Ali Mohammad Banaei-Moghaddam

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences

Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1–1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.

Evolution and biology of supernumerary B chromosomes

B chromosomes (Bs) are dispensable components of the genome exhibiting non-Mendelian inheritance and have been widely reported on over several thousand eukaryotes, but still remain an evolutionary mystery ever since their first discovery over a century ago [1]. Recent advances in genome analysis have significantly improved our knowledge on the origin and composition of Bs in the last few years. In contrast to the prevalent view that Bs do not harbor genes, recent analysis revealed that Bs of sequenced species are rich in gene-derived sequences. We summarize the latest findings on supernumerary chromosomes with a special focus on the origin, DNA composition, and the non-Mendelian accumulation mechanism of Bs.

Formation and Expression of Pseudogenes on the B Chromosome of Rye

In contrast with the prevalent view that supernumerary B chromosomes do not contain genes, this work demonstrates that the B chromosome of rye contributes to the transcriptome and also affects in trans the activity of standard A chromosome–located genes. The authors propose a model for the evolution of B chromosome–located pseudogenes. B chromosomes (Bs) are dispensable components of the genomes of numerous species. In contrast with the prevalent view that Bs do not harbor genes, our recent sequence analysis revealed that Bs of rye (Secale cereale) are rich in gene-derived sequences. We compared these gene-like fragments of the rye B with their ancestral A-located counterparts and confirmed an A chromosomal origin and the pseudogenization of B-located gene-like fragments. About 15% of the pseudogene-like fragments on Bs are transcribed in a tissue-type and genotype-specific manner. In addition, B-located sequences can cause in trans down- or upregulation of A chromosome–encoded genic fragments. Phenotypes and effects associated with the presence of Bs might be explained by the activity of B-located pseudogenes. We propose a model for the evolution of B-located pseudogenes.

High‐copy sequences reveal distinct evolution of the rye B chromosome

B chromosomes (Bs) are supernumerary chromosomes that vary in number among individuals of the same species. Because of their dispensable nature, their non-Mendelian inheritance and their origin from A chromosomes (As), one might assume that Bs followed a different evolutionary pathway from As, this being reflected in differences in their high-copy DNA constitution. We provide detailed insight into the composition and distribution of rye (Secale cereale) B-located high-copy sequences. A- and B-specific high-copy sequences were identified in silico. Mobile elements and satellite sequences were verified by fluorescence in situ hybridization (FISH). Replication was analyzed via EdU incorporation. Although most repeats are similarly distributed along As and Bs, several transposons are either amplified or depleted on the B. An accumulation of B-enriched satellites was found mostly in the nondisjunction control region of the B, which is transcriptionally active and late-replicating. All B-enriched sequences are not unique to the B but are also present in other Secale species, suggesting the origin of the B from As of the same genus. Our findings highlight the differences between As and Bs. Although Bs originated from As, they have since taken a separate evolutionary pathway.

Nondisjunction in Favor of a Chromosome: The Mechanism of Rye B Chromosome Drive during Pollen Mitosis

This work examines the mechanism by which rye B chromosomes accumulate, finding that a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation. B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.

Point mutation impairs centromeric CENH3 loading and induces haploid plants

Significance The generation of haploids is the most powerful means to accelerate the plant-breeding process. We elucidated whether point mutations in the centromere-specific histone H3 variant CENH3 could be harnessed for the induction of haploids. We identified plants with impaired centromere loading caused by a mutation in the centromere-targeting domain (CATD). The same mutation results in reduced loading of CENH3 in transgenic Arabidopsis and sugar beet. Arabidopsis plants carrying this single point mutation in wild-type CENH3 were used as haploid inducers. Because the identified mutation site is highly conserved and because point mutations can be generated by mutagenesis or genome editing, the described method offers opportunities for application in a wide range of crop species. The chromosomal position of the centromere-specific histone H3 variant CENH3 (also called “CENP-A”) is the assembly site for the kinetochore complex of active centromeres. Any error in transcription, translation, modification, or incorporation can affect the ability to assemble intact CENH3 chromatin and can cause centromere inactivation [Allshire RC, Karpen GH (2008) Nat Rev Genet 9 (12):923–937]. Here we show that a single-point amino acid exchange in the centromere-targeting domain of CENH3 leads to reduced centromere loading of CENH3 in barley, sugar beet, and Arabidopsis thaliana. Haploids were obtained after cenh3 L130F-complemented cenh3-null mutant plants were crossed with wild-type A. thaliana. In contrast, in a noncompeting situation (i.e., centromeres possessing only mutated or only wild-type CENH3), no uniparental chromosome elimination occurs during early embryogenesis. The high degree of evolutionary conservation of the identified mutation site offers promising opportunities for application in a wide range of crop species in which haploid technology is of interest.

Biology and Evolution of B Chromosomes

B chromosomes are dispensable and often selfish elements of the genome which follow their own evolutionary pathway. B chromosomes are a major source of intraspecific variation in nuclear DNA amounts in numerous species and the distribution of Bs among different groups of angiosperms is not random. B chromosome inheritance is irregular and non-Mendelian, and therefore polymorphisms exist with respect to the number of Bs within populations or even within different cell lines of an individual carrying Bs. Drive mechanisms play a major role in the equilibrium of B frequency in populations. The most widely accepted view is that Bs are derived from the A chromosome complement. Some evidence also suggests that Bs can be spontaneously generated in response to the new genomic conditions after interspecific hybridization. The molecular processes that gave rise to Bs during evolution remain unclear. Here, we survey current knowledge on the DNA/chromatin composition, origin, and mitotic and meiotic drive mechanisms of B chromosomes and discuss effects and transcripts associated with Bs.

The differential loading of two barley CENH3 variants into distinct centromeric substructures is cell type- and development-specific.

The organization of centromeric chromatin of diploid barley (Hordeum vulgare) encoding two (α and β) CENH3 variants was analysed by super-resolution microscopy. Antibody staining revealed that both CENH3 variants are organized in distinct but intermingled subdomains in interphase, mitotic and meiotic centromeres. Artificially extended chromatin fibres illustrate that these subdomains are formed by polynucleosome clusters. Thus, a CENH3 variant-specific loading followed by the arrangement into specific intermingling subdomains forming the centromere region appears. The CENH3 composition and transcription vary among different tissues. In young embryos, most interphase centromeres are composed of both CENH3 variants, while in meristematic root cells, a high number of nuclei contain βCENH3 mainly dispersed within the nucleoplasm. A similar distribution and no preferential arrangement of the two CENH3 variants in relationship to the spindle poles suggest that both homologs meet the same function in metaphase cells.

B chromosomes of rye are highly conserved and accompanied the development of early agriculture

BACKGROUND AND AIMS Supernumerary B chromosomes (Bs) represent a specific type of selfish genetic element. As Bs are dispensable for normal growth, it is expected to observe B polymorphisms among populations. To address whether Bs maintained in geographically distinct populations of cultivated and weedy rye are polymorphic, the distribution patterns and the transcriptional activity of different B-located repeats were analysed. METHODS Bs of cultivated and weedy rye from seven origins were analysed by fluorescence in situ hybridization (FISH) with probes specific for the pericentromeric and interstitial regions as well as the B-specific non-disjunction control region. The DNA replication, chromatin composition and transcription behaviour of the non-disjunction regions were determined. To address whether the B-marker repeats E3900 and D1100 have diverged genotypes of different origin at the sequence level, the genomic sequences of both repeats were compared between cultivated rye and weedy rye from five different origins. KEY RESULTS B chromosomes in cultivated and weedy rye have maintained a similar molecular structure at the level of subspecies. The high degree of conservation of the non-disjunction control region regarding its transcription activity, histone composition and replication underlines the functional importance of this chromosome region for the maintenance of Bs. The conserved chromosome structure suggests a monophyletic origin of the rye B. As Bs were found in different countries, it is likely that Bs were frequently present in the seed material used in early agriculture. CONCLUSIONS The surprisingly conserved chromosome structure suggests that although the rye Bs experienced rapid evolution including multiple rearrangements at the early evolutionary stages, this process has slowed significantly and may have even ceased during its recent evolution.

A relative comparison between Hidden Markov- and Log-Linear- based models for differential expression analysis in a real time course RNA sequencing data

With the advent of the Next Generation Sequencing technologies, RNA-seq has become known as an optimal approach for studying gene expression profiling. Particularly, time course RNA-seq differential expression analysis has been used in many studies to identify candidate genes. However, applying a statistical method to efficiently identify differentially expressed genes (DEGs) in time course studies is challenging due to inherent characteristics of such data including correlation and dependencies over time. Here we aim to relatively compare EBSeq-HMM, a Hidden Markov-based model, with multiDE, a Log-Linear-based model, in a real time course RNA sequencing data. In order to conduct the comparison, common DEGs detected by edgeR, DESeq2 and Voom (referred to as Benchmark DEGs) were utilized as a measure. Each of the two models were compared using different normalization methods. The findings revealed that multiDE identified more Benchmark DEGs and showed a higher agreement with them than EBSeq-HMM. Furthermore, multiDE and EBSeq-HMM displayed their best performance using TMM and Upper-Quartile normalization methods, respectively.