Distribution of CR1-like transposable element in woodpeckers (Aves Piciformes): Z sex chromosomes can act as a refuge for transposable elements

Bertocchi, Natasha Avila; Oliveira, Thays Duarte de; Garnero, Analía Del Valle; Coan, Rafael Luiz Buogo; Gunski, Ricardo José; Martins, Cesar; Torres, Fabiano Pimentel

doi:10.1007/s10577-018-9592-1

Cited by 16 publications

(12 citation statements)

References 39 publications

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“…For instance, in the human genome, the Alu distribution is not similar between chromosomes 21 and 22 [ 61 ], and L1 elements are not randomly distributed, although they seem able to target all genomic regions [ 62 ]. A similar distribution bias is also observed in Drosophila [ 63 ], catfish [ 64 ], and woodpeckers [ 65 ], among others. All these results suggest that even if TEs are potentially capable of jumping everywhere in the genomes, purifying selection against new insertion and ectopic recombination can remove several of them and reshape distribution [ 66 , 67 ].…”

Section: Long Term Co-evolution Of Transposable Elements and Genomes: Domestication And Exaptationsupporting

confidence: 75%

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

Capy

2021

Cells

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During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.

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Section: Long Term Co-evolution Of Transposable Elements and Genomes: Domestication And Exaptationsupporting

confidence: 75%

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

Capy

2021

Cells

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“…The higher density of TEs on these chromosomes might increase their probability to regulate some key sexual development genes and consequently to impact sexual development. In birds, such as woodpeckers for instance, the female specific chromosome W is enriched in CR1 insertions, which is a retrotransposon [116, 117]. In human, the Y chromosome is a hot spot for specific TE insertions [118].…”

Section: Tes Are Involved In Sex Chromosome Structure and Evolutionmentioning

confidence: 99%

Sex and the TEs: transposable elements in sexual development and function in animals

et al. 2019

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Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of sexual development genes, and how, reciprocally, they are tightly controlled in gonads. We also review how transposable elements contribute to the organization, expression and evolution of sexual development genes and sex chromosomes. This underscores the intricate co-evolution between host functions and transposable elements, which regularly shift from a parasitic to a domesticated status useful to the host.

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“…Red-bellied/Golden-fronted woodpeckers (Giller 1959;Smith 1987;Moore 1987;Moore and Price 1993;Seneviratne et al 2012Seneviratne et al , 2016. More recently, woodpeckers have gained attention for the high amount of repetitive DNA found in their genomes relative to other bird taxa (Sotero-Caio et al 2017;de Oliveira et al 2017;Bertocchi et al 2018), the result of high levels of genome-wide transposable elements (TEs), which are scarce in most bird genomes (Gao et al 2017). Manthey et al (2018) surveyed several woodpecker genomes, and found that TEs make up 17-31% of woodpecker genomes, compared to <10% for other bird species.…”

Section: Introductionmentioning

confidence: 99%

A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly

Wiley

Miller

2020

G3 Genes|Genomes|Genetics

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Woodpeckers are found in nearly every part of the world and have been important for studies of biogeography, phylogeography, and macroecology. Woodpecker hybrid zones are often studied to understand the dynamics of introgression between bird species. Notably, woodpeckers are gaining attention for their enriched levels of transposable elements (TEs) relative to most other birds. This enrichment of TEs may have substantial effects on molecular evolution. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species. Using hybrid assembly methods combining long-read Oxford Nanopore and short-read Illumina sequencing data, we generated a highly contiguous genome assembly for the Golden-fronted Woodpecker (Melanerpes aurifrons). The final assembly is 1.31 Gb and comprises 441 contigs plus a full mitochondrial genome. Half of the assembly is represented by 28 contigs (contig L50), each of these contigs is at least 16 Mb in size (contig N50). High recovery (92.6%) of bird-specific BUSCO genes suggests our assembly is both relatively complete and relatively accurate. Over a quarter (25.8%) of the genome consists of repetitive elements, with 287 Mb (21.9%) of those elements assignable to the CR1 superfamily of transposable elements, the highest proportion of CR1 repeats reported for any bird genome to date. Our assembly should improve comparative studies of molecular evolution and genomics in woodpeckers and allies. Additionally, the sequencing and bioinformatic resources used to generate this assembly were relatively low-cost and should provide a direction for development of high-quality genomes for studies of animal biodiversity.

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Distribution of CR1-like transposable element in woodpeckers (Aves Piciformes): Z sex chromosomes can act as a refuge for transposable elements

Cited by 16 publications

References 39 publications

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

Sex and the TEs: transposable elements in sexual development and function in animals

A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly

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