Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

Abstract

Some eukaryotes exhibit dramatic genome size differences between cells of different organs, resulting from programmed elimination of chromosomes. Here, we present the first transcriptome analysis of programmed chromosome elimination using laser capture microdissection (LCM)-based isolation of the central meristematic region of Aegilops speltoides embryos where B chromosome (B) elimination occurs. The comparative RNA-seq analysis of meristematic cells of embryos with (Bplus) and without Bs (B0) allowed the identification of 14,578 transcript isoforms (35% out of 41,615 analyzed transcript isoforms) that are differentially expressed during the elimination of Bs. A total of 2908 annotated unigenes were found to be up-regulated in Bplus condition. These genes are either associated with the process of B chromosome elimination or with the presence of B chromosomes themselves. GO enrichment analysis categorized up-regulated transcript isoforms into 27 overrepresented terms related to the biological process, nine terms of the molecular function aspect and three terms of the cellular component category. A total of 2726 annotated unigenes were down-regulated in Bplus condition. Based on strict filtering criteria, 341 B-unique transcript isoforms could be identified in central meristematic cells, of which 70 were functionally annotated. Beside others, genes associated with chromosome segregation, kinetochore function and spindle checkpoint activity were retrieved as promising candidates involved in the process of B chromosome elimination.

Rye B chromosomes differently influence the expression of A chromosome–encoded genes depending on the host species

“…Alteration of Nuf2 in A. thaliana affects the microtubule organization and results in lagging chromatids (Li et al 2021). Interestingly, B-specific Nuf2 transcripts are also associated with the process of programmed elimination of B chromosomes in Aegilops speltoides embryos (Boudichevskaia et al 2020). Ae.…”

Natural genetic engineering: A programmed chromosome/DNA elimination

“…Many plants, like 15% of all eukaryotic species, carry, in addition to standard chromosomes (A chromosomes), the supernumerary B chromosomes (Hanlon et al, 2018). Although B chromosomes are expandable, and without any known function, they are preferentially inherited at the super-Mendelian frequency through the "chromosome drive" mechanism (Dalla Benetta et al, 2019;Ruban et al, 2020). Recent studies on rye species showed that the sister chromatids of B chromosomes do not separate (non-disjunct) during the asymmetrical division that produces the germ cells (sperm of the pollen) and somatic (vegetative) cell, and preferentially segregate on the asymmetrical spindle to the generative pole.…”

“…This process, rerepeated through several generations, leads to the accumulation of supernumerary B chromosomes in the germ cells (Dalla Benetta et al, 2019). Ruban et al (2020) studied B chromosome behavior (elimination and drive) in developing roots and during the first mitosis of the pollen, respectively, in the goatgrass Ae.…”

“…This suggests that first B chromosomes derived from a duplication of A chromosomes that lost the euchromatic regions but retained the centromeric and pericentromeric regions, which, later in evolution, underwent mutations, translocations, inversions, and deletions, making the B chromosomes non-functional and quasi parasitic (Dalla Benetta et al, 2019;Marques et al, 2018). Application of novel, ingenious techniques such as transcriptome analysis combined with the laser capture microdissection (LCM) allowed, recently, for detailed analysis of eliminated B chromosomes in the central meristematic region of Aegilops speltoides embryos (Boudichevskaia et al 2020). By comparing RNA sequences of meristematic cells of embryos with and without B chromosomes, authors identified 14,578 transcript isoforms, i.e., 35% of 41,615 analyzed, differentially expressed during B chromosome elimination.…”

B-A Chromosome Translocations Possessing an A Centromere Partly Overcome the Root-Restricted Process of Chromosome Elimination in Aegilops speltoides

“…Independent of centromere activity, B chromosomes demonstrate nondisjunction of chromatids and lagging in anaphase, resulting in micronucleation and subsequent elimination. This process might allow root tissues to survive the detrimental expression or overexpression of B chromosome-located root-specific genes with paralogs located on standard A chromosomes ( Boudichevskaia et al, 2020 ; Ruban et al, 2020 ).…”