Biology subjects

Blin, A.

Publications and source records attributed to Blin, A..

7 recordsLinked to original sources

bioRxiv2025

Evaluation of the Ultima Genomics UG 100™ sequencing platform for clinical services

The steep reduction in the cost of genome sequencing started with the introduction of Solexa Sequencing-By-Synthesis technology in 2006 has plateaued recently due to technical limitations in the use of closed flowcells and to the cost of reagents. The Ultima Genomics UG 100 is the first sequencing machine to lower the cost of human genome sequencing to 80$. However, technical limitations in resolving long homopolymer regions undermine the application of this technology to short variant calling in clinical settings. Here, we evaluate the ability of UG 100 to identify short variants in relation to its suitability for clinical accreditation, by comparing it with the Illumina NovaSeq 6000 Systems platform. We focus specifically on the small variant calling performance in long homopolymer regions, both genome-wide and in relation to a set of medically-relevant genes that are challenging to sequence. Our analysis aims at supporting clinicians in determining whether the UG 100 platform is well-suited for their studies, and to guide clinical sequencing centers in evaluating the adoption of this emerging technology.

bioinformatics↗

bioRxiv2024

Draft genome and transcriptomic sequence data of three invasive insect species

Cydalima perspectalis (the box tree moth), Leptoglossus occidentalis (the western conifer seed bug), and Tecia solanivora (the Guatemalan tuber moth) are three economically harmful invasive insect species. This study presents their genomic and transcriptomic sequences, generated through whole- genome sequencing, RNA-seq transcriptomic data, and Hi-C sequencing. The resulting genome assemblies exhibit good quality, providing valuable insights into these species. The genome sizes are 500.4 Mb for C. perspectalis, 1.74 Gb for L. occidentalis, and 623.3 Mb for T. solanivora. These datasets are available in the NCBI Sequence Read Archive (BioProject PRJNA1140410) and serve as essential resources for population genomics studies and the development of effective pest management strategies, addressing significant gaps in the understanding of invasive insect species.

genomics↗

bioRxiv2024

Unraveling genetic load dynamics during biological invasion: insights from two invasive insect species

Many invasive species undergo a significant reduction in genetic diversity, i.e. a genetic bottleneck, in the early stages of invasion. However, this reduction does not necessarily prevent them from achieving considerable ecological success and becoming highly efficient colonizers. Here we investigated the purge hypothesis, which suggests that demographic bottlenecks may facilitate conditions (e.g., increased homozygosity and inbreeding) under which natural selection can purge deleterious mutations, thereby reducing genetic load. We used a transcriptome-based exome capture protocol to identify thousands of SNPs in coding regions of native and invasive populations of two highly successful invasive insect species, the western corn rootworm (Chrysomelidae: Diabrotica virgifera virgifera) and the harlequin ladybird (Coccinelidae: Harmonia axyridis). We categorized and polarized SNPs to investigate changes in genetic load between invasive populations and their sources. Our results differed between species. In D. virgifera virgifera, although there was a general reduction in genetic diversity in invasive populations, including that associated with genetic load, we found no clear evidence for purging of genetic load, except marginally for highly deleterious mutations in one European population. Conversely, in H. axyridis, the reduction in genetic diversity was minimal, and we detected signs of genetic load fixation in invasive populations. These findings provide new insights into the evolution of genetic load during invasions, but do not offer a definitive answer to the purge hypothesis. Future research should include larger genomic datasets and a broader range of invasive species to further elucidate these dynamics.

evolutionary biology↗

bioRxiv2020

Analysis Of Polycerate Mutants Reveals The Evolutionary Co-Option Of HOXD1 To Determine The Number And Topology Of Horns In Bovidae

In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as headgear, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

genomics↗

bioRxiv2020

Shifts from pulled to pushed range expansions caused by reductions in connectedness

AO_SCPLOWBSTRACTC_SCPLOWRange expansions are key processes shaping the distribution of species; their ecological and evolutionary dynamics have become especially relevant today, as human influence reshapes ecosystems worldwide. Many attempts to explain and predict range expansions assume, explicitly or implicitly, so-called "pulled" expansion dynamics, in which the low-density edge populations provide most of the "fuel" for the species advance. Some expansions, however, exhibit very different dynamics, with high-density populations behind the front "pushing" the expansion forward. These two types of expansions are predicted to have different effects on e.g. genetic diversity and habitat quality sensitivity. However, empirical studies are lacking due to the challenge of generating reliably pushed vs. pulled expansions in the laboratory, or discriminating them in the field. We here propose that manipulating the degree of connectivity among populations may prove a more generalizable way to create pushed expansions. We demonstrate this with individual-based simulations as well as replicated experimental range expansions (using the parasitoid wasp Trichogramma brassicae as model). By analyzing expansion velocities and neutral genetic diversity, we showed that reducing connectivity led to pushed dynamics. Low connectivity alone, i.e. without density-dependent dispersal, can only lead to "weakly pushed" expansions, where invasion speed conforms to pushed expectations, but the decline in genetic diversity does not. In empirical expansions however, low connectivity may in some cases also lead to adjustments to the dispersal-density function, recreating "classical" pushed expansions. In the current context of habitat loss and fragmentation, we need to better account for this relationship between connectivity and expansion regimes to successfully predict the ecological and evolutionary consequences of range expansions.

ecology↗

bioRxiv2019

An evaluation of pool-sequencing transcriptome-based exon capture for population genomics of non-model species

AO_SCPLOWBSTRACTC_SCPLOWExon capture coupled to high-throughput sequencing constitutes a cost-effective technical solution for addressing specific questions in evolutionary biology by focusing on expressed regions of the genome preferentially targeted by selection. Transcriptome-based capture, a process that can be used to capture the exons of non-model species, is use in phylogenomics. However, its use in population genomics remains rare due to the high costs of sequencing large numbers of indexed individuals across multiple populations. We evaluated the feasibility of combining transcriptome-based capture and the pooling of tissues from numerous individuals for DNA extraction as a cost-effective, generic and robust approach to estimating the variant allele frequencies of any species at the population level. We designed capture probes for [~]5 Mb of chosen de novo transcripts from the Asian ladybird Harmonia axyridis (5,717 transcripts). We called [~]300,000 bi-allelic SNPs for a pool of 36 non-indexed individuals. Capture efficiency was high, and pool-seq was as effective and accurate as individual-seq for detecting variants and estimating allele frequencies. Finally, we also evaluated an approach for simplifying bioinformatic analyses by mapping genomic reads directly to targeted transcript sequences to obtain coding variants. This approach is effective and does not affect the estimation of SNP allele frequencies, except for a small bias close to some exon ends. We demonstrate that this approach can also be used to predict the intron-exon boundaries of targeted de novo transcripts, making it possible to abolish genotyping biases near exon ends.

genomics↗

bioRxiv2017

Colonization History Of The Western Corn Rootworm (Diabrotica virgifera virgifera) In North America: Insights From Random Forest ABC Using Microsatellite Data

First described from western Kansas, USA, the western corn rootworm, Diabrotica virgifera virgifera, is one of the worst pests of maize. The species is generally thought to be of Mexican origin and to have incidentally followed the expansion of maize cultivation into North America thousands of years ago. However, this hypothesis has never been investigated formally. In this study, the genetic variability of samples collected throughout North America was analysed at 13 microsatellite marker loci to explore precisely the population genetic structure and colonization history of D. v. virgifera. In particular, we used up-to-date Approximate Bayesian Computation methods based on random forest algorithms to test a Mexican versus a central-USA origin of the species, and to compare various possible timings of colonization. This analysis provided strong evidence that the origin of D. v. virgifera was southern (Mexico, or even further south). Surprisingly, we also found that the expansion of the species north of its origin was recent - probably not before 1100 years ago - thus indicating it was not directly associated with the early history of maize expansion out of Mexico, a far more ancient event.

evolutionary biology↗