Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Abstract

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.

New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

“…highly repetitive region [27]. As in other species [19,20,28], even with long read sequencing, we could not assemble heterochromatic regions. Full annotation of the Brahman X and Angus Y chromosomes are available from Ensembl release v97 (UOA_Brhaman_1 and UOA_Angus_1).…”

“…The full length of the cattle Y chromosome has been estimated at ~50Mb, at least half of which is in the highly repetitive region [27]. As in other species [19,20,28], even with long read sequencing, we could not assemble the ampliconic region. highly repetitive region [27].…”

Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual

“…Chromosome preparation, staining, sorting, DNA purification, concentration and sequencing were performed as previously described in (Kuderna et al, 2019) with some modifications (see supplementary methods). Briefly, chromosomes were prepared from a lymphoblastoid cell line derived from a Chinese individual (Coriell, cat.…”

“…We recently developed a workflow to isolate and sequence native flow-sorted human Y chromosomes on an Oxford Nanopore MinION device (Kuderna et al, 2019). We sought to apply this method to other chromosomes to generate a population specific long read assembly, namely for a chromosome 1 of a Chinese individual.…”

One fly - one genome : Chromosome-scale genome assembly of a single outbred Drosophila melanogaster

“…We therefore believe this is an XXY female. Despite the abundance of Y-derived reads, our Y chromosome assembly is exceedingly fragmented, as most Y chromosome assemblies are, reflecting the challenges of assembling extremely repeat-dense chromosomes (Kuderna et al 2019) . Nonetheless, this finding highlights the value of sequencing individuals rather than pools because pooling would likely obscure this relationship of relative chromosome depths.…”