DOI: 10.5061/dryad.ncjsxkt65
title: Denovo assembly of a Japan Sea stickleback (Gasterosteus nipponicus) and a Japanese Pacific Ocean lineage of three-spined stickleback (Gasterosteus aculeatus)

description: DNA within the nucleus is organized into a well-regulated
 three-dimensional (3D) structure. However, it remains largely elusive how
 such 3D genome structures influence speciation processes. Recent studies
 have shown that 3D genome structures influence mutation rates, including
 the occurrence of chromosomal rearrangement. For example, breakpoints of
 chromosomal rearrangements are often enriched at topologically associating
 domain (TAD) boundaries. Here, we hypothesized that TAD structures may
 constrain the location of chromosomal inversions and thereby shape the
 genomic landscape of divergence between species with ongoing gene flow,
 because inversions can contribute to barriers to gene flow. To test this
 hypothesis, we used a Japanese stickleback species
 pair, Gasterosteus nipponicus (Japan Sea stickleback)
 and G. aculeatus (three-spined stickleback). We first constructed
 high-quality genome assemblies of both species using PacBio HiFi and
 Dovetail Omni-C technologies and identified several chromosomal
 inversions. Second, population genomic analyses revealed higher genetic
 differentiation in inverted regions than in colinear regions and no gene
 flow within inversions, which contrasts with significant gene flow in
 colinear regions. Third, using Hi-C data, we revealed 3D genome structures
 of sticklebacks, such as A/B compartments and TAD. Finally, we found that
 inversion breakpoints were enriched at TAD boundaries. Thus, our study
 demonstrate that 3D genome constrains breakpoints of inversions that can
 act as barriers to gene flow in the stickleback. Further integration of 3D
 genome analyses with population genomics has the potential to provide
 novel insights into the mechanisms by which 3D genome influences
 speciation processes.
description: # Genome assemblies of Gasterosteus nipponicus and Gasterosteus aculeatus
 used in "3D genome constrains breakpoints of inversions that can act
 as barriers to gene flow in the stickleback" We assembled genomes of
 the two Gasterosteus species in Japan; G. nipponicus and G. aculeatus. We
 used PacBio HiFi and Dovetail Omni-C technologies to make chromosome-scale
 assemblies. ## General information [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.ncjsxkt65) 1. Title of Dataset:
 Genome assemblies of Gasterosteus nipponicus and Gasterosteus aculeatus 2.
 Author Information * Principal Investigator Name: Jun Kitano Institution:
 National Institute of Genetics Address: Mishima, Shizuoka, Japan Email:
 [jkitano@nig.ac.jp](mailto:jkitano@nig.ac.jp) * Data curation Name: Yo
 Yamasaki Institution: National Institute of Genetics Address: Mishima,
 Shizuoka, Japan Email: [yamasaki@nig.ac.jp](mailto:yamasaki@nig.ac.jp) 1.
 Date of sample collection * G. nipponicus: 15/5/2023 * G. aculeatus:
 24/5/2022 1. Geographic location of data collection * G. nipponicus:
 Hamanaka, Hokaido, Japan * G. aculeatus: Akkeshi, Hokkaido, Japan 1.
 Information about funding sources that supported the collection of the
 data * JSPS Kakenhi (22H04983, 20J01503, 21H02542, and 22KK0105) * JST
 CREST (JPMJCR20S2) ## File extension and its contents "XXX" in
 the following descriptions indicates prefix of the file. * XXX.fa\ FASTA
 file of genome assembly. * XXX.masked.fa\ Following regions of XXX.fa were
 hardmasked: highly repetitive regions on chrXII and chrXXI,
  puseudo-autosomal regions, neo-Y part of the fused Y chromosome of G.
 nipponicus. * XXX.hardmasked.fa\ Repeat masked XXX.fa by RepeatModeler and
 RepeatMasker pipeline. Repetitive regions were masked by N. *
 XXX.softmasked.fa\ Repeat masked XXX.fa RepeatModeler and RepeatMasker
 pipeline. Repetitive regions were masked by small letters. * XXX.gff\
 Annotation of gene positions in XXX.fa. * XXX.centromere.bed\ Annotation
 of centromere positions in XXX.fa. * XXX.GAP.bed\ Positions of assembly
 gaps indicated by N. * XXX.compartment_KR_100kb.bed\ Regions of A/B
 compartment. Calculation was conducted with Knight-Ruiz normalization and
 100kb bin by FAN-C v0.9.1. * POvsJS_inversions.XXcoordinate.masked.bed\
 Inversions detected by G. aculeatus vs G. nipponicus alignment. One
 inversion found on highly repetitive region on chrXXI was removed. ###
 Note * Mean of columns in XXX.compartment_KR_100kb.bed is as follows; ```
 - 1st column: chromosome - 2nd column: domain start position - 3rd column:
 domain end position - 4th column: assignment of compartment types for the
 domain (A or B) - 5th column: the average eigenvector entry values of all
 bins in the domain - 6th column: no entry ``` * XXX.TAD_25kb_Level1.bed\
 Regions of topologically associated domains (TAD) estimated by
 SpectralTAD. Only primary TADs are included. * XXX.TAD_25kb_Level2.bed
 Regions of topologically associated domains (TAD) estimated by
 SpectralTAD. TADs which estimated as secondary TAD are included. Some are
 completely matched with primary TADs. ### Note * Mean of columns in
 XXX.TAD_25kb_Level1.bed and XXX.TAD_25kb_Level2.bed is as follows; ``` -
 1st column: chromosome - 2nd column: domain start position - 3rd column:
 domain end position - 4th column: TAD hierarchy. "1" indicate
 primary TAD, "2" indicate secondary TAD ``` ## Description of
 the data and file structure There are six groups of datasets. Details of
 data collection and analysis methods are described in the manuscripts. ###
 1. JSv20240517\_dryad Genome assembly of G. nipponicus. We selected one
 chromosome-scale haplotype with fewer gaps for each autosome, and
 chromosome-scale X and Y_IX chromosomes were also selected from following
 phased assembly sets (i.e. JS_male_hap1.v20240517.fa and
 JS_male_hap2.v20240517.fa) #### Files * JSv20240517.fa *
 JSv20240517.masked.fa\ Some highly repetitive regions masked
 JSv20240517.fa. Masked regions were as follows: first 3,207,000 bp of
 chrY_IX, 21,72,300-44,829,387 bp region on the chrY_IX,
 20,676,000-21,892,999 bp and 22,110,000-29,005,999 bp on chrXII,
 580,259-3,826,000 bp region of chrXXI * JSv20240517.hardmasked.fa *
 JSv20240517.softmasked.fa * JSv20240517.gff * JSv20240517.centromere.bed *
 JSv20240517.GAP.bed * JSv20240517.compartment_KR_100kb.bed *
 JSv20240517.TAD_25kb_Level1.bed * JSv20240517.TAD_25kb_Level2.bed *
 POvsJS_inversions.JScoordinate.masked.bed ### 2.
 Gnipponicus\_male\_hap1\_20240517\_dryad Haplotype set 1 of G. nipponicus.
 Included sex chromosome is X (chrXIX). #### Files *
 JS_male_hap1.v20240517.fa * JS_male_hap1.v20240517.hardmasked.fa *
 JS_male_hap1.v20240517.softmasked.fa * JS_male_hap1.v20240517.gff ### 3.
 Gnipponicus\_male\_hap2\_20240517\_dryad Haplotype set 2 of G. nipponicus.
 Included sex chromosome is Y (chrY_IX). #### Files *
 JS_male_hap2.v20240517.fa * JS_male_hap2.v20240517.hardmasked.fa *
 JS_male_hap2.v20240517.softmasked.fa * JS_male_hap2.v20240517.gff ### 4.
 POv20240517\_dryad Genome assembly of G. aculeatus. We selected one
 chromosome-scale haplotype with fewer gaps for each autosome, and
 chromosome-scale X and Y chromosomes were also selected from following
 phased assembly sets (i.e. PO_male_hap1.v20240517.fa and
 PO_male_hap2.v20240517.fa). #### Files * POv20240517.fa *
 POv20240517.masked.fa\ Some highly repetitive regions masked
 POv20240517.fa. Masked regions were as follows: the first 3,236,000 bp of
 chrY, 21,026,999-23,662,723 bp on chrXII, 4,361,000-8,588,000 bp region of
 chrXXI * POv20240517.hardmasked.fa * POv20240517.softmasked.fa *
 POv20240517.gff * POv20240517.centromere.bed * POv20240517.GAP.bed *
 POv20240517.compartment_KR_100kb.bed * POv20240517.TAD_25kb_Level1.bed *
 POv20240517.TAD_25kb_Level2.bed *
 POvsJS_inversions.POcoordinate.masked.txt ### 5.
 Gaculeatus\_male\_hap1\_20240517\_dryad Haplotype set 1 of G. aculeatus.
 Included sex chromosome is Y (chrY). #### Files *
 PO_male_hap1.v20240517.fa * PO_male_hap1.v20240517.hardmasked.fa *
 PO_male_hap1.v20240517.softmasked.fa * PO_male_hap1.v20240517.gff ### 6.
 Gaculeatus\_male\_hap2\_20240517\_dryad Haplotype set 2 of G. aculeatus.
 Included sex chromosome is X (chrXIX). #### Files *
 PO_male_hap2.v20240517.fa * PO_male_hap2.v20240517.hardmasked.fa *
 PO_male_hap2.v20240517.softmasked.fa * PO_male_hap2.v20240517.gff ##
 Sharing/Access information 1. Licenses/restrictions placed on the data:
 CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that
 cite or use the data:\ Yo Y. Yamasaki, Atsushi Toyoda, Mitsutaka Kadota,
 Shigehiro Kuraku, Jun Kitano 3D genome constrains breakpoints of
 inversions that can act as barriers to gene flow in the stickleback ###
 Links to other publicly accessible locations of the data: * All raw
 sequence data are available from DDBJ: G. nipponicus HiFi and Omni-C data,
 PRJDB19945; G. aculeatus HiFi and Omni-C data, PRJDB19949; iconHi-C for G.
 nipponicus and G. aculeatus, PRJDB19958.