Genomic insights into the chromosomal elongation in a family of Collembola
Creators: name: Zhang, Feng
name: Jin, Jianfeng
name: Zhan, Zhihong
name: Wei, Xiping
name: Pan, Zhixiang
name: Zhao, Yuxin
name: Yu, Daoyuan
Publisher: name: Zenodo
Year: 2024
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 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>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 a decrease in purifying selection (higher dN/dS) than conserved regions. Enrichment analysis revealed that duplicated genes of ElChr were primarily associated with proliferation and growth, which may explain 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 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 ChinaCrossref Funder Registry ID: https://ror.org/01h0zpd94Award Number: 31970434
Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: https://ror.org/01h0zpd94Award Number: 32270470
Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: https://ror.org/01h0zpd94Award Number: 41971063
Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: https://ror.org/01h0zpd94Award Number: 42271059
description: Genome assembly

De novo 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.

Genome annotation

We used the MAKER v. 3.01.03 to predict PCGs, which integrates ab initio, 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 ab initio 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 (Daphnia magna, Cloeon dipterum, Zootermopsis nevadensis, Drosophila melanogaster, Rhopalosiphum maidis, Tribolium castaneum, Sinella curviseta, 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.