Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.

Autor:	Benham PM; Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA.; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA., Cicero C; Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA., Escalona M; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Beraut E; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA., Fairbairn C; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA., Marimuthu MPA; DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA., Nguyen O; DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA., Sahasrabudhe R; DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA., King BL; Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA., Thomas WK; Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA., Kovach AI; Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA., Nachman MW; Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA.; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA., Bowie RCK; Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA.; Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2024 Apr 02; Vol. 16 (4).
DOI:	10.1093/gbe/evae067
Abstrakt:	Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution. Competing Interests: Conflict of Interest None. (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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