Chromosome-Level Genome Assembly of the Bioluminescent Cardinalfish Siphamia tubifer: An Emerging Model for Symbiosis Research.
| Autor: | Gould AL; Ichthyology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA., Henderson JB; Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA., Lam AW; Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, California 94118, USA. |
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| Jazyk: | angličtina |
| Zdroj: | Genome biology and evolution [Genome Biol Evol] 2022 Apr 10; Vol. 14 (4). |
| DOI: | 10.1093/gbe/evac044 |
| Abstrakt: | The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer-P. mandapamensis association to be used as a model for symbiosis research. (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.) |
| Databáze: | MEDLINE |
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