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The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.
Genome Biol Evol. 2018 04 01; 10(4):1088-1103.GB

Abstract

The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

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Authors+Show Affiliations

Malmstrøm M
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway. Zoological Institute, University of Basel, Switzerland.
Britz R
Department of Life Sciences, Natural History Museum, London, United Kingdom.
Matschiner M
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway. Zoological Institute, University of Basel, Switzerland.
Tørresen OK
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.
Hadiaty RK
Ichthyology Laboratory, Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia.
Yaakob N
Forest Research Institute Malaysia (FRIM), Kepong, Selangor Darul Ehsan, Malaysia.
Tan HH
Lee Kong Chian Natural History Museum, National University of Singapore, Singapore.
Jakobsen KS
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.
Salzburger W
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway. Zoological Institute, University of Basel, Switzerland.
Rüber L
Naturhistorisches Museum Bern, Switzerland. Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland.

MeSH

AnimalsBody SizeCyprinidaeEvolution, MolecularGenes, HomeoboxGenomePhylogenyZebrafish

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29684203

Citation

Malmstrøm, Martin, et al. "The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes." Genome Biology and Evolution, vol. 10, no. 4, 2018, pp. 1088-1103.
Malmstrøm M, Britz R, Matschiner M, et al. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biol Evol. 2018;10(4):1088-1103.
Malmstrøm, M., Britz, R., Matschiner, M., Tørresen, O. K., Hadiaty, R. K., Yaakob, N., Tan, H. H., Jakobsen, K. S., Salzburger, W., & Rüber, L. (2018). The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biology and Evolution, 10(4), 1088-1103. https://doi.org/10.1093/gbe/evy058
Malmstrøm M, et al. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biol Evol. 2018 04 1;10(4):1088-1103. PubMed PMID: 29684203.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. AU - Malmstrøm,Martin, AU - Britz,Ralf, AU - Matschiner,Michael, AU - Tørresen,Ole K, AU - Hadiaty,Renny Kurnia, AU - Yaakob,Norsham, AU - Tan,Heok Hui, AU - Jakobsen,Kjetill Sigurd, AU - Salzburger,Walter, AU - Rüber,Lukas, PY - 2018/03/13/accepted PY - 2018/4/24/entrez PY - 2018/4/24/pubmed PY - 2018/10/3/medline SP - 1088 EP - 1103 JF - Genome biology and evolution JO - Genome Biol Evol VL - 10 IS - 4 N2 - The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/29684203/The_Most_Developmentally_Truncated_Fishes_Show_Extensive_Hox_Gene_Loss_and_Miniaturized_Genomes_ DB - PRIME DP - Unbound Medicine ER -