Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution.

Autor: Lin CY; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Marlétaz F; Center for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom., Pérez-Posada A; Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.; Living Systems Institute, University of Exeter, Exeter, United Kingdom., Martínez-García PM; Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain., Schloissnig S; Vienna Biocenter, Institute of Molecular Pathology, Vienna, Austria., Peluso P; Pacific Biosciences, Menlo Park, California, United States of America., Conception GT; Pacific Biosciences, Menlo Park, California, United States of America., Bump P; Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America., Chen YC; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Chou C; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Lin CY; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Fan TP; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Tsai CT; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan., Gómez Skarmeta JL; Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain., Tena JJ; Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain., Lowe CJ; Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America.; Chan-Zuckerberg Biohub, San Francisco, California, United States of America., Rank DR; Pacific Biosciences, Menlo Park, California, United States of America., Rokhsar DS; Chan-Zuckerberg Biohub, San Francisco, California, United States of America.; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America.; Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan., Yu JK; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan., Su YH; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
Jazyk: angličtina
Zdroj: PLoS biology [PLoS Biol] 2024 Jun 03; Vol. 22 (6), pp. e3002661. Date of Electronic Publication: 2024 Jun 03 (Print Publication: 2024).
DOI: 10.1371/journal.pbio.3002661
Abstrakt: Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
Competing Interests: D.S.R. is the paid consultant and shareholder of Dovetail Genomics. The other authors have declared that no competing interests exist.
(Copyright: © 2024 Lin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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