Repetitive DNA: The Dark Matter of Avian Genomics

Weissensteiner, Matthias H.; Suh, Alexander

doi:10.1007/978-3-030-16477-5_5

Cited by 22 publications

(17 citation statements)

References 269 publications

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“…Although they provide an unprecedented view on the structure and evolution of many coding regions (Zhang et al., 2014), short reads hardly inform on the entire complexity of a genome (Thomma et al., 2016). Indeed, the systematic absence from genome assemblies and the difficulty in characterizing the nature of many such genomic regions (e.g., centromeres, telomeres, other repeats and highly heterochromatic regions) gave these “unassemblable” sequences the evocative name of genomic “dark matter” (Johnson et al., 2005; Weissensteiner & Suh, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…In both species, it is likely that the assembled sequences cover the euchromatic portions of the W. Birds have a ZW sex chromosome system in which the female is the heterogametic sex and the female‐specific W is analogous to the mammalian male‐specific Y chromosome. Comparable to the mammalian Y (Charlesworth et al., 2000), the W chromosome is highly repetitive and difficult to assemble (Weissensteiner & Suh, 2019). Previous studies focusing on the repetitive content of the avian W in chicken (Bellott et al., 2017) and collared flycatcher (Smeds et al., 2015) showed in both cases a repeat density of about 50%.…”

Section: Discussionmentioning

confidence: 99%

“…Technological biases are therefore impeding the complete reconstruction of genomes and substantial regions are systematically missing from genome assemblies. These missing “unassemblable” regions are often referred to as the genomic “dark matter” (Sedlazeck et al., 2018; Weissensteiner & Suh, 2019). It is key now for the genomics field to overcome these limitations and investigate this dark matter.…”

Section: Introductionmentioning

confidence: 99%

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona

Blom

et al. 2020

Molecular Ecology Resources

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118

135

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Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome. Telomere‐to‐telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona

Blom

et al. 2020

Molecular Ecology Resources

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118

135

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“…However, satellite diversity and abundance are difficult to identify because of repeat complex structures [ 239 ]. Due to reduced genome size, avian genomes are characterized by considerably lower percentages of repeats compared to other vertebrates [ 240 ]. In different species of birds such as Colaptes melanochloros (Gmelin, 1788 [ 241 ]) (2 n = 84) and Colaptes campestris (Vieillot, 1818 [ 242 ]), SatDNA repeats are accumulated with centromeric and telomeric regions in both macro- and microchromosomes along with clusters of 18S rDNA [ 243 ].…”

Section: Distribution Of Repeated Sequences Between Macro- and Microchromosomesmentioning

confidence: 99%

Why Do Some Vertebrates Have Microchromosomes?

Srikulnath

Ahmad

Singchat

et al. 2021

Cells

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With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.

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“…The lack of knowledge regarding SVs on the W chromosome is tied to assembly issues since its repetitive content surpasses 70% in non-ratite birds (36), making it one of the most difficult-to-assemble avian chromosomes (27). The true levels of genetic variability on the W might have been hidden in past studies as part of the so-called genomic “dark matter” in contemporary genome assemblies (25, 27, 47). Assessing the level of W-linked variability with new long-read or multiplatform reference assemblies is necessary to better understand the magnitude of occurrence rate variation for different types of mutations (2) and to inform models of sex chromosome evolution (22).…”

Section: Introductionmentioning

confidence: 99%

The hidden structural variability in avian genomes

Peona

Blom

Frankl-Vilches

et al. 2022

Preprint

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Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and dele-tions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chro-mosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turn-over of transposable element insertions, especially endogenous retroviruses.

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Repetitive DNA: The Dark Matter of Avian Genomics

Cited by 22 publications

References 269 publications

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Why Do Some Vertebrates Have Microchromosomes?

The hidden structural variability in avian genomes

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