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The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages

Citation

Gainett, Guilherme et al. (2021), The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages, Dryad, Dataset, https://doi.org/10.5061/dryad.ht76hdrds

Abstract

Chelicerate arthropods exhibit dynamic genome evolution, with ancient whole genome duplication (WGD) events affecting several orders. Yet, genomes remain unavailable for a number of poorly studied orders, such as Opiliones (daddy-long-legs), which has hindered comparative study. We assembled the first opilionid draft genome for the species Phalangium opilio, which bears elongate, prehensile appendages, made possible by numerous distal articles called tarsomeres. Here, we show that the genome of P. opilio exhibits a single Hox cluster and no evidence of WGD. To investigate the developmental genetic basis for the quintessential trait of this group—the elongate legs—we interrogated the function of the Hox genes Deformed (Dfd) and Sex combs reduced (Scr), and a homolog of Epidermal growth factor receptor (Egfr). Knockdown of Dfd incurred homeotic transformation of two pairs of legs into pedipalps, with dramatic shortening of leg segments in the longest leg pair, whereas homeosis in L3 is only achieved upon double Dfd+Scr knockdown. Knockdown of Egfr incurred shortened appendages and the loss of tarsomeres. The similarity of Egfr loss-of-function phenotypic spectra in insects and this arachnid suggest that repeated cooption of EGFR signaling underlies the independent gains of supernumerary tarsomeres across the arthropod tree of life.

Usage Notes

README.txt

Associated files for Phalangium opilio (v1) genome assembly and annotation. 

#### Fasta file containing the Phalangium opilio genome assembly:
1. Phalangium_opilio_v1_NCBI.fa
#### GFF & GTF annotation files for the Phalangium opilio (v1) genome:
2. Phalangium_opilio_v1_NCBI.gff3
3. Phalangium_opilio_v1_NCBI.gtf
#### Fasta files containing the extracted protein sequences and CDS for the Phalangium opilio (v1) genome. Extracted with gffread v0.12.3 (commands: gffread Phalangium_opilio_v1_NCBI.gff3 -x Phalangium_opilio_v1_NCBI.cds -y Phalangium_opilio_v1_NCBI.aa -g Phalangium_opilio_v1_NCBI.fa).
4. Phalangium_opilio_v1_NCBI.aa
5. Phalangium_opilio_v1_NCBI.cds
#### GFF annotation file for the manual annotations for the Phalangium opilio (v1) Hox genes: 
6. Phalangium_opilio_v1_manual_annotations.gff 
#### Fasta files containing the extracted protein sequences and CDS for the Phalangium opilio genome. Extracted with gffread v0.12.3 (commands: gffread Phalangium_opilio_v1_manual_annotations.gff -x Phalangium_opilio_v1_manual_annotations.cds -y Phalangium_opilio_v1_manual_annotations.aa -g Phalangium_opilio_v1_NCBI.fa).
gffread).
7. Phalangium_opilio_v1_manual_annotations.aa
8. Phalangium_opilio_v1_manual_annotations.cds
#### Fasta file containing the soft masked Phalangium opilio genome assembly:
9. Phalangium_opilio_v1_softmasked_NCBI.fa
#### Annotated proteins exported from Blast2Go, Busco and NCBI annotations after a 98% sequence identity filtering in CDHIT: 
10. Phalangium_opilio_v1_Blast2Go_annotated_genes_plus_busco.annotated_CDHIT098.aa

11. EGFR tree

12. EGFR peptide alignment

13. HCR_Gainett.xlsx: Target sequence fragments (fasta) used to design HCR probes for the P0-lab, Po-Dfd and Po-Scr.

####Gffread citation:
Pertea G and Pertea M. GFF Utilities: GffRead and GffCompare. F1000Research 2020, 9:304 DOI: 10.12688/f1000research.23297.1

gff, gff3, and gtf file columns follow standar convention: https://m.ensembl.org/info/website/upload/gff.html

Funding

National Science Foundation, Award: IOS-1552610

National Science Foundation, Award: IOS-2019141

Global Genome Initiative, Award: GGI-Exploratory-2016-047

Global Genome Initiative, Award: GGI-Exploratory-2016-047