Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution

Abstract

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.

Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds

“…Finally, the obtained interspecies FISH hybridization datasets were amended with information available from other relevant studies for six more species, including five other Neognathae/Neoaves representatives: smooth-billed ani (Crotophaga ani, Cuculiformes) [27], budgerigar (Melopsittacus undulatus, Psittaciformes) [16], saker falcon (Falco cherrug, Falconiformes) [16], peregrine falcon (Falco peregrinus, Falconiformes) [16,25], pigeon (Columba livia, Columbiformes) [23,35], and one Palaeognathae species, ostrich (Struthio camelus, Struthioniformes) [16]. This expanded dataset for 12 birds was employed for reconstructing in silico the Neognathae/Neoaves ancestral karyotypes using information about positions/orders of BACs on macrochromosomes, as well.…”

“…The correct tree topology (in Newick format) was tested using the ETE v3 toolkit [37] (Figure S1). As we established in our previous reconstruction studies [6,19,20,23], MLGO outputs were, by inference and manually, curated and adjusted further to interpret and correct software-assisted reconstruction results using the most parsimonious explanation of the available data.…”

“…Avian karyotypes have been investigated over the last decades by whole chromosome painting using different probes sets [3,4]. These analyses have been an important tool to detect chromosomal similarities and differences between species and changes in each lineage since they diverged from common ancestors, which can also be virtually reconstructed using software algorithms (e.g., [6,[19][20][21][22][23]). However, this approach has been applied to less than 1% of species, and so many avian orders have no information concerning chromosomal homology based on molecular cytogenetics [4,5].…”

Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae

“…Because the BAC-FISH was proved to be an advantageous and sensitive tool for karyotype evolution studies [7,11,[13][14][15][33][34][35][36], we used this method for verification of the evolutionary chromosomal rearrangements in Cervidae. The four species of Cervini analysed in this study share the fusion of BTA17;19 previously described on the basis of banding patterns and chromosome painting [7,13,14,37].…”

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

“…While genome evolution has been extensively studied in mammals 15 and birds 16,17 , the relative lack of phylogenetically diverse chromosome-scale frog genomes has limited the study of genome evolution in anuran amphibians. Here, we report a high-quality assembly for X. tropicalis and three new chromosome-scale genome assemblies for the direct-developing Puerto Rican coquí (Eleutherodactylus coqui), the túngara frog (Engystomops pustulosus), which is a model for vocalization, and the Zaire dwarf clawed frog (Hymenochirus boettgeri), which has an unusually small embryo and is a model for regulation of cell and body sizes.…”