2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 3rd, 2025
Version: 1
Graduate School of Agricultural and Life Sciences, The University of Tokyo
genomics
biorxiv

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

Hirase, S.Open in Google Scholar•Makino, T.Open in Google Scholar•Takeuchi, T.Open in Google Scholar•Kadota, M.Open in Google Scholar•Kuraku, S.Open in Google Scholar•Kikuchi, K.Open in Google Scholar

Structural variation is increasingly recognized as a pivotal contributor to genomic diversity in marine invertebrates, yet its extent and evolutionary significance remain poorly characterized in many species. Haplotype-phased genome assembly is an excellent method for studying such variations by comparing homologous chromosomes. In this study, we constructed a haplotype-phased genome assembly for the western Pacific abalone, Haliotis gigantea, using high-fidelity (HiFi) long-read sequencing and high-resolution chromosome conformation capture (Hi-C) data. The primary and alternative assemblies each comprised 18 long scaffolds (>50 Mb), consistent with the species\' diploid chromosome number (2n = 36), and contained 96.5% and 96.2% complete single-copy Metazoa Benchmarking Universal Single-Copy Orthologs genes, respectively, indicating high assembly quality. Comparative analysis of the two haplotypes revealed three homologous chromosomes with large-scale non-syntenic regions caused by extensive segmental duplications, with each enriched in distinct gene domains. These non-syntenic chromosomes likely originated in abalone evolution, as they were conserved across both closely and distantly related species. Our findings highlight the evolutionary importance of non-syntenic structural variation in shaping genome architecture and suggest that such variation may play a broader role in functional diversification across abalones.

Similar Papers

biorxiv
Fri Apr 04 2025
Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis
The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell transcriptomics and chromatin accessibility, together with genome-wide profiling of DNA methylation and 3D chromosomal contact across mouse corticogenesis (E13-E18) to elucidate cell fate transitions. Us...
Shapira, Y.
•
Noack, F.
•
Vangelisti, S.
•
Chong, F.
...•
Bonev, B.
biorxiv
Fri Apr 04 2025
BRCA1 is a molecular correlate of cell proliferation in human brain development and in Group 3 and 4 medulloblastoma
The role of the BRCA1-mediated DNA damage repair pathway in regulating human brain development remains unknown, although it has been studied in mouse development. We report evidence for breast cancer type 1 susceptibility protein (BRCA1) being a molecular correlate of proliferation in human neural progenitor cells and in medulloblastoma (MB), a malignant pediatric hindbrain cancer whose cells rese...
Cheong, I.
•
Sun, X.
•
Lau, L.
•
Kishore, N.
...•
Pai, S.
biorxiv
Thu Apr 03 2025
Improving interpretability of transcription factor binding models with DNA shape features
Deep learning models in genomics that predict molecular phenotypes from DNA sequence traditionally focus on one-hot encoded representations. Here, we develop a novel model that extends this approach by incorporating DNA structural attributes indicative of local shape alongside canonical sequence inputs. This augmentation provides an additional axis for model interpretability and aids in identifyin...
Keivanfar, R. L.
•
Yang, F.
•
Pollard, K. S.
•
Ioannidis, N. M.
biorxiv
Thu Apr 03 2025
Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic plasticity and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to challenges in resolving repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telo...
Greif, G.
•
Diaz-Viraque, F.
•
Chiribao, M. L.
•
Sanz-Rodriguez, C.
•
Robello, C.
biorxiv
Thu Apr 03 2025
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus
Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates treatment of S. aureus infections. Understanding S. aureus population structure and the distribution of genetic lineages is central to understanding the biology, epidemiology, and pathogenesis of this organism. This study exploited a large, publicly available dataset of ...
Hadjirin, N. F.
•
Yassine, I.
•
Bray, J. E.
•
Maiden, M. C. J.
...•
Brueggemann, A. B.
biorxiv
Thu Apr 03 2025
Expression spectrum of TE-derived transcripts in human adult tissues
Abstract Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains ...
Miao, B.
•
Zhang, B.
•
WU, T. P.
•
Luo, X.
...•
Yang, Y.
biorxiv
Thu Apr 03 2025
Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature
Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to identify N. gonorrhoeae lineages in a consistent manner is essential for surveillance of this increasingly antimicrobial resistant organism, and to facilitate efficient...
Unitt, A.
•
Krisna, M. A.
•
Parfitt, K. M.
•
Jolley, K. A.
...•
Harrison, O. B.
biorxiv
Thu Apr 03 2025
Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach
Background Chromatin accessibility, measured via single-nucleus Assay for Transposase-Accessible Chromatin with sequencing (snATAC-seq), can reveal the underpinnings of transcriptional regulation across heterogeneous cell states. As the number and scale of snATAC-seq datasets increases, we need robust computational pipelines to integrate samples within a dataset and datasets across studies. These ...
Weinand, K.
•
Langan, E. M.
•
Curtis, M.
•
Raychaudhuri, S.
biorxiv
Thu Apr 03 2025
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at deciphering sequence features and grammar that underlie their spatiotemporal activity. To enable end-to-end enhancer modeling and design, we developed a software and modeling package, called CREsted. It combi...
Kempynck, N.
•
De Winter, S.
•
Blaauw, C. H.
•
Konstantakos, V.
...•
Aerts, S.