Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
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...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Journal article |
| Language: | English |
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Cold Spring Harbor Laboratory Press
2022
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| _version_ | 1797109118673092608 |
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| author | Mulhair, PO Crowley, L Boyes, DH Harper, A Lewis, OT Holland, PWH |
| author2 | Darwin Tree of Life Consortium |
| author_facet | Darwin Tree of Life Consortium Mulhair, PO Crowley, L Boyes, DH Harper, A Lewis, OT Holland, PWH |
| author_sort | Mulhair, PO |
| collection | OXFORD |
| description | 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 <i>lab</i> gene is repositioned and the <i>ro</i> gene is next to <i>pb</i>. 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 <i>zen</i>-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. |
| first_indexed | 2024-03-07T07:37:27Z |
| format | Journal article |
| id | oxford-uuid:1b9e2682-c2e0-4313-a65d-1b1d8bb21566 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:37:27Z |
| publishDate | 2022 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | oxford-uuid:1b9e2682-c2e0-4313-a65d-1b1d8bb215662023-03-30T14:49:43ZDiversity, duplication, and genomic organization of homeobox genes in LepidopteraJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:1b9e2682-c2e0-4313-a65d-1b1d8bb21566EnglishSymplectic ElementsCold Spring Harbor Laboratory Press2022Mulhair, POCrowley, LBoyes, DHHarper, ALewis, OTHolland, PWHDarwin Tree of Life ConsortiumHomeobox 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 <i>lab</i> gene is repositioned and the <i>ro</i> gene is next to <i>pb</i>. 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 <i>zen</i>-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. |
| spellingShingle | Mulhair, PO Crowley, L Boyes, DH Harper, A Lewis, OT Holland, PWH Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title | Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title_full | Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title_fullStr | Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title_full_unstemmed | Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title_short | Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera |
| title_sort | diversity duplication and genomic organization of homeobox genes in lepidoptera |
| work_keys_str_mv | AT mulhairpo diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera AT crowleyl diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera AT boyesdh diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera AT harpera diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera AT lewisot diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera AT hollandpwh diversityduplicationandgenomicorganizationofhomeoboxgenesinlepidoptera |