Identification and characterization of rye genes not expressed in allohexaploid triticale

Abstract

BackgroundOne of the most important evolutionary processes in plants is polyploidization. The combination of two or more genomes in one organism often initially leads to changes in gene expression and extensive genomic reorganization, compared to the parental species. Hexaploid triticale (x Triticosecale) is a synthetic hybrid crop species generated by crosses between T. turgidum and Secale cereale. Because triticale is a recent synthetic polyploid it is an important model for studying genome evolution following polyploidization. Molecular studies have demonstrated that genomic sequence changes, consisting of sequence elimination or loss of expression of genes from the rye genome, are common in triticale. High-throughput DNA sequencing allows a large number of genes to be surveyed, and transcripts from the different homeologous copies of the genes that have high sequence similarity can be better distinguished than hybridization methods previously employed.ResultsThe expression levels of 23,503 rye cDNA reference contigs were analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye, as well as in five 454-cDNA data sets created from triticale seedling shoot, ovary, stigma, pollen and seed tissues to identify the classes of rye genes silenced or absent in the recent synthetic hexaploid triticale. Comparisons between diploid rye and hexaploid triticale detected 112 rye cDNA contigs (~0.5%) that were totally undetected by expression analysis in all triticale tissues, although their expression was relatively high in rye tissues. Non-expressed rye genes were found to be strikingly less similar to their closest BLASTN matches in the wheat genome or in the other Triticum genomes than a test set of 200 random rye genes. Genes that were not detected in the RNA-seq data were further characterized by testing for their presence in the triticale genome by PCR using genomic DNA as a template.ConclusionGenes with low similarity between rye sequences and their closest matches in the Triticum genome have a higher probability to be repressed or absent in the allopolyploid genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1480-x) contains supplementary material, which is available to authorized users.

Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale

“…These were then assembled de novo and sorted into “plant-“(80.4%) and “fungal”-derived (15.2%) via BLAST analyses against the C. purpurea genome, a rye cDNA database [25] and NCBI databases. Transcripts mapping to both, plant and fungal sequences, were excluded (4.5%).…”

“…After quality control (Q ≥ 20) the cleaned reads were mapped to “de novo” assembled transcripts. The transcripts were sorted into putatively plant, putatively fungal transcript and transcripts of unclear origin via blast searches against the C. purpurea genome (http://pedant.gsf.de/pedant3htmlview/pedant3view?Method=analysis&Db=p3_p76493_Cla_purpu), NCBI databases and a collection of rye cDNA contigs [25]. BGI Hongkong Co. removed all reads mapping as well to “fungal” as to “plant” de novo assembled transcripts from the clean reads.…”

Mobile Introns Shape the Genetic Diversity of Their Host Genes

“…As a consequence of this manual inspection, we conservatively excluded strain YJM1250, which exhibits an unusual multinucleotide difference at the 5′ end of exon 6, which would have further exacerbated the SNP density gradient reported below. We also excluded strain YJM1399, whose mitochondrial genome was previously found to be more closely related to S. paradoxus (Wolters et al 2015). Polymorphic sites in cob and cox1 were therefore identified from the alignment of 92 sequences.…”

“…Found in transfer RNA (tRNA), ribosomal RNA (rRNA) and (occasionally) protein-coding genes in bacteria and archaea, they are particularly numerous in mitochondrial genomes of fungi and plants where they have invaded genes encoding components of the electron transport chain (ETC) (Lambowitz and Belfort 1993). In many instances, fungal self-splicing introns have remained mobile, as demonstrated by experiments that track invasion capacity by crossing intron-containing with intron-free yeast strains (Jacquier and Dujon 1985; Wenzlau et al 1989; Lazowska et al 1994; Paschke et al 1994) and intron presence/absence polymorphisms across natural populations of Saccharomyces cerevisiae (Wolters et al 2015), Schizosaccharomyces pombe (Zimmer et al 1987), and Lachancea kluyveri (Jung et al 2012). For the majority of self-splicing introns in S. cerevisiae , spreading to an intron-free location is initiated by a homing endonuclease that is encoded in the intron itself and binds a large (∼20–30 bp), often singular target motif with high affinity (Jacquier and Dujon 1985; Moran et al 1992).…”

Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and thePh1locus

“…Kallisto was used for mapping because in wheat, it accurately distinguishes reads from homoeologues carrying genes with a sequence identity between 95-97 % (Ramírez-González et al, 2018). Therefore, kallisto is capable of distinguishing wheat and rye reads, which are more divergent (91 % sequence identity within genes (Khalil et al, 2015)). The percentage of reads pseudoaligned to this transcriptome was similar across samples, with a mean value of 71% for wheat-rye hybrids and triticale ( Table S2 ).…”