Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

Abstract

Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

B Chromosomes in Grasshoppers: Different Origins and Pathways to the Modern Bs

“…Small unique DNA fragments of the main genome could probably also be inserted into the B s without forming C-negative region. This phenomenon was described in studies of some B s in mammals [ 19 , 20 , 21 ].…”

“…For example, the C-positive Ba1 in E. plorans contained small regions painted with euchromatic DNA probe ( Figure 10 a,d). The sequencing of microdissected libraries of mammalian B s revealed DNA fragments homologous to a unique DNA located in different chromosomes of the basic set [ 19 , 20 , 21 ]. The question “are the C-negative regions of the B s the remnants of large euchromatic regions earlier present in the B or are they the result of multiple insertions/duplications of a small euchromatic chromosome region?” remains open.…”

“…Probably both types of B s are present in natural populations. Furthermore, in some B s small insertions of DNA fragments from euchromatic regions of A s seem to be too small to form visible C-negative regions in these B s [ 19 , 20 ].…”

“…At least a half of these genes are transcriptionally active [ 71 ]. It should be noted that these genes are involved in cell division processes as well as the genes of B s of vertebrates [ 19 , 20 , 21 , 72 , 73 , 74 ]. However, the exact location and flanking regions of these genes are mostly unknown.…”

“…The ITS from the autosome S11 appeared to be the closest one to the ITS from the B chromosome [ 18 ]. We should also note that sequencing of B s in six mammalian species showed that B s can contain DNA fragments from different A s [ 19 , 20 , 21 ], which significantly puzzles the question of the B s origin.…”