Genome assembly and annotations of Yoshiicerus persimilis

Gene duplication is an important mechanism for organism evolution and adaptation. Whole-genome duplication (WGD) is considered as a major driver of species diversification. It has been reported that ancient WGD events occurred during the evolution of basal hexapod; the inferred pattern based on gene-tree and molecular-clock analyses remains challenging. Therefore, the lack of chromosome-scale genome has limited the characterization of WGD directly upon the synteny evidence. In order to get direct evidence from intra-chromosome synteny, we constructed the first chromosome-level genome of basal hexapod (Yoshiicerus persimilis, Collembola). We observed only large-scale gene duplications in chromosome 1, but not within/among other five chromosomes. These duplications were involved in proliferation and growth.

Methods
The chromosome-level genome was assembled using PacBio long reads and Hi-C data. Protein-coding genes (PSGs) were predicted under three lines of evidence including ab initio, RNA-seq and protein homology, and all the above evidence was integrated by Maker genome annotation pipeline. The repetitive sequences of the genome was constructed using RepeatModeler, Repbase and RepeatMasker. Non-coding RNAs, including rRNAs, snRNAs and miRNAs were identified by aligning the genome of Yoshiicerus persimilis to the Rfam database. The tRNAs were predicted using tRNAscan-SE. Motifs and domains in the PCGs were retrieved by performing InterProScan. The software eggNOG-mapper was also used for functional category annotation of the predicted PCGs based on the eggNOG database.