DOI: 10.5061/dryad.547d7wmmq
title: Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones (<em>Haliotis</em>)

description: 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 resource for studying
 such variations by comparing homologous chromosomes. Here, we focus on
 abalones (genus Haliotis) that are iconic marine invertebrates originating
 in the Cretaceous period. They have long drawn attention for their
 ecological roles, distinctive morphology, and cultural and economic value.
 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 (&gt;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 that may be related to adaptive
 evolution. These non-syntenic chromosomes likely originated in abalone
 evolution, as they were conserved across both closely and distantly
 related species, and led to the accumulation of duplicated genes in
 abalones. Our genome assembly highlights the evolutionary importance of
 non-syntenic structural variation in shaping genome architecture and
 suggests that such variation may play a broader role in functional
 diversification, adaptation, and consequent prosperity across abalones.
description: # Ancestral origin and structural characteristics of non-syntenic
 homologous chromosomes in abalones (*Haliotis*) Dataset DOI:
 [10.5061/dryad.547d7wmmq](https://doi.org/10.5061/dryad.547d7wmmq) ##
 Description of the data and file structure This includes fasta files and
 script files used for genome assembly of Haliotis gigantea and the
 downstream analyses based on the assembly. ### data.zip #####
 megai_hifi_only.bp.p_utg.fa.gz fasta file of unitig outputted by hifiasm
 ##### megai_hifi_only.bp.p_utg_HiC.fasta.gz fasta file of haplotype-phased
 genome assembly outputted by 3D-DNA (all scaffolds) ### scripts.zip (See
 Zenodo link in related works) ##### **HiC_scaffolding_main.sh** A script
 used for haplotype-phased genome assembly ##### repeat2braker2_main.sh A
 script used for repeat masking and gene annotation #####
 post_analyses_main.sh A script used for downstream analyses based on this
 assembly ##### BUSCO_synteny A folder including subscripts for
 constructing a synteny plot between primary and alternative assemblies
 based on BUSCO. ##### interproscan A folder including subscripts and
 materials for interprocan analyses. ##### MCscanX A folder including
 subscripts for MCscanX analyses. ##### NGenomeSyn A folder including
 subscripts for NGenomeSyn analyses. ##### nucmer A folder including
 subscripts for nucmer output.