Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes)

Kretschmer, Rafael; Franz, Ismael; Souza, Marcelo Santos de; Garnero, Analía Del Valle; Gunski, Ricardo José; Oliveira, Edivaldo Herculano Corrêa de; O’Connor, Rebecca E.; Griffin, Darren K.; Freitas, Thales Renato Ochotorena de

doi:10.3390/cells10102650

Cited by 8 publications

(10 citation statements)

References 33 publications

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“…BAC probes from microchromosomes have been used in several bird orders and have significantly contributed to our knowledge about microchromosome organization and evolution [ 14 , 16 , 17 , 18 , 27 , 34 , 35 ]. Interchromosomal rearrangements involving these tiny chromosomes were found only in some orders, such as Falconiformes, Psittaciformes, Caprimulgiformes, Cuculiformes, Suliformes, and Passeriformes, always in species with a relatively low diploid number for birds (usually lower than 2n = 74), indicating that the decrease in the diploid number was due to microchromosome fusions.…”

Section: Discussionmentioning

confidence: 99%

Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species

Souza

Barcellos

Santos

et al. 2022

Animals

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Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds—Calidris canutus, Jacana jacana, and Vanellus chilensis—combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10–28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in C. canutus, we found two microchromosomes involved in chromosome fusions, they were present as single pairs in V. chilensis. We also described a new chromosome number for C. canutus (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species.

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Section: Discussionmentioning

confidence: 99%

Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species

Souza

Barcellos

Santos

et al. 2022

Animals

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“…As such, genome-wide AT–GC disequilibrium may be driven in part by an overall reduction in recombination rate. More detailed studies on specific chromosomal rearrangements within Falconidae, and potentially other birds ( Kretschmer et al 2021 ), will be necessary to explore this hypothesis.…”

Section: Discussionmentioning

confidence: 99%

Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux

Wilcox

Arca-Ruibal

Samour

et al. 2022

Genome Biology and Evolution

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Falcons are diverse birds of cultural and economic importance. They have undergone major lineage-specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in substitutions towards higher AT content; this bias is predominantly but not exclusively driven by hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased-gene-conversion in determining genomic equilibrium.

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“…While several studies demonstrated that interchromosomal rearrangements involving macro-and microchromosomes have played a role in the karyotype evolution of Ciconiiformes, Falconiformes, and Psittaciformes, recent studies have also observed this type of rearrangement in Caprimulgiformes, Cuculiformes, Suliformes, and Passeriformes species [140,142]. However, in these studies, only one representative species was investigated (Caprimulgiformes, Cuculiformes, and Suliformes) or the rearrangements were found only in one species (Passeriformes).…”

Section: Caprimulgiformes Cuculiformes Suliformes and Passeriformesmentioning

confidence: 99%

A Bird’s-Eye View of Chromosomic Evolution in the Class Aves

O’Connor,

Kretschmer,

Romanov

et al. 2024

Cells

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Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome (“chromosomic”) organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The ‘signature’ avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.

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Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes)

Cited by 8 publications

References 33 publications

Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species

Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species

Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux

A Bird’s-Eye View of Chromosomic Evolution in the Class Aves

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