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

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 harvestman 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 homologue 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 signalling underlies the independent gains of supernumerary tarsomeres across the arthropod tree of life.

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royalsocietypublishing.org/journal/rspb
Research
Cite this article: Gainett G, González VL,
Ballesteros JA, Setton EVW, Baker CM, Barolo
Gargiulo L, Santibáñez-López CE, Coddington
JA, Sharma PP. 2021 The genome of a daddy-
long-legs (Opiliones) illuminates the evolution
of arachnid appendages. Proc. R. Soc. B 288:
20211168.
https://doi.org/10.1098/rspb.2021.1168
Received: 15 February 2021
Accepted: 14 July 2021
Subject Category:
Genetics and genomics
Subject Areas:
developmental biology, genomics, genetics
Keywords:
Hox, Deformed,Sex combs reduced,Egfr,
Chelicerata, Arachnida
Authors for correspondence:
Guilherme Gainett
e-mail: guilherme.gainett@wisc.edu
Vanessa L. González
e-mail: gonzalezv@si.edu
†
Co-first authors.
Electronic supplementary material is available
online at https://doi.org/10.6084/m9.figshare.
c.5534425.
The genome of a daddy-long-legs
(Opiliones) illuminates the evolution
of arachnid appendages
Guilherme Gainett
1,†
, Vanessa L. González
2,†
, Jesús A. Ballesteros
1
, Emily
V. W. Setton
1
, Caitlin M. Baker
1
, Leonardo Barolo Gargiulo
1
, Carlos
E. Santibáñez-López
3
, Jonathan A. Coddington
2
and Prashant P. Sharma
1
1
Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
2
Global Genome Initiative, Smithsonian Institution, National Museum of Natural History, 10th and Constitution,
NW, Washington, DC 20560-0105, USA
3
Department of Biological and Environmental Sciences, Western Connecticut State University, 181 White St,
Danbury, CT 06810, USA
GG, 0000-0002-9040-4863; VLG, 0000-0002-1593-4469; CMB, 0000-0002-9782-4959;
LBG, 0000-0001-6084-6372; CES-L, 0000-0001-6062-282X; PPS, 0000-0002-2328-9084
Chelicerate arthropods exhibit dynamic genome evolution, with ancient
whole-genome duplication (WGD) events affecting several orders. Yet, gen-
omes remain unavailable for a number of poorly studied orders, such as
Opiliones (daddy-long-legs), which has hindered comparative study. We
assembled the first harvestman 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 homologue of Epider-
mal 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 signalling underlies the independent gains
of supernumerary tarsomeres across the arthropod tree of life.
1. Introduction
The advent of genomic resources has revealed complex dynamics in the evolution of
chelicerate genomes. A group of six terrestrial orders (Arachnopulmonata), which
includes spiders, scorpions, and pseudoscorpions, exhibit an ancient shared
whole-genome duplication (WGD), as evidenced by the architecture of Hox clusters,
analyses of synteny, patterns of microRNA enrichment, gene expression patterns
and gene tree topologies [1–6] (figure 1a). Separately, genomes of all four living
Xiphosura (horseshoe crabs) suggest a lineage-specific twofold genome duplication
in this order, with one of these duplications occurring relatively recently [7–9].
While genomes of Acariformes and Parasitiformes (mites and ticks) suggest that
these two orders were not included in the genome duplication events, they often
deviate from typical arthropod datasets. As examples, the acariform mite Tetrany-
chus urticae exhibits extreme genome compaction (90 Mb), in tandem with the loss
of many transcription factors, which has been linked to miniaturization [10]. Simi-
larly, the genome of the parasitiform mite Galendromus occidentalis exhibits an
atomized Hox cluster, degradation of synteny and high rates of intron gain and
loss [11].
© 2021 The Author(s) Published by the Royal Society. All rights reserved.