Skip to content

Research at St Andrews

A revised spiralian homeobox gene classification incorporating new polychaete transcriptomes reveals a diverse TALE class and a divergent Hox gene

Research output: Contribution to journalArticle

DOI

Open Access permissions

Open

Abstract

The diversity of mechanisms and capacity for regeneration across the Metazoa present an intriguing challenge in evolutionary biology, impacting on the burgeoning field of regenerative medicine. Broad taxonomic sampling is essential to improve our understanding of regeneration, and studies outside of the traditional model organisms have proved extremely informative. Within the historically under-studied Spiralia, the Annelida have an impressive variety of tractable regenerative systems. The biomeralising, blastema-less regeneration of the head appendage (operculum) of the serpulid polychaete keelworm Spirobranchus (formerly Pomatoceros) lamarcki is one such system. To profile potential regulatory mechanisms, we classified the homeobox gene content of opercular regeneration transcriptomes. As a result of retrieving several difficult-to-classify homeobox sequences, we performed an extensive search and phylogenetic analysis of the TALE and PRD-class homeobox gene content of a broad selection of lophotrochozoan genomes. These analyses contribute to our increasing understanding of the diversity, taxonomic extent, rapid evolution, and radical flexibility of these recently discovered homeobox gene radiations. Our expansion and integration of previous nomenclature systems helps to clarify their cryptic orthology. We also describe an unusual divergent S. lamarcki Antp gene, a previously unclassified lophotrochozoan orphan gene family (Lopx), and a number of novel Nk class orphan genes. The expression and potential involvement of many of these lineage- and clade-restricted homeobox genes in S. lamarcki operculum regeneration provides an example of diversity in regenerative mechanisms, as well as significantly improving our understanding of homeobox gene evolution.
Close

Details

Original languageEnglish
Pages (from-to)2151–2167
Number of pages17
JournalGenome Biology and Evolution
Volume10
Issue number9
Early online date7 Jul 2018
DOIs
Publication statusPublished - 1 Sep 2018

    Research areas

  • Spirobranchus lamarcki, Regeneration, Operculum, Biomineralization, NK genes, PRD class genes

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Amphioxus functional genomics and the origins of vertebrate gene regulation

    Marletaz, F., Firbas, P., Maeso, I., Tena, J., Bogdanovic, O., Perry, M., Wyatt, C., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R., van Heeringen, S., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I. & 41 othersPermanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon Florian, A., Subirana, L., Balwierz, P. J., Duckett, P., Farahani, E., Aury, J. M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutierrez, E., Canestro, C., Castro, F., D'Aniello, S., Ferrier, D. E. K., Huang, S., Laudet, V., Marais, G., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I. M. L., Takahashi, T., Mirabeau, O., Xu, A., Yu, J-K., Carninci, P., Martinez-Morales, J., Crollius, H., Kozmik, Z., Weirauch, M., Garcia-Fernandez, J., Lister, R., Lenhard, B., Holland, P., Escriva, H., Gomez-Skarmeta, J. L. & Irimia, M., 21 Nov 2018, In : Nature. 564, 7734, p. 64-70 29 p.

    Research output: Contribution to journalArticle

  2. Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage

    Barton-Owen, T., Ferrier, D. E. K. & Somorjai, I. M. L., 20 Jun 2018, In : Scientific Reports. 8, 11 p., 9414.

    Research output: Contribution to journalArticle

  3. Light sheet microscopy with acoustic sample confinement

    Yang, Z., Cole, K. L. H., Qiu, Y., Somorjai, I. M. L., Wijesinghe, P., Nylk, J., Cochran, S., Spalding, G. C., Lyons, D. A. & Dholakia, K., 8 Feb 2019, In : Nature Communications. 10, 8 p., 669.

    Research output: Contribution to journalArticle

  4. Space and time in Hox/ParaHox gene cluster evolution.

    Ferrier, D. E. K., 2019, Perspectives on Evolutionary Developmental Biology: Essays for Alessandro Minelli. Fusco, G. (ed.). Padova: Padova University Press, p. 245-258

    Research output: Chapter in Book/Report/Conference proceedingChapter

  5. Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

    Szabó, R. & Ferrier, D. E. K., 27 Dec 2018, In : BMC Evolutionary Biology. 18, 13 p., 203.

    Research output: Contribution to journalArticle

Related by journal

  1. Inter and Intraspecific genomic divergence in Drosophila montana shows evidence for cold adaptation

    Parker, D., Wiberg, R. A. W., Trivedi, U., Tyukmaeva, V. I., Gharbi, K., Butlin, R. K., Hoikkala, A., Kankare, M. & Ritchie, M., 1 Aug 2018, In : Genome Biology and Evolution. 10, 8, p. 2086–2101

    Research output: Contribution to journalArticle

  2. Shared transcriptional control and disparate gain and loss of aphid parasitism genes

    Thorpe, P., Escudero-Martinez, C. M., Cock, P. J. A., Eves-van den Akker, S. & Bos, J. I. B., 1 Oct 2018, In : Genome Biology and Evolution. 10, 10, p. 2716-2733

    Research output: Contribution to journalArticle

  3. Assessing recent selection and functionality at long noncoding RNA loci in the mouse genome

    Wiberg, R. A. W., Halligan, D. L., Ness, R. W., Necsulea, A., Kaessmann, H. & Keightley, P. D., Aug 2015, In : Genome Biology and Evolution. 7, 8, p. 2432-2444 13 p.

    Research output: Contribution to journalArticle

  4. The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae)

    Cunningham, C. B., Ji, L., Wiberg, R. A. W., Shelton, J., McKinney, E. C., Parker, D. J., Meagher, R. B., Benowitz, K. M., Roy-Zokan, E. M., Ritchie, M. G., Brown, S. J., Schmitz, R. J. & Moore, A. J., 1 Dec 2015, In : Genome Biology and Evolution. 7, 12, p. 3383-3396 14 p.

    Research output: Contribution to journalArticle

ID: 252585510