 74 non-IBD controls (ii) 780 blood samples from a non-CD adult population and (iii) 40 ileal biopsies (17 CD cases and 23 non-IBD controls) from the group (i). Genome-wide DNAm profiling and genotyping were performed using the Illumina MethylationEPIC and Illumina Multi-Ethnic arrays. SNP-CpG associations were tested via linear models adjusted for age, gender, disease status, disease subtype, estimated cell type, and three genotype-based principal components. We used a Bonferroni-adjusted significance threshold to identify significantly associated SNP-CpG pairs, but also considered larger sets identified by a false discovery rate criterion. Results: We observed 535,448 SNP-CpG associations between 287,881 SNPs and 12,843 CpG sites (P<8.21x10-14). These associations and their effects are highly consistent across different ages, races, disease states, and tissue types, suggesting that the vast majority of these mQTLs participate in common gene regulation. However, genes near CpGs associated with IBD SNPs were enriched for 18 KEGG pathways relevant to IBD-linked immune function and inflammatory responses. We observed suggestive evidence for a small number of tissue-specific associations and disease-specific ileal associations in the ileum, though larger studies will be needed to confirm these results. Conclusion: The vast majority of blood-derived mQTLs are commonly shared across individuals. However, we have identified a subset of such, which may be involved in processes related to CD. Independent cohort studies will be required to validate these findings. ### Competing Interest Statement The authors have declared no competing interest.

6550: Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus
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Posted 17 Jun 2020

Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus
101 downloads bioRxiv genomics

P. Simmonds, L. Cuypers, W.L. Irving, J. McLauchlan, G.S. Cooke, E. Barnes, STOP-HCV Consortium, M.A. Ansari

Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute associated with formation of large scale RNA structure in their genomic RNA. We developed novel methods to analyse and visualise genome-scale ordered RNA structure (GORS) predicted from the increasingly large datasets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localised exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally entirely distinct, even between subtypes 1a and 1b. Dynamic remodelling was further evident from comparison of HCV strains in different host genetic background. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in the IFNL4 gene compared to the CC (non-expressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represents an important new element in RNA virus evolution and the adaptive interplay between virus and host. ### Competing Interest Statement The authors have declared no competing interest.

6551: High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs
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Posted 02 Nov 2020

High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs
101 downloads bioRxiv genomics

Benjamin R Holmes, David K Gifford, Richard Sherwood, Lin Lin

Genomic enhancer elements play a role in modulating gene expression by interacting with effector proteins known as transcription factors. We present a new computational method, "STARR-scan", which identifies transcription factor motif appearances in synthetic DNA constructs that are correlated with enhancer activity. Using a tiled STARR-seq assay, we demonstrate that STARR-scan can suggest the biological function of transcription factors previously suspected to activate the APOBEC-3B gene. Using the same methodology, STARR-scan can suggest transcription factors with previously unknown biological activity which may regulate the APOBEC-3B gene. These novel factors may have biological significance in our understanding of cancer biology. ### Competing Interest Statement The authors have declared no competing interest.

6552: Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences
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Posted 26 Oct 2020

Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences
101 downloads bioRxiv genomics

Abdoulie Kanteh, Jarra Manneh, Sona Jabang, Kujabi Mariama A., Sanyang Bakary, Oboh Mary A., Abdoulie Bojang, Haruna Jallow, Davis Nwakanma, Ousman Secka, Anna Rocca, Alfred Amambua-Ngwa, Martin Antonio, Ignatius Baldeh, Karen Forrest, Ahmadou Lamin Samateh, Umberto D’Alessandro, Abdul Karim Sesay

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility. This study generated Whole Genome data to determine the origin and pattern of transmission of SARS-CoV-2 from the first six cases tested in The Gambia. Total RNA from SARS-CoV-2 was extracted from inactivated nasopharyngeal-oropharyngeal swabs of six cases and converted to cDNA following the ARTIC COVID-19 sequencing protocol. Libraries were constructed with the NEBNext ultra II DNA library prep kit for Illumina and Oxford Nanopore Ligation sequencing kit and sequenced on Illumina MiSeq and Nanopore GridION, respectively. Sequencing reads were mapped to the Wuhan reference genome and compared to eleven other SARS-CoV-2 strains of Asian, European and American origins. A phylogenetic tree was constructed with the consensus genomes for local and non-African strains. Three of the Gambian strains had a European origin (UK and Spain), two strains were of Asian origin (Japan). In The Gambia, Nanopore and Illumina sequencers were successfully used to identify the sources of SARS-CoV-2 infection in COVID-19 cases.

6553: Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species
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Posted 03 Sep 2020

Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species
101 downloads bioRxiv genomics

Pierre Marin, Angelo Jaquet, Justine Picarle, Marie Fablet, Vincent Merel, Marie-Laure Delignette-Muller, Mariana Galvão Ferrarini, Patricia Gibert, Cristina Vieira

Background Adaptation to rapid environmental changes must occur within a short time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and successfully adapted to novel environmental conditions. Here we investigated how invasive and non-invasive populations of D. suzukii deal with an oxidative stress at both the phenotypic and molecular level. We also investigated the impact of transposable element insertions on the differential gene expression between genotypes in response to oxidative stress. Results Invasive populations lived longer in the untreated condition than non-invasive Japanese populations. As expected, lifespan was greatly reduced following exposure to paraquat, but this reduction varied among genotypes (a genotype by environment interaction, GEI) with invasive genotypes appearing more affected by exposure than non-invasive genotypes. We also performed transcriptomic sequencing of selected genotypes upon and without paraquat and detected a large number of genes differentially expressed, distinguishing the genotypes in the untreated environment. While a small core set of genes were differentially expressed by all genotypes following paraquat exposure, much of the response of each population was unique. Interestingly, we identified a set of genes presenting genotype by environment interaction (GEI). Many of these differences may reflect signatures of history of past adaptation. Transposable elements (TEs) were not activated after oxidative stress and differentially expressed (DE) genes were significantly depleted of TEs. Conclusion In the decade since the invasion from the south of Asia, invasive populations of D. suzukii have diverged from populations in the native area regarding their genetic response to oxidative stress. This suggests that such transcriptomic changes could be involved in the rapid adaptation to local environments. ### Competing Interest Statement The authors have declared no competing interest.

6554: PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets
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Posted 07 Oct 2020

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets
101 downloads bioRxiv genomics

Léa Pradier, Tazzio Tissot, Anna-Sophie Fiston-Lavier, Stéphanie Bedhomme

Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. The detection of plasmids in large sets of genomes is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance genes propagation. Several bioinformatics methods have been developed to detect plasmids. However, they suffer from low sensitivity (i.e., most plasmids remain undetected) or low precision (i.e., these methods identify chromosomes as plasmids), and are overall not adapted to identify plasmids in whole genomes that are not fully assembled (contigs and scaffolds). Here, we present PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in unassembled genomes. This tool is based on the determination of homologies against a database of plasmid sequences, which allow a random forest classifier to discriminate plasmid contigs. Without knowing the taxonomical origin of the samples, PlasForest identifies contigs as plasmids or chromosomes with an accuracy of 98%. Notably, it can detect 96% of plasmid contigs over 50kb with 3.3% of false positives. PlasForest outperforms other currently available tools on test datasets by being both sensitive and precise. We implemented this tool in a user-friendly pipeline that can identify plasmids in large datasets in a reasonable amount of time. ### Competing Interest Statement The authors have declared no competing interest.

6555: Cyclical Regression Covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasite Plasmodium falciparum
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Posted 18 Apr 2020

Cyclical Regression Covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasite Plasmodium falciparum
101 downloads bioRxiv genomics

Gabriel J. Foster, Katrina Button-Simons, Katelyn Vendrely, Jeanne Romero-Severson, Michael T Ferdig

Background: The cyclical nature of parasite gene expression in the intraerythrocytic development cycle (IDC) in human blood confounds the accurate detection of specific transcriptional differences due to drug resistance in Plasmodium falciparum. Here, we propose the use of cyclical regression covariates to eliminate the major confounding of developmentally driven transcriptional changes with changes due to drug response. We show that elimination of this confounding can reduce both Type I and Type II errors, and demonstrate the effect of approach on real data. Results: We apply this method to two publicly available datasets, and demonstrate its ability to reduce the potential confounding of differences in expression due the species-specific intraerythrocytic development cycle from strain-specific differences in drug response. We show that the application of cyclical regression covariates has minimal impact on the pool of transcripts identified as significantly different in a dataset generated from single timepoint clinical blood samples with low variance for developmental stage and a profound impact on another clinical data set with more variance among the samples for developmental stage. Conclusions: Cyclical regression covariates have immediate application to studies where in-vitro synchronization of all samples to the same developmental timepoint is not feasible, primarily parasite transcriptome sequencing direct from clinical blood samples, a widely used approach to frontline detection of emerging drug resistance. ### Competing Interest Statement The authors have declared no competing interest.

6556: SINE Retrotransposons Import Polyadenylation Signals to 3'UTRs in Dog (Canis familiaris)
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Posted 01 Dec 2020

SINE Retrotransposons Import Polyadenylation Signals to 3'UTRs in Dog (Canis familiaris)
101 downloads bioRxiv genomics

Jessica D. Choi, Lelani A. Del Pinto, Nathan B. Sutter

Background: Messenger RNA 3' untranslated regions (3'UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3'UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy number. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may help terminate transcript in some dog genes. Results: Dog 3'UTRs have several peaks of AATAAA PAS frequency within 40 bp of the 3'UTR end, including four bp-interval peaks at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. While density of antisense-oriented Can-SINEs in 3'UTRs is fairly constant with distances from 3'end, sense-oriented Can-SINEs are common at the 3'end but nearly absent farther upstream. There are nine Can-SINE sub-types in the dog genome and the consensus sequence sense strands (head to tail) all carry at least three PASs while antisense strands usually have none. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp for target site duplications (TSDs). We find that all Can-SINE types favor integration at TSDs beginning with A(4). The count of AATAAA PASs differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3'UTR ends are very likely to carry AATAAA on the mRNA sense strand while those farther upstream are not. We also identified loci where Can-SINE insertion has truncated or altered a dog 3'UTR compared to the human ortholog. Conclusion: Dog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3'UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3'UTR regions but are retained at the far downstream end of 3'UTRs, which we infer reflects their role as termination sequences for these transcripts.

6557: Phylogenetic and evolutionary analysis reveals the recent dominance of ciprofloxacin resistant S. sonnei and local persistence of S. flexneri clones in India
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Posted 07 Jun 2020

Phylogenetic and evolutionary analysis reveals the recent dominance of ciprofloxacin resistant S. sonnei and local persistence of S. flexneri clones in India
100 downloads bioRxiv genomics

Dhiviya Prabaa Muthuirulandi Sethuvel, Ankur Mutreja, Agila Kumari Pragasam, Karthick Vasudevan, Dhivya Murugan, Shalini Anandan, Joy Sarojini Michael, Kamini Walia, Balaji Veeraraghavan

Shigella is the second leading cause of bacterial diarrhea worldwide. Recently S. sonnei seems to be replacing S. flexneri in low and middle-income countries undergoing economic development. Despite this, studies focusing on these species at genomic level remain largely unexplored. Here we compared the genome sequences of S. flexneri and S. sonnei isolated from India with the publically available genomes of global strains. Our analysis provide evidence for the long term persistence of all PGs of S. flexneri and the recent dominance of ciprofloxacin-resistant S. sonnei lineage in India. Within S. flexneri PGs, majority of the study isolates belonged to PG3 within the predominance of serotype 2. For S. sonnei, the current pandemic involves globally distributed MDR clones that belong to Central Asia lineage III. The presence of such epidemiologically-dominant lineages in association with stable AMR determinants results in the successful survival in the community. ### Competing Interest Statement The authors have declared no competing interest.

6558: MADS-box genes galore in wheat genome: phylogenomics, evolution and stress associated functions
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Posted 23 Oct 2020

MADS-box genes galore in wheat genome: phylogenomics, evolution and stress associated functions
100 downloads bioRxiv genomics

Qasim Raza, Awais Riaz, Rana Muhammad Atif, Babar Hussain, Zulfiqar Ali, Hikmet Budak

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. However, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the latest publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies, without a single FLOWERING LOCUS C homolog present in the wheat genome. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more recent evolutionary origin was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that will accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits. ### Competing Interest Statement The authors have declared no competing interest.

6559: A highly rifampicin resistant Mycobacterium tuberculosis strain emerging in Southern Brazil
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Posted 03 Sep 2020

A highly rifampicin resistant Mycobacterium tuberculosis strain emerging in Southern Brazil
100 downloads bioRxiv genomics

Maria Lucia Rossetti, Pedro Eduardo Almeida da Silva, Richard Steiner Salvato, Ana Júlia Reis, Sun Hee Schiefelbein, Andrea von Groll, Regina Bones Barcellos, Raquel Maschmann, Leonardo Esteves, Fernanda Spies, Rubia Raubach Trespach, Elis Regina Dalla Costa, Hermes Luís Neubauer de Amorim

Here we described phenotypical, molecular and epidemiological features of a highly rifampicin-resistant Mycobacterium tuberculosis strain emerging in Southern Brazil, that carries an uncommon insertion of 12 nucleotides at the codon 435 in the rpoB gene. Employing a whole-genome sequencing-based study on drug-resistant Mycobacterium tuberculosis strains, we identified this emergent strain in 16 (9.19%) from 174 rifampicin-resistant clinical strains included. Nine of these 16 strains were available to minimum inhibitory concentration determination and for all of them was found a high rifampicin-resistance level (≥ to 32 mg/L). This high resistance level could be explained by structural changes into the RIF binding site of RNA polymerase caused by the insertions, and consequent low-affinity interaction with rifampicin complex confirmed through protein modeling and molecular docking simulations. Epidemiological investigation showed that most of the individuals (56.25%) infected by the studied strains were prison inmate individuals or that spent some time in prison. The phylogenomic approach revealed that all strains carrying on the 12 nucleotide insertion belonged to the same genomic cluster, evidencing a communal transmission chain involving inmate individuals and community. We stress the importance of tuberculosis genomic surveillance and the introduction of measures to interrupt the Mycobacterium tuberculosis transmission chain in this region. ### Competing Interest Statement The authors have declared no competing interest.

6560: Draft Genome Sequences of Seven Strains of Dickeya dadantii, a Quick Decline-causing Pathogen in Fruit Trees, Isolated from Japan
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Posted 25 May 2020

Draft Genome Sequences of Seven Strains of Dickeya dadantii, a Quick Decline-causing Pathogen in Fruit Trees, Isolated from Japan
100 downloads bioRxiv genomics

Takashi Fujikawa, Hiroe Hatomi, Nobuyoshi Ota

Plant pathogenic bacterium Dickeya dadantii causes quick decline in fruit trees (apple, Japanese pear, and peach). In this study, we report on the draft genome sequences of seven strains of D. dadantii isolated from fruit trees with typical quick decline symptoms in Japan. ### Competing Interest Statement The authors have declared no competing interest.

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