Biology subjects

Iampietro, C.

Publications and source records attributed to Iampietro, C..

14 recordsLinked to original sources

bioRxiv2026

Cromosomal genomes assemblies of twelve sheep breeds

The sheep research community benefits from a genome assembly that has been refined over the last 15 years. However, the rich diversity of sheep breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, twelve breeds were selected to represent (mostly French) sheep genetic diversity: Basco-Bearnaise, Black Belly, Blanche du Massif Central, Corse, Ile de France, Lacaune, Manech Tete Noire, Noire du Velay, Ouessant, Rambouillet, Vendeen, Soay. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. The reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Lacaune breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 11 standard sheep assemblies that pave the way for pangenome construction and structural variant functional studies.

genomics↗

bioRxiv2026

Goat genome assemblies, nine breeds for pangenome contribution

The goat research community benefits from one of the most comprehensive livestock genome assemblies, ARS1. However, the rich diversity of goat breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate very high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, nine goat breeds were selected to represent French goat genetic diversity: Alpine, Boer, Creole, Fosses, Poitevine, Provencale, Pyreneenne, Rove and Saanen. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. There reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Alpine breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 8 standard goat assemblies that pave the way for pangenome construction and structural variant functional studies.

genomics↗

bioRxiv2026

New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

genomics↗

bioRxiv2025

Chromosome-scale genome assembly of Xiphinema index uncovers an unparalleled epigenetic toolkit in invertebrates

Nematodes constitute the most speciose animal phylum, occupying an exceptionally broad range of biomes and encompassing free-living microbe-feeders, predators, and notorious plant or animal parasites. However, the limited availability of genome-scale resources for early-branching nematode clades has constrained our understanding of the molecular determinants underlying these multiple evolutionary adaptations. Here, we present the genome of the plant-parasitic nematode Xiphinema index, constituting the first telomere-to-telomere assembly for the order Dorylaimida, an early-branching nematode lineage. Phylogenetic analyses reveal that horizontal gene transfers (HGT) have played a pivotal role in the emergence of plant parasitism in this phylum. Remarkably, we identify the first documented case of a plant-derived HGT in a nematode genome. This gene encodes a predicted secreted parasitic effector, underscoring the diversity of evolutionary events that contributed to the parasitic arsenal. Our results suggest that, beyond bacteria and fungi, plants themselves have provided crucial genes for parasitism that may now be used by the nematodes to manipulate them. Our comparative genomic analyses across more than 70 nematode species further uncover an unprecedented epigenetic toolkit in an invertebrate genome. Indeed, X. index harbors a complete set of canonical DNA methyltransferases, a full-length ATRX chromatin remodeler, and 3D-chromatin architectural CTCF protein coding homolog. Consistent with this repertoire, we detected methylation at CpG genome-wide, which inversely correlates with gene expression and chromatin accessibility. Together, these findings reveal a vertebrate-like epigenetic machinery in an early-branching nematode and call for a fundamental reassessment of the prevailing epigenetic paradigm in nematodes and, more broadly, in animals.

genomics↗

bioRxiv2025

Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

BackgroundThe current cattle reference genome, derived from a single Hereford cow, does not capture the full spectrum of genetic diversity present within the species. Moreover, detecting structural variations (SVs [≥] 50 nucleotides long) remains challenging using only standard approaches of either short or long-read sequence approaches against a linear reference genome. Recent advances in long-read sequencing technologies and graph-based assembly now enable the construction of breed-specific pangenomes, revealing previously uncharacterized genomic regions that may contribute to important agricultural traits. ResultsIn this study we constructed a cattle pangenome graph using 16 high-quality haplotype-resolved genome assemblies originating from nine breeds representing the diversity of French cattle populations, and including Yak (Bos grunniens) as a close outgroup species. Using a trio-based strategy combined with complementary sequencing technologies and bioinformatics methods, we identified and characterized 101,219 structural variations. Of these, 33,634 were classified as non-reference unique insertions (NRUIs), adding several megabases of novel genomic sequences absent from the current Hereford reference genome. Analysis of the distribution of these NRUIs revealed significant genome-wide enrichment within QTL regions associated with milk production and morphological traits, suggesting their contribution to the genetic basis of economically relevant phenotypes. Furthermore, their functional annotation highlighted two NRUIs located within the intronic regions of ARMH3 and EPHA5, both specific to the Normande breed and significantly associated with milk production and morphological traits, respectively. ConclusionsOur findings demonstrate the value of pangenome approaches to uncover functionally relevant SVs, particularly NRUIs, that are systematically not in the current reference genome. By linking these variants to economically important traits, our work underscores the need to incorporate breed diversity into future genomic analyses and reference-building efforts in cattle.

genetics↗

bioRxiv2025

Comprehensive detection of structural variations in long and short reads dataset of French cattle

Structural variants (SVs) correspond to different types of genomic variants larger than 50 bp. Many findings suggest the use of long rather than short reads to improve the accuracy of SV detection. Here, we present the results of an in-depth analysis for detection of SVs, mainly large insertions and deletions, in 14 French bovine breeds, based on whole-genome data comprising 176 long-read and 571 short-read samples, with 154 individuals having both long- and short-read data available. We first investigated possible biases on the performances of well-known SV detection tools, namely CUTESV, PBSV, and SNIFFLES, using long reads from different technologies, including PacBio HiFi, Oxford ONT, and PacBio CLR. We subsequently highlighted the abilities of tools for detecting SVs (DELLY, LUMPY, and MANTA) and for genotyping known SVs (GRAPHTYPER, SVTYPER, PARAGRAPH, and VG toolkit) using short-read data. We then show how the incremental composition of samples in the reference panel affected the SV genotyping for six validation individuals sequenced in short reads. We then searched for the optimal parameters and created the final SV reference panel consisting of 25,191 deletions and 30,118 insertions. Finally, we emphasized the landscape of the genotyped SVs segregating across 571 short-read individuals of 14 breeds.

genomics↗

bioRxiv2025

Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes

BackgroundThe current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represent a limit when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of short or long-read sequence mapping to the current bovine genome assembly. ResultsIn this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current Hereford reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic, including 21,840 insertions and 21,340 deletions. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed several well-known QTLs across the genome for the Holstein, Montbeliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed. This SV is a 6.2 kb deletion affecting the 5UTR, first exon and part of first intron of MATN3 gene, suggesting a potential regulatory and coding effect. ConclusionsOur study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits.

genetics↗

bioRxiv2025

Benchmarking long-read genome assemblers for three sequencing protocols and three agricultural species

Today, long read technologies make it possible to produce telomere-to-telomere genome assemblies. These assemblies permit more accurate whole genome analyses, including on repeated regions. The genome assembly process can chain several steps such as read correction, contigs assembly, contig polishing, scaffolding and gap filling, among others. Each step usually requires at least one software package, and input sequences. For the end user, it is not necessarily clear which combination of tools, together with read types, will work best for a given genome. In this work, we will focus on contig production, which is a central and complex task of the assembly process. It aims at producing the longest, errorless, sequences, called contigs, from reads. While it is possible to produce contigs from short reads, long reads are now widely preferred, since they produce much longer contigs. In this work, we evaluate several contig producing software packages (usually named assemblers), on long reads generated by two sequencers using three protocols, for three eukaryotic, complex species with different characteristics. Our aim is twofold. First, we would like to give readers insight on the impact of sequencing technology and assembler combinations, in order to help them make their choice for a given genome. Second, we would like to present different assembly metrics and provide a critical view on their interpretation.

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

New insights into past and future invasion of Drosophila suzukii using novel genomic resources and statistical methods to combine individual and pool sequencing data

Global change is accelerating biological invasions, making it crucial to understand how species adapt in new environments to improve management strategies. Genomic data provide valuable insights into adaptation through Genotype-Environment Association (GEA) studies, which identify genes and biological processes tied to invasion success, and through geometric Genomic Offset (gGO) statistics, which estimate genetic (mal)adaptation to new environments. Here, we investigate genetic adaptation in the invasive pest Drosophila suzukii using novel genomic resources and statistical methods. We use a new chromosome-level genome assembly and data from 37 populations, combining publicly available and newly generated pooled and individual sequencing data, analyzed with an enhanced version of BayPass software, tailored for such hybrid datasets. First, we identify genomic regions showing genetic differentiation between native and invasive populations. Then, using a GEA with 29 environmental covariates, we estimate the gGO between the source environments and the invaded areas, shedding light on the potential adaptive challenges D. suzukii faced during previous invasions. In addition, we estimate gGO for geographical areas not yet invaded to predict future invasion risks, and identify regions from which preadapted populations may originate. Our results reveal numerous genomic regions associated with the invasive status from genome scans. However, when considering broader patterns of adaptation to specific environmental variables through gGO analyses, we find that D. suzukii populations likely faced only limited adaptive challenges across their major invasion range, while certain uninvaded regions still remain at high risk of future invasion. Our study offers significant insights into D. suzukii adaptation and provides a practical population genomics framework to predict biological invasions, applicable to various species.

evolutionary biology↗

bioRxiv2024

metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads

BackgroundTo study communities of micro-organisms taxonomically and functionally, metagenomic analyses are now often used. If there is no reference gene catalogue, a de novo approach is required. Because genomes are easier to interpret than contigs, the recovery of metagenome-assembled genomes (MAGs) by binning of contigs from metagenomic data has recently become a common task for microbial studies. However, during this process, there is a significant loss of information between the assembly and the binning of contigs. This is why it is important to produce taxonomic and functional matrices for all contigs and not just those included in correct bins. In addition, Pacbio HiFi reads (long and of good quality) are now a possible, albeit more expensive, alternative to short Illumina reads. We therefore developed a workflow that is easy to install with dependencies fixed using singularity images and easy to use on a computing cluster, that is capable of analyzing either short or long reads, and that should allow analysis at the contig and/or bin level, depending on the users choice. Following is a presentation of metagWGS, a fully automated workflow for metagenomic data analysis. It uses a new tool for refining bins (called Binette) that we will demonstrate is more efficient than competing tools. MethodsmetagWGS is a Nextflow workflow distributed with two singularity images and complete documentation to facilitate its installation and use. Because the main original features of metagWGS concern binning (short and long reads) and the analysis of HiFi reads, we compared metagWGS with the MAG construction workflow proposed by PacBio to a public dataset used by Pacbio to promote its workflow. ResultsmetagWGS differs from existing workflows by (i) offering flexible approaches for the assembly; (ii) supporting short reads (Illumina) or PacBio HiFi reads; (iii) combining multiple binning algorithms with a new bin refinement tool, referred to as "Binette", to achieve high-quality genome bins; and (iv) providing taxonomic and functional annotation for all genes, all contigs built and bins. metagWGS produces more medium (708) and high-quality (255) bins on 11 public metagenomic samples from human gut data than the Pacbio HiFi dedicated workflow, referred to as the HiFi-MAGS-pipeline (659 medium quality bins and 231 high quality bins), primarily due to the better performance of Binette.

bioinformatics↗

bioRxiv2023

Massive detection of cryptic recessive genetic defects in cattle mining millions of life histories

We present a data-mining framework designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

genetics↗

bioRxiv2022

Genome structures resolve the early diversification of teleost fishes

Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies. One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.

evolutionary biology↗

bioRxiv2022

An ancient truncated duplication of the anti-Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex determination system. Here, we generated novel genomic resources for 12 Pangasiid species and provided a first characterization of their SD system. Based on an Oxford Nanopore long-read chromosome-scale high quality genome assembly of the striped catfish Pangasianodon hypophthalmus, we identified a duplication of the anti-Mullerian hormone receptor type II gene (amhr2), which was further characterized as being sex-linked in males and expressed only in testicular samples. These first results point to a male-specific duplication on the Y chromosome (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Short-read genome sequencing and reference-guided assembly of 11 additional Pangasiid species, along with sex-linkage studies, revealed that this truncated amhr2by duplication is also conserved as a male-specific gene in many Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiid catfishes, a finding that highlights the recurrent usage of the transforming growth factor {beta} pathway in teleost sex determination and brings another empirical case towards the understanding of the dynamics or stability of sex determination systems.

genomics↗