Heather S Bruce

Marine Biological Laboratory | MBL · Eugene Bell Center for Regenerative Biology and Tissue Engineering

An iconic feature of insects is the apparent lack of legs on the abdomen, which is believed to be due to the repression of the leg-patterning gene Distalless (Dll) by abdominal Hox genes. However, in contrast to these molecular observations, it is not widely appreciated that the embryos of most insect groups do in fact form paired protrusions on mo...

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalpal segment (lab-1) and in patterning the first walking leg identity (Dfd-1),...

An iconic feature of insects is the apparent lack of legs on the abdomen, which is believed to be due to the repression of the leg-patterning gene Distalless (Dll) by abdominal Hox genes. However, in contrast to these molecular observations, it is not widely appreciated that the embryos of most insect groups do in fact form paired protrusions on mo...

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata, with emphasis on the Hox logic of the anterior prosomal segments, which bear the mouthparts. Previous investigations of individual paralogs of labial ( lab ) and Deformed ( Dfd ) in the spider Parasteatoda tepidariorum have shown t...

In the embryo of Carabus insulicola, Kobayashi et al. (2013: J. Morphol., 274, 1323-1352) revealed that the subcoxa can be divided into subcoxae-1 and 2 by the paracoxal suture (PCXS), and these subcoxae form the larval pleuron. Mashimo and Machida (2017: Sci. Rep., 7, 12597), however, rejected the appendicular nature of subcoxa-1 and interpreted t...

Understanding how novel structures arise is a central question in evolution. Novel structures are often defined as structures that are not derived from (homologous to) any structure in the ancestor.¹ The carapace of the crustacean Daphnia magna is a bivalved “cape” of exoskeleton. Shiga et al.² proposed that the carapace of crustaceans like Daphnia...

Emerging research organisms enable the study of biology that cannot be addressed using classical "model" organisms. New data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emergi...

Understanding how novel structures arise is a central question in evolution. The carapace of the waterflea Daphnia is a bivalved cape of exoskeleton that has been proposed to be one of many novel arthropod structures that arose through repeated co-option of genes that also pattern insect wings. To determine whether the Daphnia carapace is a novel s...

This protocol largely follows the HCR v3.0 protocol for whole-mount Drosophila embryos (Choi et al. 2018) with a few adaptations that simplify the procedure and improve signal to noise ratio in our hands.

Understanding how novel structures arise is a central question in evolution. The carapace of the waterflea Daphnia is a bivalved “cape” of exoskeleton that surrounds the animal, and has been proposed to be one of many novel structures that arose through repeated co-option of genes that also pattern insect wings. To determine whether the Daphnia car...

Understanding how novel structures arise is a central question in evolution. The carapace of the waterflea Daphnia is a bivalved “cape” of exoskeleton that surrounds the animal, and has been proposed to be one of many novel structures that arose through repeated co-option of genes that also pattern insect wings. To determine whether the Daphnia car...

How to align leg segments between the four groups of arthropods (insects, crustaceans, myriapods, and chelicerates) has tantalized researchers for over a century. By comparing the loss-of-function phenotypes of leg patterning genes in diverged arthropod taxa, including a crustacean, insects, and arachnids, arthropod legs can be aligned in a one-to-...

The origin of insect wings has long been debated. Central to this debate is whether wings are a novel structure on the body wall resulting from gene co-option, or evolved from an exite (outgrowth; for example, a gill) on the leg of an ancestral crustacean. Here, we report the phenotypes for the knockout of five leg patterning genes in the crustacea...

How to align leg segments between the four groups of arthropods (insects, crustaceans, myriapods, and chelicerates) has tantalized researchers for over a century. By comparing the loss-of-function phenotypes of leg patterning genes in diverged arthropod taxa, including a crustacean, insects, and spiders, we show that all arthropod legs can be align...

The origin of insect wings has long been debated. Central to this debate is whether wings evolved from an epipod (outgrowth, e.g., a gill) on ancestral crustacean leg segments, or represent a novel outgrowth from the dorsal body wall that co-opted some of the genes used to pattern the epipods. To determine whether wings can be traced to ancestral,...

Catalog of repeat elements in Parhyale genome assembly.Description of repeat content in the Parhyale genome.DOI: http://dx.doi.org/10.7554/eLife.20062.008

List of proteins currently unique to Parhyale.List of proteins in Parhyale without identity to other species.DOI: http://dx.doi.org/10.7554/eLife.20062.013

Polymorphism in Parhyale devlopmental genes.Description of polymorphism in previously identfied Parhyale developmental genes.DOI: http://dx.doi.org/10.7554/eLife.20062.018

RFAM based annotation of the Parhyale genome.RFAM annotation of the Parhyale genome.DOI: http://dx.doi.org/10.7554/eLife.20062.039

iPython Notebook for variant analysis. Analysis of polymorphism in Parhyale using genome reads, transcriptome data and sanger sequenced BACs. DOI: http://dx.doi.org/10.7554/eLife.20062.049

List of Parhyale transcription factors by family.List of Parhyale transcript IDs for all transcription factors in the proteome, grouped by transcription factor family.DOI: http://dx.doi.org/10.7554/eLife.20062.023

Homeobox transcription factors.Annotation of homeobox transcription factor genes in Parhyale.DOI: http://dx.doi.org/10.7554/eLife.20062.025

Catalog of GH family genes in Parhyale.IDs of all Parhyale GH genes and analyis of GH family membership across available malacostracan data sets.DOI: http://dx.doi.org/10.7554/eLife.20062.032

iPython Notebook for Parhyale genome assembly. Includes bioinformatic processsing of raw read data, k-mer analysis, contig assembly, scaffolding and CEGMA cased representation analyis. DOI: http://dx.doi.org/10.7554/eLife.20062.046

iPython Notebook for RNA. Analysis of microRNAs and putative lncRNAs in Parhyale. DOI: http://dx.doi.org/10.7554/eLife.20062.051

Software and Data.List of programs and bioinformatic tools and publicly available sequence data used in this study.DOI: http://dx.doi.org/10.7554/eLife.20062.009

Orthofinder analysis.Orthofinder analysis using the Parhyale predicted proteome.DOI: http://dx.doi.org/10.7554/eLife.20062.015

Wnt, TGFβ and FGF signaling pathways .Parhyale transcript IDs for Wnt, Wnt ligand, FGF, FGFR and TGFβ pathway genes.DOI: http://dx.doi.org/10.7554/eLife.20062.024

iPython Notebook for repeat analysis. Includes repeat analysis of the Parhyale genome using Repeat Modeller and Repeat Masker. DOI: http://dx.doi.org/10.7554/eLife.20062.047

iPython Notebook of orthology analysis. Protein orthology analysis between Parhyale and other species DOI: http://dx.doi.org/10.7554/eLife.20062.050

List of genes likely to be specific to the MalacostracaList of genes likely to be specific to the Malacostraca.DOI: http://dx.doi.org/10.7554/eLife.20062.014

Catalog of innate immunity related genes in Parhyale.Parhyale IDs and numbers of immune related genes in comparison to other species.DOI: http://dx.doi.org/10.7554/eLife.20062.035

Genes involved with epigenetic modification.Catalog of Parhyale genes involved in DNA methylation and histone modifications.DOI: http://dx.doi.org/10.7554/eLife.20062.043

iPython Notebook for transcriptome and annotation. Parhyale transcriptome assembly, genome annotation and generation of canonical proteome dataset. DOI: http://dx.doi.org/10.7554/eLife.20062.048

ELife digest The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissue...

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacost...

Hox genes play crucial roles in establishing regional identity along the anterior–posterior axis in bila-terian animals, and have been implicated in generating morphological diversity throughout evolution. Here we report the identification, expression, and initial genomic characterization of the complete set of Hox genes from the amphipod crustacea...

Crustaceans possess a diverse array of specialized limbs. Although shifts in Hox gene expression domains have been postulated to play a role in generating this limb diversity, little functional data have been provided to understand the precise roles of Hox genes during crustacean development. We used a combination of CRISPR/Cas9-targeted mutagenesi...

The diverse array of body plans possessed by arthropods is created by generating variations upon a design of repeated segments formed during development, using a relatively small "toolbox" of conserved patterning genes. These attributes make the arthropod body plan a valuable model for elucidating how changes in development create diversity of form...