Rich polymorphic variants of alpha satellite 34mer higher order repeats in hg38 assembly of human chromosome Y

A challenging problem in human population genetics is related to the unique role of human Y chromosome, with properties that distinguish humans from other species. Centromeres in primate genomes are constituted of tandem repeats of [~] 171 bp alpha satellite monomers, commonly organized into higher order repats (HORs). Because of gaps in DNA sequencing, HOR regions as genomic \"black holes\" have been understudied in spite of crucial importance. Only recently the sequencing of more complete satellite DNAs becomes accessible. In human Y chromosome the largest alpha satellite higher order repeat unit 34/36mer was found, but its polymorphic variants were not investigated. Here, we study the human Y chromosome centromeric genomic sequence from hg38 assembly using our novel ALPHAsub algorithm for simple identification of alpha satellite arrays and robust GRM algorithm for HOR identification in repeat sequences. We determine the monomer alignment scheme for alpha satellite HOR array based on canonical 34mer HOR, discovering a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions.\n\nAuthor SummaryThe centromere is important for segregation of chromosomes during cell division in eukaryotes. Its destabilization results in chromosomal missegregation, aneuploidy, hallmarks of cancers and birth defects. In primate genomes centromeres contain tandem repeats of [~] 171 bp alpha satellite DNA, commonly organized into higher order repeats (HORs). In this work, we used our bioinformatics algorithms to study the human Y chromosome centromeric genomic sequence and we discover a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions. These results could help to understand the role of alpha satellites and alpha HOR structures in centromeric organization and function, in particular their role in creating a functional kinetochore that is crucial for chromosome segregation during cell division.