A selfish chromosome breaks Mendel’s laws

It has been a century since Gotoh’s discovery of supernumerary B chromosomes in rye (Secale cereale) (Gotoh 1924). B chromosomes are mysterious genetic elements found in approximately 3000 species of fungi, plants and animals. Unlike standard (A) chromosomes, B chromosomes are non-essential and do not undergo recombination with A chromosomes, instead following an independent evolutionary path. Whereas typical A chromosomes adhere to Mendelian inheritance, giving each a 50% chance of passing into sperm or egg cells, B chromosomes often circumvent this rule. Lacking any apparent benefit to the host, B chromosomes would otherwise face elimination under selection pressure. However, many can break Mendelian laws to increase their numbers during reproduction. This process is known as chromosome drive.

In rye and many other plants, the first pollen mitosis is asymmetric. The nucleus of the haploid gamete divides into a heritable generative nucleus and a non-heritable vegetative nucleus. During this stage, rye B chromatids exhibit nondisjunction, remain lagging at anaphase, and finally preferentially enter the closer generative nucleus. In the second pollen mitosis, the generative nucleus divides to produce two sperm nuclei, each with an unreduced number of B chromosomes. Thus, B chromosome drive occurred.

Drive mechanisms in B chromosome systems have been studied in some species and contexts using various technologies, from classical genetics to cytogenetics. But despite being an ideal test case to study the underlying mechanisms of the chromosome drive, B chromosome research has only slowly been able to capitalize on the data explosion of the DNA sequencing boom: B chromosomes are highly structurally complex, and DNA repeat-enriched, all of which make them challenging to pseudomolecule-level chromosome assembly, especially before recent developments in the area of long-read sequencing. As such, gene-level insight into the specific mechanisms that control chromosome drive is severely limited, and specific gene candidates implicated in this phenomenon have not been identified so far. To identify drive-controlling factor(s) on the rye B chromosome, an international research team narrowed down the size of the B chromosome drive-control region and assembled the rye B chromosome sequence.

A small region on the B chromosome controls the drive

B chromosome drive disappears when the distal region on the long arm of the B chromosome is lost. This region was designated as the drive control region (DCR) and functions in trans as drive-deficient B chromosomes recover drive in the presence of a standard B chromosome. First, we narrowed down the size of the drive control region by fluorescence in situ hybridization (FISH) and drive frequency analysis. After comparing a diverse panel of drive-positive and drive-negative B chromosome variants, a small chromosome region was identified as controlling the drive. Next, we assemble the rye B into a single ~430 Mb-long pseudomolecule from PacBio HiFi long reads and Nanopore ultra-long reads. The drive control region is a ~40 Mb-large chromosome segment encoding  88 genes.

An unreported microtubule-associated protein DCR28 might play a role in controlling the B chromosome drive

To reduce the number of candidate genes, a tissue-specific, comparative RNA-seq analysis using B chromosome variants, both with and without the ability to drive, revealed five drive-controlling candidate genes located in the drive control region. Among them, only candidate gene DCR28 is also encoded by the B chromosome of Aegilops speltoides, which shows a similar chromosome drive during the first pollen mitosis (Wu et al. 2019). DCR28 consists of 15 members derived from an evolutionarily conserved single-copy A chromosome paralog. It was classified as a member of the microtubule-associated Futsch-like protein family, a family conserved throughout the plant kingdom with unknown function. We demonstrated that DCR28 is a microtubule-associated protein related to cell division. We consider the DCR28 gene family as a candidate to control in trans the drive of the rye B chromosome because of its B-specific and high first pollen mitosis-specific transcription activity, the post-meiotic division, where the drive of the B occurs irrespectively of the host species. Our findings could also be helpful for research into genetic diseases that are based on the unequal distribution of chromosomes.

Jianyong Chen and Andreas Houben

References:

Gotoh K (1924) Über die Chromosomenzahl von Secale cereale L. Jap J Genet 7:135-152

Wu D, Ruban A, Fuchs J, Macas J, Novak P, Vaio M, Zhou Y, Houben A (2019) Nondisjunction and unequal spindle organization accompany the drive of Aegilops speltoides B chromosomes. New Phytol 223 (3):1340-1352. doi:10.1111/nph.15875

Schema depicts the chromosome drive of the rye B chromosome. The B chromosome sister chromatids undergo nondisjunction during the first pollen mitosis, accumulating in the generative and sperm nuclei. Cross-section of pollen after in situ detection of A- and B chromosome-specific sequences.