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Benham PM, Cicero C, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, King BL, Thomas WK, Kovach AI, Nachman MW, Bowie RCK. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery. Genome Biol Evol 2024; 16:evae067. [PMID: 38566597 PMCID: PMC11088854 DOI: 10.1093/gbe/evae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
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.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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McCormack JE, Hill MM, DeRaad DA, Kirsch EJ, Reckling KR, Mutchler MJ, Ramirez BR, Campbell RML, Salter JF, Pizarro AK, Tsai WLE, Bonaccorso E. An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays ( Cyanolyca cucullata) during the Great American Biotic Interchange. Ecol Evol 2023; 13:e10411. [PMID: 37589041 PMCID: PMC10425738 DOI: 10.1002/ece3.10411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023] Open
Abstract
The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas.
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Affiliation(s)
- John E. McCormack
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Molly M. Hill
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Devon A. DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - Eliza J. Kirsch
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | | | - Brenda R. Ramirez
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Jessie F. Salter
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | - Alana K. Pizarro
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
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