Regions enriched for DNA repeats in chromosomes of Macrostomum mirumnovem, a species with a recent Whole Genome Duplication.

N B Rubtsov,K S Zadesenets

doi:10.18699/vj20.657

Abstract

The free-living flatworm Macrostomum mirumnovem is a neopolyploid species whose genome underwent a recent Whole Genome Duplication (WGD). In the result of chromosome fusions of the ancient haploid chromosome set, large metacentric chromosomes were formed. In addition to three pairs of small metacentrics, the current karyotype of M. mirumnovem contains two pairs of large metacentric chromosomes, MMI1 and MMI2. The generation of microdissected DNA libraries enriched for DNA repeats followed by DNA probe preparation and fluorescent in situ hybridization (FISH) were performed. The DNA probes obtained marked chromosome regions enriched for different DNA repeats in the M. mirumnovem chromosomes. The size and localization of these regions varied in different copies of large chromosomes. They varied even in homologous chromosomes, suggesting their divergence due to genome re-diploidization after a WGD. Besides the newly formed chromosome regions enriched for DNA repeats, B chromosomes were found in the karyotypes of the studied specimens of M. mirumnovem. These B chromosomes varied in size and morphology. FISH with microdissected DNA probes revealed that some Bs had a distinct DNA content. FISH could paint differently B chromosomes in different worms and even in the same sample. B chromosomes could carry a bright specific fluorescent signal or could show no fluorescent signal at all. In latter cases, the specific FISH signal could be absent even in the pericentromeric region of the B chromosome. Possible mechanisms of B chromosome formation and their further evolution are discussed. The results obtained indicate an important role that repetitive DNAs play in genome re-diploidization initiating a rapid differentiation of large chromosome copies. Taking together, karyotype peculiarities (a high level of intraspecific karyotypic diversity associated with chromosome number variation, structural chromosomal rearrangements, and the formation of new regions enriched for DNA repeats) and some phenotypic features of M. mirumnovem (small body size, short lifecycle, easy maintenance in the laboratory) make this species a perspective model in the studies of genomic and karyotypic evolution in species passed through a recent WGD event.

Highlights

Comparative genomics opened up new possibilities for studies of mechanisms of whole-genome duplication (WGD), as well as its consequences after the large-scale changes of genome involving almost all of the genes
By generation of microdissected DNA probes enriched with DNA repetitive sequences, we studied the distribution of these DNA repeats in the M. mirumnovem chromosomes
The regions painted by the DNA probes S3 or S4 will be called S3D- or S4D-regions, respectively, i. e. the regions detected by fluorescent in situ hybridization (FISH) using the DNA probes S3 and S4

Summary

Introduction

Comparative genomics opened up new possibilities for studies of mechanisms of whole-genome duplication (WGD), as well as its consequences after the large-scale changes of genome involving almost all of the genes. The genomes of modern species are paleoploids, and they contain only traces of WGDs (Dehal, Boore, 2005). There are two main mechanisms of WGD: autopolyploidy resulted in autotetraploid genome formation, and allopolyploidization, i. E. doubling of hybrid genome after interspecific hybridization In the latter case, a new allo polyploid genome contains both parental genomes, and it can retain many traits of its hybrid ancestor. The key role of WGD in genome evolution in animals was considered in the recent review (Zadesenets, Rubtsov, 2018)

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Conclusion