Genomic insights into the chromosomal elongation in a family of Collembola
Creators: name: Zhang, Feng
name: Jin, Jianfeng
name: Zhan, Zhihong
name: Zhao, Yuxin
name: Yu, Daoyuan
Publisher: name: Zenodo
Year: 2023
Subjects: soil arthropod
exceptionally large chromosome
segmental duplication
transposon proliferation
chromosome size evolution

description: Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 3 to 11. Tomoceridae is one of the oldest collembolan families, and previous karyotype studies indicated that this family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of <em>Yoshiicerus persimilis</em> with a size of 334.44 Mb and BUSCO completeness of 97.0%. Both genomes of <em>Y. persimilis </em>and <em>Tomocerus qinae</em> (recently published) have an exceptionally large chromosome (ElChr&gt;100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses revealed a high degree of homology between the two ElChr, with 95.08% (2,224) of 1:1:1 orthologous genes shared between them. The ElChr elongation was caused by segmental duplication and transposon proliferation, with genes in these regions experiencing stronger selection pressure (higher dN/dS) than conserved regions. Enrichment analysis revealed that duplicated genes of ElChr were primarily associated with proliferation and growth, which explains their larger body size. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers within Entomobryomorpha. This study provides important insights into the mechanisms of chromosome evolution and offers a valuable omics resource for Collembola.
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).Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809<br>Award Number: 31970434Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809<br>Award Number: 32270470Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809<br>Award Number: 41971063Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809<br>Award Number: 42271059
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.