DOI: 10.5061/dryad.70rxwdc48
title: Genomic insights into the chromosomal elongation in a family of Collembola

description: Collembola is a highly diverse and abundant group of soil arthropods with
 chromosome numbers ranging from 5 to 11. Previous karyotype studies
 indicated that the Tomoceridae family possesses an exceptionally long
 chromosome. To better understand chromosome size evolution in Collembola,
 we obtained a chromosome-level genome of Yoshiicerus persimilis with a
 size of 334.44 Mb and BUSCO completeness of 97.0% (n = 1,013). Both
 genomes of Y. persimilis and Tomocerus qinae (recently published) have an
 exceptionally large chromosome (ElChr &gt;100 Mb), accounting for
 nearly one-third of the genome. Comparative genomic analyses suggest that
 chromosomal elongation occurred independently in two species approximately
 10 million years ago, rather than in the ancestor of the Tomoceridae
 family. The ElChr elongation was caused by large tandem and segmental
 duplications, as well as transposon proliferation, with genes in these
 regions experiencing weaker purifying selection (higher dN/dS) than
 conserved regions. Moreover, inter-genomic synteny analyses indicated that
 chromosomal fission/fusion events played a crucial role in the evolution
 of chromosome numbers (ranging from 5 to 7) within Entomobryomorpha. This
 study provides a valuable resource for investigating the chromosome
 evolution of Collembola.
description: <strong>Genome
 assembly</strong>
 <em>De novo</em> assembly of PacBio long reads was performed by
 Raven v. 1.6.0. The assembly was then polished with one round of long
 reads using Flye v. 2.8.3 and two rounds of Illumina short reads using
 NextPolish v. 1.3.1. Primary contigs were anchored into chromosomes using
 3D-DNA v. 180922.
 <strong>Genome
 annotation</strong>
 We used the MAKER v. 3.01.03
 to predict PCGs, which integrates <em>ab initio</em>, RNA-seq,
 and protein homology evidence. BRAKER v. 2.1.6  and GeMoMa v. 1.7.1
 predictions combining protein and transcriptome evidence were integrated
 as the <em>ab initio</em> input passed to MAKER. BRAKER
 trained Augustus v. 3.3.4 and GeneMark-ES/ET/EP 4.68_lic integrating
 evidence from the OrthoDB10 v1 database. GeMoMa with parameters “GeMoMa.c
 = 0.3 GeMoMa.p = 12” utilized eight species (<em>Daphnia magna, Cloeon dipterum,
 Zootermopsis nevadensis, Drosophila melanogaster, Rhopalosiphum maidis,
 Tribolium castaneum, Sinella curviseta</em>, and FCSH) as the
 protein homology-based reference. RNA-seq alignments were produced using
 HISAT2 v. 2.2.0. RNA-seq data were further assembled into transcripts with
 the genome-guided assembler StringTie v. 2.1.6. MAKER used the protein
 sequences from the aforementioned eight species as protein homology
 evidence. PCGs were annotated by aligning protein
 sequences to the UniProtKB database using Diamond v. 2.0.8 with an e-value
 threshold of 1e-5. Furthermore, protein domains were predicted by
 InterProScan 5.48–83.0 based on five public databases: Pfam, SMART,
 Superfamily, Gene3D, and CDD. EggNOG-mapper v. 2.1.5 was also employed for
 functional category annotation based on the eggNOG v. 5.0.2
 database.
description: The sequencing reads are
 deposited at NCBI (SRR13480398–SRR13480401 and SRR25299242) under
 BioProject PRJNA630033. The genome assembly is deposited at GenBank under
 accessions JABJWA000000000. Additionally, the results of annotation for
 repeated sequences, gene structure, and functional prediction have been
 deposited in Figshare
 (https://doi.org/10.6084/m9.figshare.23722086).
description: genome.fa.masked.gz Repeat-masked genome assembly repeats.gff.gz Repeat
 annotation iprscan.tsv.gz InterProscan results
 eggnog.emapper.annotations.gz eggNOG annotation results gene.maker.gff.gz
 Annotation file of MAKER-annotated protein-coding genes cds.maker.fasta.gz
 Coding sequences of MAKER-annotated protein-coding genes
 proteins.maker.fasta.gz Amino-acid sequences of MAKER-annotated
 protein-coding genes transcripts.maker.fasta.gz Transcripts of
 MAKER-annotated protein-coding genes