Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.10.31.564804

Unraveling the Genomic and Environmental Diversity of the Ubiquitous Solirubrobacter

Jara-Servin, A.·Mejia, G.·Romero, M. F.·Peimbert, M.·Alcaraz, L. D.
View original source ↗Export metadata ↓

Abstract

2.Solirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions of Solirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) of Solirubrobacter in Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity of Solirubrobacter across various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlighting Solirubrobacters adaptability. We observed that Solirubrobacters prevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity, Solirubrobacter might be a versatile yet overlooked keystone species in its environments, meriting further recognition and study. 3. Impact statementThis study explored the enigmatic world of Solirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets of Solirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed that Solirubrobacter environmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants. 4. Data summaryData, scripts and statistical analysis available in GitHub: https://github.com/genomica-fciencias-unam/Solirubrobacter Sequences, phylogenetic analysis, raw data structures: https://doi.org/10.6084/m9.figshare.24446521 16S rRNA gene raw data: https://www.ncbi.nlm.nih.gov/sra/PRJNA603586 https://www.ncbi.nlm.nih.gov/sra/PRJNA603590 Shotgun metagenomes: https://www.ncbi.nlm.nih.gov/bioproject/603603 All supporting data, code, and protocols are within the article, supplementary files, and described repositories.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jara-Servin, A., Mejia, G., Romero, M. F., Peimbert, M., Alcaraz, L. D.. 2023-11-02. Unraveling the Genomic and Environmental Diversity of the Ubiquitous Solirubrobacter. https://doi.org/10.1101/2023.10.31.564804

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

PfPHAST: Plasmodium falciparum Public Health Amplicon Sequencing Tool, a Streamlined Panel for Malaria Genomic Surveillance

Genomic tools can support malaria control policy through surveillance of Plasmodium falciparum populations, tracking antimalarial drug resistance, pfhrp2/3 deletions that compromise rapid diagnostic tests, and selection at the circumsporozoite protein (PfCSP) vaccine target, as well as through molecular correction of therapeutic efficacy studies (TES). Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing (MAD4HatTeR), a comprehensive amplicon sequencing panel covering up to 276 targets, supports these applications but is tailored to research rather than routine programmatic use. We developed P. falciparum Public Health Amplicon Sequencing Tool (PfPHAST), a 56-target derivative of MAD4HatTeR spanning drug resistance loci, pfhrp2/3 deletion, PfCSP genotyping, non-falciparum species identification, and 20 high-heterozygosity microhaplotype loci for TES classification. We compared PfPHAST and MAD4HatTeR using laboratory strain controls, including two-strain dilution series and a five-strain mixture, across parasite densities of 100 to 10,000 parasites/L. At matched per-target depth, PfPHAST achieved a higher quality-control pass rate than MAD4HatTeR (94.4% versus 90.0%) and distributed reads more evenly across targets. The panels showed comparable recall and precision for drug resistance codons and microhaplotypes, reaching near-complete recall above 40% within-sample allele frequency (WSAF) at all densities, with reduced sensitivity for minor alleles below 10% WSAF at low parasite density in both panels. Observed and expected WSAF correlated strongly for both panels, and both resolved a five-strain polyclonal mixture, including a 5% minor strain. By concentrating sequencing capacity on targets of greatest programmatic relevance, PfPHAST offers a scalable, lower-cost alternative to comprehensive research panels without sacrificing performance on shared targets, complementing MAD4HatTeR for routine molecular malaria surveillance.

genomics↗
bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗