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Background Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the extent of its genomic variation and its difference from allopolyploidies remains unknown. Methods Here, we explored this issue using the bread wheat cultivar SR3, a derivative of an asymmetric somatic hybrid between the cultivar JN177 and an accession of tall wheatgrass (Thinopyrum elongatum). The ESTs (expressed sequence taqs) were large-scale sequenced using the cDNA library constructed in each of SR3 and JN177. Point mutations and indels (insertions and deletions) of SR3 were calculated, and their difference from the genetic variation of bread wheat and its ancestors were compared, with aim to analyze the extent and pattern of sequence variation induced by somatic hybridization. Results Both point mutations and indels (insertions and deletions) were frequently induced by somatic hybridization in the coding sequences. While the genomic shock caused by allopolyploidization tends to favor deletion over insertion, there was no evidence for such a preference following asymmetric somatic hybridization. The GC content of sequence adjacent to indel sites was also distinct from what has been observed in allopolyploids. Conclusions This study demonstrates that asymmetric somatic hybridization induces high frequency of genetic variation in a manner partially different from allopolipoidization. Asymmetric somatic hybridization provides appropriate material to comprehensively explore the nature of the genetic variation induced by genomic shock. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1974-6) contains supplementary material, which is available to authorized users.

Background Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at present rather unclear. Results To explore this relationship, the sequences of a set of genes containing between zero and nine introns was extracted from the published genome sequences of three algal species, one moss, one fern and six angiosperms (three monocotyledonous species and three dicotyledonous species). In the algal genomes, the frequency of synonymous codons of the form NNG/NNC (codons with G and C at the third position) was positively related to intron number, but that of NNA/NNT was inversely correlated; the opposite was the case in the land plant genomes. The frequency of NNC/NNG was higher and that of NNA/NNT lower in two terminal exons than in the interstitial exons in the land plant genes, but the rule showed to be opposite in the algal genes. SCUB patterns in the interstitial and two terminal exons mirror the different evolutionary relationships between these plant species, while the first exon shows the highest level of conservation is therefore concluded to be the one which experiences the heaviest selection pressure. The phenomenon of SCUB may also be related to DNA methylation induced conversion of CG to AT. Conclusions These data provide some evidence of linkage between SCUB, the evolution of introns and DNA methylation, which brings about a new perspective for understanding how genomic variation is created during plant evolution.