Biology subjects

Lledo, J.

Publications and source records attributed to Lledo, J..

5 recordsLinked to original sources

bioRxiv2025

An annotated chromosome-level genome assembly ofthe Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)

The genus Ostrinia (Lepidoptera: Crambidae) comprises two of the most important maize pests worldwide, the Asian and the European corn borers. Here, we present an annotated, chromosome-level genome assembly for the most closely related species, the Adzuki bean borer Ostrinia scapulalis, which feeds on various dicotyledon plants. The previous reference genome assembly for this species was generated from short-read sequencing data, resulting in high fragmentation and low completeness. Combining PacBio long read and Hi-C sequencing, we generated a 476 Mb genome with 48 contigs organised into 31 chromosomes (30 autosomes and one Z sex chromosome), with a contig N50 of 16.1 Mbp and BUSCO completeness exceeding 98%. We further combined published and novel RNA-seq data encompassing multiple life stages, tissues, and sexes to annotate 14,261 gene models, reaching a proteome BUSCO completeness of 95%. This highly contiguous reference genome assembly provides a much-improved resource for carrying comparative genomic approaches and better understanding speciation and host plant adaptation in the Ostrinia genus.

evolutionary biology↗

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↗

bioRxiv2024

Unveiling the genome assembly of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii

Root-knot nematodes of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to the agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control root-knot nematodes (RKN) is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on M. enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest implementing regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of Meloidogyne enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting genome assembly spans 273 Mbp with 556 contigs, a GC% of 30 {+/-} 0.042 and an N50 value of 2.11Mb, constituting a useful platform for comparative, population and functional genomics.

genomics↗

bioRxiv2023

Chromosome-level genome assembly of the European Green woodpecker Picus viridis

The European Green Woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here we assembled a highly contiguous genome assembly for this species using a combination of short and long reads sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a [~]30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the Picus viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers.

genomics↗

bioRxiv2022

Genome assembly of three Amazonian Morpho butterflyspecies reveals Z-chromosome rearrangements betweenclosely-related species living in sympatry

The genomic processes enabling speciation and the coexistence of species in sympatry are still largely unknown. Here we describe the whole genome sequencing and assembly of three closely-related species from the butterfly genus Morpho: Morpho achilles (Linnaeus, 1758), M. helenor (Cramer, 1776) and M. deidamia (Hubner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing colour pattern, suggesting local mimicry. By sequencing, assembling and annotating their genomes, we aim at uncovering pre-zygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the three species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in pre-zygotic isolation like genes controlling colour discrimination (L-opsin). Altogether, the assembly and the annotation of these three new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.

genomics↗