Genomic Organization of Repetitive DNA in Woodpeckers (Aves, Piciformes): Implications for Karyotype and ZW Sex Chromosome Differentiation

Abstract

Birds are characterized by a low proportion of repetitive DNA in their genome when compared to other vertebrates. Among birds, species belonging to Piciformes order, such as woodpeckers, show a relatively higher amount of these sequences. The aim of this study was to analyze the distribution of different classes of repetitive DNA—including microsatellites, telomere sequences and 18S rDNA—in the karyotype of three Picidae species (Aves, Piciformes)—Colaptes melanochloros (2n = 84), Colaptes campestris (2n = 84) and Melanerpes candidus (2n = 64)–by means of fluorescence in situ hybridization. Clusters of 18S rDNA were found in one microchromosome pair in each of the three species, coinciding to a region of (CGG)10 sequence accumulation. Interstitial telomeric sequences were found in some macrochromosomes pairs, indicating possible regions of fusions, which can be related to variation of diploid number in the family. Only one, from the 11 different microsatellite sequences used, did not produce any signals. Both species of genus Colaptes showed a similar distribution of microsatellite sequences, with some difference when compared to M. candidus. Microsatellites were found preferentially in the centromeric and telomeric regions of micro and macrochromosomes. However, some sequences produced patterns of interstitial bands in the Z chromosome, which corresponds to the largest element of the karyotype in all three species. This was not observed in the W chromosome of Colaptes melanochloros, which is heterochromatic in most of its length, but was not hybridized by any of the sequences used. These results highlight the importance of microsatellite sequences in differentiation of sex chromosomes, and the accumulation of these sequences is probably responsible for the enlargement of the Z chromosome.

Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes)

“…In addition, our data reinforced the view that the existence of one pair of microchromosomes bearing 18S rDNA clusters is apparently an ancestral character retained in Columbidae, and that repetitive sequences did preferentially accumulate in the centromeric regions of macro and microchromosomes, as well as in the W chromosomes. Additionally, despite the fact that studies with repetitive sequences in birds are still incipient, the comparison of our data with the ones for Psittaciformes, Piciformes and Galliformes ( Matsubara et al , 2015 ; de Oliveira et al , 2017 ; Furo et al , 2017 ) shows interesting variation in accumulation sites for some of them, reinforcing microsatellites as important markers for studies on karyotype evolution.…”

“…In Piciformes, a large accumulation of 10 sequences was observed on autosomes and especially on the Z sex chromosome in three woodpecker species (Picidae). The Z chromosome corresponds to the larger element of their karyotype due to the accumulation of such sequences, which increased its size ( de Oliveira et al , 2017 ). On the other hand, in Myiopsitta monachus (Psittaciformes, Psittacidae) these sequences accumulated preferentially in the W sex chromosome, which has the same size of the Z chromosome, unlike most Neognathae bird species ( Furo et al , 2017 ).…”

A highly contiguous genome for the Golden-fronted Woodpecker (Melanerpes aurifrons) via a hybrid Oxford Nanopore and short read assembly

“…These include flickers [10][11][12][13][14][15], sapsuckers (Sphyrapicus; [10][11][12][13][14][15], Nuttall's/Ladder-back woodpeckers [16] and Redbellied/Golden-fronted woodpeckers [10][11][12][13][14][15]. More recently, woodpeckers have gained attention for the high amount of repetitive DNA found in their genomes relative to other bird taxa [17][18][19], the result of high levels of genome-wide transposable elements (TEs), which are scarce in most bird genomes [20]. Manthey et al [21] surveyed several woodpecker genomes, and found that TEs make up 17-31% of woodpecker genomes, compared to <10% for other bird species.…”

De Novo Assembly of a Chromosome-Scale Reference Genome for the Northern FlickerColaptes auratus

“…However, we note that one-to-one synteny to the Gallus assembly was lacking for the larger chromosomes, indicative of chromosomal splitting since the Gallus-Colaptes common ancestor has occurred. Members of Picidae are known for containing a high number of chromosomes, particularly micro-chromosomes (Kaul and Ansari 1978), and karyotypes of Colaptes have been shown to consistently have a larger number of chromosomes when compared to Gallus (Pollock and Fechheimer 1976;de Oliveira et al 2017).…”