Biology subjects

Ben Hamadou, A.

Publications and source records attributed to Ben Hamadou, A..

5 recordsLinked to original sources

bioRxiv2026

Systematic benchmarks reveal DNA polymerase combinations for high-quality genome assembly

Background: A fundamental challenge in biodiversity genomics is generating long-read sequencing data and high-quality genome assemblies from samples lacking gold-standard flash-frozen tissue, including ethanol-preserved specimens, minimally invasive biopsies, and small-bodied organisms. Amplification-based library preparation enables long-read sequencing of such samples, but assembly quality critically depends on the polymerase used for amplification. Results: We present a systematic benchmark of eleven long-range DNA polymerases for PacBio HiFi sequencing and genome assembly across three taxonomically diverse species: a springtail, a sea slug, and a bat. We show that polymerase choice substantially affects assembly contiguity and gene completeness, primarily caused by polymerase-intrinsic GC-dependent amplification bias and read coverage heterogeneity. Five polymerases consistently produced assemblies with comparatively high contiguity and completeness, with some enzymes outperforming the polymerase currently used in the PacBio Ampli-Fi protocol. Importantly, combining reads amplified with different polymerases frequently resulted in superior assemblies, because polymerases complement each other by covering regions where others drop out. Combining reads amplified with different polymerases, we generated haplotype-resolved assemblies of the ~1 Gb giant springtail and ~2 Gb bat genome and improved the sea slug reference genome. Using the human GIAB benchmark, we further show that optimized amplification strategies improve variant-calling accuracy, highlighting their utility in medical and clinical research. To facilitate polymerase benchmarking across additional taxa, we provide the polymeval pipeline (https://github.com/casparbein/polymeval), which automates the computational workflow. Conclusion: Our study demonstrates that optimized amplification-based HiFi sequencing generates assemblies with >1 Mb contig N50 and >90% gene completeness, providing a toolkit to produce long-read genome assemblies from challenging samples.

genomics↗

bioRxiv2025

A Prelude to Conservation Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel (Pteromyini: Pteromys volans)

The Siberian flying squirrel (Pteromys volans) represents the only European Pteromyini species. Thus, it is biogeographically unique due to its specialised anatomy and biology as a volant rodent. As a result of habitat fragmentation and destruction, Siberian flying squirrels experience severe and ongoing population declines throughout most of their distribution. While considered Least Concern throughout their immense Eurasian distribution, this species is red-listed as Vulnerable and even Critically Endangered in parts of its range. More knowledge about the population structure and overall biology is needed to improve conservation efforts for this umbrella and flagship species of old-growth boreal forests. Here, we present the first chromosome-level genome assembly of any Pteromyini, represented by P. volans (Uoulu_pteVol_1.0). The final assembly has a total length of 2.85 Gbp in 19 chromosome-scale scaffolds with only minor differences in the chromosomal structure compared to other Sciuridae. All chromosome-scale scaffolds show indications for telomeres at both ends; the N50 value and busco as well as k-mer completeness scores are high with 157.39 Mbp and 97 - 99 %, respectively, indicating chromosome-level quality of the assembly. Based on whole-genome data from 17 rodent species, P. volans clusters according to known evolutionary relationships. Additionally, we present a new 16,511 bp long mitogenome unveiling differences from known conspecific mitogenomes. We propose the utility of the new reference genome for further research and development of conservation-applied genetic methods.

genomics↗

bioRxiv2024

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome

BackgroundThe time required for sequencing and de novo assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian de novo genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a model: The Whippet. FindingsWe present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%. ConclusionsSequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.

genomics↗

bioRxiv2024

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BackgroundSequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data. ResultsIn this study, we present the chromosome-level genome assembly and annotation of the marine sacoglossan species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the Long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are 100-fold and 4-fold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa. We detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds. ConclusionsWe can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

genomics↗

bioRxiv2022

A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

genomics↗