DOI: 10.5061/dryad.ht76hdrds
title: The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages

description: 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.
description: README.txt Associated files for Phalangium
 opilio (v1) genome assembly and annotation.  #### Fasta
 file containing the Phalangium opilio genome assembly:<br> 1.
 Phalangium_opilio_v1_NCBI.fa<br> #### GFF & GTF annotation
 files for the Phalangium opilio (v1) genome:<br> 2.
 Phalangium_opilio_v1_NCBI.gff3<br> 3.
 Phalangium_opilio_v1_NCBI.gtf<br> #### 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).<br>
 4. Phalangium_opilio_v1_NCBI.aa<br> 5.
 Phalangium_opilio_v1_NCBI.cds<br> #### GFF annotation file for the
 manual annotations for the Phalangium opilio (v1) Hox genes: <br> 6.
 Phalangium_opilio_v1_manual_annotations.gff <br> #### 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).<br> gffread).<br> 7.
 Phalangium_opilio_v1_manual_annotations.aa<br> 8.
 Phalangium_opilio_v1_manual_annotations.cds<br> #### Fasta file
 containing the soft masked Phalangium opilio genome assembly:<br> 9.
 Phalangium_opilio_v1_softmasked_NCBI.fa<br> #### Annotated proteins
 exported from Blast2Go, Busco and NCBI annotations after a 98% sequence
 identity filtering in CDHIT: <br> 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:<br> 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