Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

Mulhair, Peter O.; Crowley, Liam; Boyes, Douglas H. ORCID:; Harper, Amber; Lewis, Owen T.; Holland, Peter W.H.; Darwin Tree of Life Consortium, . 2023 Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera. Genome Research, 33 (1). 32-44.

Before downloading, please read NORA policies.
N534730JA.pdf - Published Version
Available under License Creative Commons Attribution 4.0.

Download (3MB) | Preview


Homeobox genes encode transcription factors with essential roles in patterning and cell fate in developing animal embryos. Many homeobox genes, including Hox and NK genes, are arranged in gene clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary genome assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large order of insects. Here we analyze an extensive data set of high-quality genomes to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which the lab gene is repositioned and the ro gene is next to pb. A topologically associating domain spans much of the gene cluster, suggesting deep regulatory conservation of the Hox cluster arrangement in this insect order. Most Lepidoptera have four Shx genes, divergent zen-derived loci, but these loci underwent dramatic duplication in several lineages, with some moths having over 165 homeobox loci in the Hox gene cluster; this expansion is associated with local LINE element density. In contrast, the NK gene cluster content is more stable, although there are differences in organization compared with other insects, as well as major rearrangements within butterflies. Our analysis represents the first description of homeobox gene content across the order Lepidoptera, exemplifying the potential of newly generated genome assemblies for understanding genome and gene family evolution.

Item Type: Publication - Article
Digital Object Identifier (DOI):
UKCEH and CEH Sections/Science Areas: Biodiversity (Science Area 2017-)
ISSN: 1088-9051
Additional Information. Not used in RCUK Gateway to Research.: Open Access paper - full text available via Official URL link.
NORA Subject Terms: Ecology and Environment
Related URLs:
Date made live: 31 Oct 2023 10:13 +0 (UTC)

Actions (login required)

View Item View Item

Document Downloads

Downloads for past 30 days

Downloads per month over past year

More statistics for this item...