Zadesenets, K. S. | bioRxiv Science

bioRxiv2023

Unravelling genome organization of neopolyploid flatworm Macrostomum lignano

Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of genome doubling through allo- or autopolyploidization could lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are undoubtedly important for understanding one of the crucial stages of genome evolution. However, assembling neopolyploid appears to be a challenging task because its genome consists of two homologous (or homeologous) chromosome sets and therefore contains the extended paralogous regions with a high homology level. Post-WGD evolution of polyploids includes rediploidization, first part of which is cytogenetic diploidization led to the formation of species, whose polyploid origin might be hidden by disomic inheritance and diploid-like meiosis. Earlier we uncovered the hidden polyploid origin of free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Despite the different mechanisms for their genome doubling, cytogenetic diploidization in these species accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we reported unusual subgenomic organization of M. lignano through generation and sequencing of two new laboratory sublines of DV1 that differ only by a copy number of the large chromosome MLI1. Using non-trivial assembly-free comparative analysis of their genomes, including adapted multivariate k-mer analysis, and self-homology within the published genome assembly of M. lignano, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists in (1) presence of three subgenomes, emerged via formation of large fused chromosome and its variants, and (2) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.

genomics↗

bioRxiv2018

Germline-Restricted Chromosome (GRC) is Widespread among Songbirds

The genome of flying birds, the smallest among amniotes, reflects overweight of the extensive DNA loss over the unrestricted proliferation of selfish genetic elements, resulted in a shortage of repeated sequences and lack of B-chromosomes. The only exception of this rule has been described in zebra finch, which possesses a large germ-line restricted chromosome (GRC), transmitted via oocytes, eliminated from male postmeiotic cells and absent in somatic cell. It is considered as a rarity and its origin, content and function remain unclear. We discovered that all songbirds possess GRC: in various size and genetic content it is present in all fifteen songbird species investigated and absent from germ-line genomes of all eight species of other bird orders examined. Our data based on fluorescent in situ hybridization of DNA probes derived from GRCs of four different Passeri species and their sequencing indicate that the GRCs show low homology between avian species. They contain fragments of the somatic genomes, which include various unique and repetitive sequences. We propose that the GRC has formed in the common ancestor of the extant songbirds and undergone subsequent divergence. GRC presence in the germ line of every songbird studied indicate that it could contain genetic element(s) indispensable for gametogenesis, which are yet to be discovered.

evolutionary biology↗