Gene annotation and RepeatMasker outputs for the Japanese eel (<i>Anguilla japonica</i>) chromosome-scale genome assembly J-eel 3.4

<p dir="ltr">Companion data and reproducibility files for the chromosome-scale genome assembly of the Japanese eel (<i>Anguilla japonica</i>), assembly version J-eel 3.4, described in the Scientific Data Data Descriptor by Nomura and Fujiwara.</p><p><br></p><p dir="ltr">Repeat annotation</p><p dir="ltr">J-eel3.4.fa.out.gz, J-eel3.4.fa.out.gff.gz, and J-eel3.4.fa.masked.gz: RepeatMasker tabular output, GFF3 annotation, and soft-masked genome for the repeat analysis reported in the Data Descriptor (RepeatModeler 2.0.4 with -LTRStruct; RepeatMasker 4.1.4 in default mode with rmblastn 2.13.0+; de novo library eel3.4-families.fa).</p><p><br></p><p dir="ltr">eel3.4-families.fa: the de novo repeat-family library used for that analysis.</p><p><br></p><p dir="ltr">rmod.log: the RepeatModeler execution log.</p><p><br></p><p dir="ltr">README_repeat_annotation_20260905.md, REPEAT_RUN_PROVENANCE_20260905.tsv, and REPEAT_UPLOAD_MANIFEST.tsv: methods, run-identification, and checksum documentation for the repeat files.</p><p><br></p><p dir="ltr">Gene annotation</p><p dir="ltr">J-eel3.4.gene_annotation.gff.gz: gene annotation in GFF3 format.</p><p><br></p><p dir="ltr">Assembly history and reproducibility</p><p dir="ltr">J_eel3_4_revision_reproducibility_package_fig5_update_20260914.zip: reconstructed assembly provenance, software versions and parameters, manual-curation records, compact summaries and command records for mapping, controlled raw- and trimmed-read GenomeScope2 analyses, Merqury, BUSCO, annotation QC, assembly self-alignment, read-backed base-accuracy analyses, and the source evidence used to generate revised Fig. 5.</p><p><br></p><p dir="ltr">J-eel3.1.fa.gz, J-eel3.2.fa.gz, and J-eel3.3.fa.gz: intermediate assembly FASTA files used to document the assembly history.

Checksums are included in the reproducibility archive.</p><p><br></p><p dir="ltr">The deposited J-eel 3.4 sequence set contains 19 chromosome-scale sequences, one mitochondrial sequence, and 87 unplaced sequences. DDBJ has issued Finished Level sequence accessions AP053221–AP053327 under submission NSUB003923; these records replace the earlier WGS records BAAJLN010000001–BAAJLN010000107. Raw sequencing data are linked to BioProject PRJDB18266 and INSDC study DRP018890.</p><p><br></p><p dir="ltr">Large primary read and alignment files are not duplicated in this record.