The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

Bours, Andrea; Pruisscher, Peter; Bascón-Cardozo, Karen; Odenthal-Hesse, Linda; Liedvogel, Miriam

doi:10.1038/s41598-023-43090-1

Cited by 5 publications

(4 citation statements)

References 35 publications

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“…Recent proliferation of LTR elements was especially pronounced in the Bell’s sparrow. Recent proliferation of LTR elements more closely aligns with patterns of TE expansion observed in the zebra finch (Kapusta & Suh 2017) and the blackcap ( Sylvia atricapilla ; Bours et al 2023). The reasons for recent LTR expansions in songbirds versus other avian lineages (e.g.…”

Section: Discussionsupporting

confidence: 63%

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

Benham,

Cicero,

Escalona

et al. 2023

Preprint

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Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repetitive regions of the genome should provide novel insights into patterns of TE diversity. Here we report the generation of highly contiguous reference genomes using PacBio long read and Omni-C technologies for three species of sparrows in the family Passerellidae. To assess the influence of sequencing technology on TE annotation, we compared these assemblies to three chromosome-level sparrow assemblies recently generated by the Vertebrate Genomes Project and nine other sparrow species generated using a variety of short- and long-read technologies. All long-read based assemblies were longer in length (range: 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb). Assembly length was strongly correlated with the amount of repeat content, with longer genomes showing much higher levels of repeat content than typically reported for the avian order Passeriformes. Repeat content for the Bell’s sparrow (31.2% of genome) was the highest level reported to date for a songbird genome assembly and was more in line with woodpecker (order Piciformes) genomes. CR1 LINE elements retained from an expansion that occurred 25-30 million years ago were the most abundant TEs in the song sparrow genome. Although the other five sparrow species also exhibit evidence for a spike in CR1 LINE activity at 25-30 million years ago, LTR elements stemming from more recent expansions were the most abundant elements in these species. LTRs were uniquely abundant in the Bell’s sparrow genome deriving from two recent peaks of activity. Higher levels of repeat content (79.2-93.7%) were found on the W chromosome relative to the Z (20.7-26.5) or autosomes (16.1-30.9%). These patterns support a dynamic model of transposable element expansion and contraction underpinning the seemingly constrained and small sized genomes of birds. 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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Section: Discussionsupporting

confidence: 63%

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

Benham,

Cicero,

Escalona

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Recent proliferation of LTR elements was especially pronounced in Bell's sparrow. Recent proliferation of LTR elements more closely aligns with patterns of TE expansion observed in the zebra finch ( Kapusta and Suh 2017 ) and the Eurasian blackcap ( Sylvia atricapilla ; Bours et al 2023 ). The reasons for recent LTR expansions in songbirds versus other avian lineages (e.g.…”

Section: Discussionsupporting

confidence: 63%

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

Benham,

Cicero,

Escalona

et al. 2024

Genome Biology and Evolution

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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: 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for the 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 (79.2-93.7%) 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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“…SVs frequently occurred in repetitive regions of the genome. Specifically, we annotated SVs using a repeat library manually curated for the Eurasian blackcap ( Bascón-Cardozo et al, 2022 ; Bours et al, 2022 ). Thirty-seven percent of the variants overlapped one or more repetitive elements in this library.…”

Section: Resultsmentioning

confidence: 99%

Structural genomic variation and migratory behavior in a wild songbird

Delmore,

Van Doren,

Ullrich

et al. 2023

Evolution Letters

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Structural variants (SVs) are a major source of genetic variation; and descriptions in natural populations and connections with phenotypic traits are beginning to accumulate in the literature. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (a) characterized the genome-wide distribution, frequency, and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (b) used these SVs to study the genetics of seasonal migration. We detected >15 K SVs. Many SVs overlapped repetitive regions and exhibited evidence of purifying selection suggesting they have overall deleterious effects on fitness. We used estimates of genomic differentiation to identify SVs exhibiting evidence of selection in blackcaps with different migratory strategies. Insertions and deletions dominated the SVs we identified and were associated with genes that are either directly (e.g., regulatory motifs that maintain circadian rhythms) or indirectly (e.g., through immune response) related to migration. We also broke migration down into individual traits (direction, distance, and timing) using existing tracking data and tested if genetic variation at the SVs we identified could account for phenotypic variation at these traits. This was only the case for 1 trait—direction—and 1 specific SV (a deletion on chromosome 27) accounted for much of this variation. Our results highlight the evolutionary importance of SVs in natural populations and provide insight into the genetic basis of seasonal migration.

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The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

Cited by 5 publications

References 35 publications

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

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

Structural genomic variation and migratory behavior in a wild songbird

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