Avian Chromosomal Evolution

Damas, Joana; O’Connor, Rebecca E.; Griffin, Darren K.; Larkin, Denis M.

doi:10.1007/978-3-030-16477-5_4

Cited by 9 publications

(10 citation statements)

References 115 publications

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“…Our synteny plots reflect the relative stability of avian chromosome structure relative to other groups of organisms [62,64]. These results expand upon the high syntenic relationship found for the genomes of other passerines [67,96], as well as for non-passerine birds (e.g., Struthio camelus [93] and G. gallus [67]).…”

Section: Analysis Of Syntenysupporting

confidence: 72%

“…These results expand upon the high syntenic relationship found for the genomes of other passerines [67,96], as well as for non-passerine birds (e.g., Struthio camelus [93] and G. gallus [67]). It was expected that the level of synteny between F. peregrinus and S. habroptilus with the R. melanosticta genome would be lower than for other genomes; Falconiformes and Psitacifformes have highly rearranged genomes within Aves [64,93]. Regardless of their high level of rearrangement, the chromosome 1 fragment of the R. melanosticta genome that mapped to chromosome 4 in all birds was located in chromosome 2 of F. peregrinus, which is homologous to chromosome 4 in other birds.…”

Section: Analysis Of Syntenymentioning

confidence: 99%

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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

2019

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Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

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Section: Analysis Of Syntenysupporting

confidence: 72%

Section: Analysis Of Syntenymentioning

confidence: 99%

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

2019

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“…Pair 2 of P. cayana, which is homologous to GGA2, also showed an inversion, which was observed with probes corresponding to LAL2 (Fig 7B). These findings are in accordance with the fact that intrachromosomal rearrangements are frequent in avian genomes and may contribute to the phenotypic diversity of different bird species [28,29].…”

Section: Plos Onesupporting

confidence: 90%

Chromosomal evolution and phylogenetic considerations in cuckoos (Aves, Cuculiformes, Cuculidae)

et al. 2020

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The Cuckoos have a long history of difficult classification. The species of this order have been the subject of several studies based on osteology, behavior, ecology, morphology and molecular data. Despite this, the relationship between Cuculiformes and species of other orders remains controversial. In this work, two species of Cuculidae, Guira guira (Gmelin, 1788) and Piaya cayana (Linnaeus, 1766), were analyzed by means of comparative chromosome painting in order to study the chromosome evolution of this group and to undertake the first chromosome mapping of these species. Our results demonstrate high chromosomal diversity, with 2n = 76 in G. guira, with fission and fusion events involving ancestral syntenies, while P. cayana presented only fissions, which were responsible for the high diploid number of 2n = 90. Interestingly, there were no chromosomal rearrangements in common between these species. Our results, based on Giemsa staining, were compared with previous data for other cuckoos and also with taxa proposed as sister-groups of Cuculiformes (Otidiformes, Musophagiformes and Opisthocomiformes). Cytogenetic comparisons demonstrated that cuckoo species can be divided into at least three major groups. In addition, we found no evidence to place Cuculiformes close to the groups proposed previously as sister-groups.

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“…The karyotypes and genome sizes of birds have remained considerably stable over more than 100 million years' evolution of modern birds (Zhang et al 2014;Ellegren 2010; Ferguson-Smith, and de Oliveira 2018; Kapusta, Suh, and Feschotte 2017;Damas et al 2019).…”

Section: Introductionmentioning

confidence: 99%

“…The karyotypes and genome sizes of birds have remained considerably stable over more than 100 million years’ evolution of modern birds (Zhang et al 2014; Ellegren 2010; Kretschmer, Ferguson-Smith, and de Oliveira 2018; Kapusta, Suh, and Feschotte 2017; Damas et al 2019). A typical avian karyotype consists of about 40 pairs of chromosomes (2n = 80), among which about 30 paris are microchromosomes (smaller than 20 Mb).…”

Section: Introductionmentioning

confidence: 99%

Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

Huang

Furo

Peona

et al. 2021

Preprint

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The karyotype of most birds has remained considerably stable during more than 100 million years evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of three parrot genomes (monk parakeet, blue-fronted amazon, budgerigar), we uncovered frequent chromosome fusions and fissions among parrots, with most of them being lineage-specific. In particular, at least 12 chromosomes recurrently experienced inter-chromosomal fusions in different parrot lineages. Two conserved vertebrate genes, ALC1 and PARP3, with known functions in the repair of double-strand breaks and maintenance of genome stability, were specifically lost in parrots. The loss of ALC1 was associated with multiple deletions and an accumulation of CR1-psi, a novel subfamily of transposable elements (TEs) that recently amplified in parrots, while the loss of PARP3 was associated with an inversion. Additionally, the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. The newly formed neo-sex chromosomes were validated by our chromosomal painting, genomic and phylogenetic analyses. Transcriptome profiling for multiple tissues of males and females did not reveal signals of female-specific selection driving the formation of neo-sex chromosomes. Finally, we identified one W-specific satellite repeat that contributed to the unusual enlargement of the W chromosome in monk parakeet. Together, the combination of our genomic and cytogenetic analyses highlight the role of TEs and genetic drift in promoting chromosome rearrangements, gene loss and the evolution of neo-sex chromosome in parrots.

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Avian Chromosomal Evolution

Cited by 9 publications

References 115 publications

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Chromosomal evolution and phylogenetic considerations in cuckoos (Aves, Cuculiformes, Cuculidae)

Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

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