Biology subjects

Ponnikas, S.

Publications and source records attributed to Ponnikas, S..

4 recordsLinked to original sources

bioRxiv2023

Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions

Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyse the genomes of twelve great reed warblers (Acrocephalus arundinaceus) in a three-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated towards the telomeric ends of the chromosomes. While the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared to maternal chromosomes. The frequency of crossovers was similar between intergenic and genic regions, but within genes, they occurred more frequently in exons than in introns. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias towards the sub-telomeric regions, particularly on the paternal side. These findings emphasise the importance of thoroughly screening the entire length of chromosomes to characterise the recombination landscape and uncover potential sex-biases in recombination. Article summaryThe genetic exchange between the paternal and maternal chromosomes during meiosis - recombination - plays a crucial role in evolution by generating new haplotypes that natural selection can act upon. By analysing genomic data of a three-generation family of great reed warblers, we detected precise locations of approximately 200 recombination events in the genome of these birds. This unveiled a prominent sex-bias with recombination occurring more often towards chromosome ends in males than in females.

evolutionary biology↗

bioRxiv2020

Extreme variation in recombination rate and genetic variation along the Sylvioidea neo-sex chromosome

In the majority of bird species, recombination between the sex chromosome pairs in heterogametic females (ZW) is restricted to a small pseudoautosomal region (PAR), whereas recombination is ongoing along the entire Z chromosome in the homogametic males (ZZ). Recombination has a strong impact on the sequence evolution by affecting the extent of linkage, level of genetic diversity and efficacy of selection. Species within the Sylvioidea superfamily are unique among birds in having extended Z and W chromosomes ("neo-sex chromosomes") formed by a fusion between the ancestral sex chromosomes and a part of chromosome 4A. So far the recombination landscape of the Sylvioidea neo-sex chromosomes remains unknown, despite its importance for understanding sequence evolution. Here, we use linkage mapping in a multi-generation pedigree to assemble, and assess the recombination rate along the entire Z chromosome of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). This resulted in an 87.54 Mbp and 90.19 cM large Z including the ancestral-Z, where the small PAR (0.89 Mbp) is located, and the added-Z. A striking result was an extreme variation in recombination rate along the Z in male great reed warblers with high rates at both telomeric ends, but an apparent lack of recombination over a substantial central section, covering 77% of the chromosome. This region showed a drastic loss of nucleotide diversity and accumulation of repeats compared to the highly recombining regions. Nonetheless, the evolutionary rate of genes (measured by dN/dS) did not differ between these regions, suggesting that the efficacy of selection on protein-coding sequences is not reduced by lack of recombination.

genetics↗

bioRxiv2020

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. Sylvioidea songbirds is an emerging model for understanding avian sex chromosome evolution because a unique chromosome fusion event [~]24 Myr ago has formed enlarged "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). We confirm that the added region has been translocated to both Z and W, and show that the added-W part has been heavily reorganised within itself and with the ancestral-W. Next, we show that recombination between Z and W continued after the fusion event, and that recombination suppression took [~]10 Myr to be completed and arose locally and non-linearly along the sex chromosomes. This pattern is inconsistent with that of large inversions and instead suggests gradual and mosaic recombination suppression. We find that the added-W mirrors the ancestral-W in terms of repeat accumulation, loss of genetic variation, and gene degeneration. Lastly, we show that genes being maintained on W are slowly evolving and dosage sensitive, and that highly conserved genes across broad taxonomic groups, regardless of sex-linkage, evolve slower on both Z and W. This study reveals complex expansion of recombination suppression along avian sex chromosomes, and that the evolutionary trajectory of sex-linked genes is highly predictable and governed partly by sex-linkage per se, partly by their functional properties.

evolutionary biology↗

bioRxiv2019

Genomics of expanded avian sex chromosomes shows that certain chromosomes are predisposed towards sex-linkage in vertebrates

Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that certain genomic regions are predisposed towards sex-linkage. However, to test this hypothesis detailed studies of independently originated sex-linked regions and their gene content are needed. Here we address this problem through comparative genomics of birds where multiple chromosomes appear to have formed neo-sex chromosomes: larks (Alaudidae; Sylvioidea). We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between (parts of) four avian chromosomes (Z, 3, 4A and 5). We found evidence of five evolutionary strata where recombination has been suppressed at different time points, and that these time points correlate with the level of Z-W gametolog differentiation. We show that there is extensive homology to sex chromosomes in other vertebrate lineages: three of the fused chromosomes (Z, 4A, 5) have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A) and mammals (Z, 4A). Moreover, we found that the fourth chromosome, chromosome 3, was significantly enriched for genes with predicted sex-specific functions. These results support a key role of chromosome content in the evolution of sex chromosomes in vertebrates.

evolutionary biology↗