Biology subjects

Sollitto, M.

Publications and source records attributed to Sollitto, M..

5 recordsLinked to original sources

bioRxiv2026

Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs

Recent developments in genome sequencing and assembly technologies have enabled the automated assembly of vertebrate chromosomes from telomere to telomere. However, for some long, highly similar repeats, genome assemblers may lack sufficient information to unambiguously resolve the sequence, leaving tangles in the assembly graph and gaps in the final assembly. In recently published genomes, such gaps are often closed by manual graph curation, a process that is labor-intensive, error-prone, and sometimes infeasible. This can leave important genomic repeats, such as recently duplicated genes, misassembled or excluded from the final assembly. Here we present the Trivial Tangle Traverser (TTT) algorithm that finds optimized resolutions of assembly graph tangles. TTT uses depth of coverage and read-to-graph alignment information in a two-stage process to identify evidence-based traversals that are consistent with the underlying data. First, sequence multiplicities are estimated through mixed-integer linear programming, after which an Eulerian path is found in the derived multigraph and optimized through a gradient-descent-like approach. We evaluate TTT traversals on the HG002 human reference genome and demonstrate its use to characterize a previously unassembled amplified gene array in the zebra finch genome. AvailabilityTTT is available at https://github.com/marbl/TTT

bioinformatics↗

bioRxiv2026

The Distribution and Diversity of LuxI/LuxR Quorum Sensing Systems in Proteobacteria (Pseudomonadota)

In Pseudomonadota (formerly Proteobacteria), the N-acyl homoserine lactone (AHL) quorum sensing (QS) system involves LuxI/LuxR modules, where LuxI synthesizes AHLs and LuxR-AHL regulates target gene expression. Despite extensive characterization in many bacterial species, the distribution, genomic organization, and taxonomic comprehensiveness of LuxI/R systems remains unexplored at scale. In this study, we present the first large-scale, genome-wide assessment of LuxI/R QS systems across over 30,000 publicly available genomes at chromosome-level and manually curated spanning 938 genera. Using pfam-based domain annotation, we mapped the distribution, occurrence, and copy number of LuxI/R homologs. LuxI/R systems were identified in [~]32% of surveyed genera, with notable enrichment in symbiotic and plant-associated taxa such as Rhizobium, Burkholderia, and Pseudomonas, and remarkable conservation in pathogenic taxa such as Yersinia, Aeromonas, and Acinetobacter. Conversely, entire genera, including Escherichia, Salmonella, and Klebsiella, among others, lacked LuxI/R systems across all sequenced strains, suggesting evolutionary loss, niche-specific signaling strategies, or reliance on alternative currently unknown communication systems. Our results also revealed genera with multiple, non-redundant and taxonomically not-related LuxI/R pairs per genome, indicating modular architectures and unpredictable events of horizontal gene transfer events and genetic arrangements. This study delineates the complex distribution and conservation patterns of LuxI/R circuits, providing a resource for future studies into AHL-mediated QS regulation, and microbial community interactions across diverse environments. HighlightsO_LILuxI/LuxR quorum-sensing systems show an uneven distribution across Pseudomonadota (formerly Proteobacteria) and evolved through expansion, conservation, and loss, reflecting diverse ecological strategies C_LIO_LIAmong [~]31,815 high-quality Proteobacterial genomes, 6,400 (20.1%), corresponding to C_LIO_LI[~]303 genera ([~]32%), encoded at least one complete LuxI/LuxR pair. C_LIO_LIMultiple, highly variable LuxI/R copies, up to seven per genome, reveal extensive horizontal gene transfer and mosaic evolutionary histories, especially in rhizobial and plant-associated taxa. C_LIO_LIPhylogenetic analyses distinguish genera with conserved QS architectures from those with fragmented, lineage-independent LuxI/R repertoires, possibly highlighting diverse ecological pressures shaping QS. C_LI

microbiology↗

bioRxiv2025

The complete genome of a songbird

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding [~]90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

genomics↗

bioRxiv2025

Coexisting with humans: genomic and behavioural consequences in a small and isolated bear population

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

genomics↗

bioRxiv2025

Evaluation of sequencing reads at scale using rdeval

MotivationLarge sequencing data sets are produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical. ResultsAs part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community need for efficient sequencing data evaluation by developing rdeval, a standalone tool to quickly compute and dynamically display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in read sketches, with dramatic compression gains. Statistics can then be efficiently recalled from sketches for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain is marginal, and BAM achieves the best compromise between data compression and accessing speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdevals functionalities using human and VGP read data from different sequencing platforms and species. For PacBio long-read sequencing, our analysis shows dramatic improvements both in read length and quality over time, and a benefit of additional coverage for genome assembly. Availability and implementationRdeval is implemented in C++ for data processivity and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available using ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates. Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗