Biology subjects

Malinovskaya, L.

Publications and source records attributed to Malinovskaya, L..

3 recordsLinked to original sources

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2025

Mechanisms and timing of programmed DNA elimination in songbirds

It is commonly assumed that multicellular organisms contain the same genetic information in all the cells of an individual. However, there is a growing list of species in which parts of the genome are removed from some cells of the organism through a process called programmed DNA elimination. In songbirds, an entire chromosome, called the germline-restricted chromosome (GRC), is lost from all somatic cells during early embryonic development. Nevertheless, the mechanisms, timing and consequences of this elimination remain largely unexplored. Here, we studied GRC elimination using two songbird species, the zebra finch (Taeniopygia guttata) and the Bengalese finch (Lonchura domestica), as model systems. We found that chromosome elimination occurs during the cleavage stage and is completed before egg laying and blastoderm formation. Elimination is associated with delayed attachment of the GRC to the mitotic spindle, changes in its histone modifications, and failure of chromatid separation in anaphase. The lagging GRC is then sequestered into a micronucleus with a defective envelope lacking the essential protein lamin B1, where the DNA is fragmented and degraded. Although the genetic basis of GRC elimination remains to be elucidated, our results suggest that changes of the GRC centromere together with epigenetic modifications of histones play a crucial role in GRC elimination from somatic cells. As the timing of elimination coincides with the germline/soma distinction, we propose that GRC elimination may play an important role in this crucial developmental process in songbirds.

genetics↗

bioRxiv2022

Pachytene karyotypes of 17 species of birds

Karyotypes of less than 10% of bird species are known. Using immunolocalization of the synaptonemal complex, the core structure of meiotic chromosomes at the pachytene stage, and centromere proteins we described male pachytene karyotypes of seventeen species of birds. This method enables higher resolution than the conventional analyses of metaphase chromosomes. We provided the first descriptions of the karyotypes of three species (Rook, Blyths reed warbler and European pied flycatcher), corrected the published data on the karyotypes of ten species and confirmed them for four species. All passerine species examined have highly conservative karyotypes, 2n=80-82 with seven pairs of macrochromosomes and 33-34 pairs of microchromosomes. In all of them but not in the Common cuckoo we revealed single copies of the germline restricted chromosomes varying in size and morphology even between closely related species. This indicates a fast evolution of this additional chromosome. The interspecies differences concern the sizes of the macrochromosomes, morphology of the microchromosomes and sizes of the centromeres. The pachytene cells of the Gouldian finch, Brambling and Common linnet contained heteromorphic synaptonemal complexes indicating heterozygosity for inversions or centromere shifts. The European pied flycatcher, Gouldian finch and Domestic canary have extended centromeres in several macro- and microchromosomes.

genetics↗