B Chromosomes in Free-Living Flatworms of the Genus Macrostomum (Platyhelminthes, Macrostomorpha)

Transcribing the enigma: the B chromosome as a territory of uncharted RNAs

B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.

Unraveling the Unusual Subgenomic Organization in the Neopolyploid Free-Living Flatworm Macrostomum lignano

Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, 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 of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.