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.
Highlights
The genetic information is believed to be uniform in somatic and gamete precursor cells in most organisms
Elimination of A. speltodies B chromosomes occurs in the central meristematic zone between the developing apical meristem and embryonic root [3]
To evaluate whether the process of B chromosome elimination affects the transcriptome of developing embryos, the central meristematic regions of 17 to 20 days after anthesis (DAA) embryos of mother plants with and without B chromosomes were isolated by laser capture microdissection (LCM) (Figure 2), and RNA-seq was performed for transcriptome profiling
Summary
The genetic information is believed to be uniform in somatic and gamete precursor cells in most organisms. Some species demonstrate regular elimination of specific DNA fragments as a part of the developmental program This occurs either as a loss of entire chromosomes, chromosome fragments or DNA sequences, often during the differentiation of somatic and germline cells. B chromosomes (Bs) can be observed in some plant, animal and fungi species as a dispensable addition to the basic karyotype Their presence may be neutral in regard to the phenotypic characteristics of the host or it may exert detrimental effects on the fitness and fertility, often depending on the number of Bs in individuals [4]. Some B chromosome-specific genes of Ae. speltoides were identified [3], no information about genes involved in chromosome elimination exists It is not known whether this process affects the transcriptome of developing embryos in an indirect way. Genes associated with chromosome segregation stand out as candidates involved in the process of B chromosome elimination
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