Genome annotation of Arctia plantaginis (ArcPla_EST)

The wood tiger moth, Arctia plantaginis, is an important model organism for the study of polymorphism in warning colour. One major colour locus has been identified but studying its association with other traits as well as signatures of selection has been limited by the lack of a contiguous reference genome. A previous assembly consisted of more than 1000 scaffolds. We present the first chromosome level genome assembly (1) based on PacBio-HiFi data and linkage map information. The final assembly spans 589 Mb consisting of 31 telomere-to-telomere chromosomes with a N50 scaffold length of 21.2 MB. The BUSCO analysis (n = 5,760) indicated a high completeness of 98.1 % with 97.5 % present as single copy and 0.6 % as duplicated. 17,456 genes were identified and 42.18 % of the genome was classified as repetitive. This new assembly provides an important resource for future research using genomic tools for studying the genetic basis and evolutionary mechanisms underlying colour polymorphisms in this species. We used Liftoff v1.6.3 (2) to lift over the previous annotation from the W-reference, iArcPla.TrioW.annotation.gtf', (3) to the new genome assembly, with the option to detect additional gene copies. A total of 17,456 genes (excluding additional copies) were successfully lifted over from the previous reference (97.4 %) to the new assembly. Overall, 27.0 % of the genome is within genes and 4.7 % within coding regions. The average length of single-copy genes was 8,946 bp, with an average of 6.5 coding sequences (CDS) per gene. Average CDS length was 238.5 bp. The final annotation can be found in 'ArcPla_EST_v2_annotation.gtf' The repeat annotation ('ArcPla_EST_repeats.gz') was generated using RepeatModeler2 v.2.0.6 26 (4). 1) Yen, E. C. et al. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 9 (2020). 2) Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639-1643 (2021). 3) Yen E C et al.(2020): Supporting data for "A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning" GigaScience Database. https://doi.org/10.5524/100774 4) Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. P Natl Acad Sci USA 117, 9451-9457 (2020).