Extensive tRNA Gene Changes in Synthetic Brassica napus

Abstract

Allopolyploidization, where two species come together to form a new species, plays a major role in speciation and genome evolution. Transfer RNAs (abbreviated tRNA) are typically 73 to 94 nucleotides in length, and are indispensable in protein synthesis, transferring amino acids to the cell protein synthesis machinery (ribosome). To date, the regularity and function of tRNA gene sequence variation during the process of allopolyploidization has not been well understood. In this study, the inter-tRNA gene corresponding to tRNA amplification polymorphism (ITAP) method was used to detect changes in tRNA gene sequences in the progeny of interspecific hybrids between Brassica rapa and B. oleracea, mimicking the original B. napus (canola) species formation event. Cluster analysis showed that tRNA gene variation during allopolyploidization did not appear to have a genotypic basis.Significant variation occurred in the early generations of synthetic Brassica napus (F 1 and F 2 generations), but fewer alterations were observed in the later generation (F 3 ).The variation-prone tRNA genes tended to be located in AT-rich regions. BlastN analysis of novel tRNA gene variants against a Brassica genome sequence database showed that the variation of these tRNA-gene-associated sequences in allopolyploidization might result in variation of gene structure and function, e.g. metabolic process and transport.

The Potential of Molecular Indicators of Plant Virus Infection: Are Plants Able to Tell Us They Are Infected?

“…These regions were modified by selecting the region table within the software and setting regions for analysis to extend the LMW-RNA region to 200 nt and to encompass the composition of LMW-RNA components; that is 50-80 nt for transfer RNAs (tRNAs of 73-94 nt), 85-100 nt for small nucleolar RNAs (snoRNAs, e.g., U14 of 84-106 nt) and 110-180 nt for ribosomal RNAs (rRNAs; 5.8 S of 154 nt and 5 S of 120 nt) in addition to the sRNA region already set (10-40 nt). The LMW-RNA component regions were set to encompass the average nt size reported for each LMW-RNA component across the literature [70,71].…”

Exploring the gene pool ofBrassica napusby genomics‐based approaches

“…Synthetic B. napus (A r A r C o C o ) is known to be meiotically unstable with frequent chromosomal exchanges between the A and C subgenomes, which can result in genomic rearrangements and structural variants (Song et al ., 1995 ; Szadkowski et al ., 2010 ; Xiong et al ., 2011 ). Other changes may involve gene expression and epigenetic modifications (Chen and Pikaard, 1997 ; Gaeta et al ., 2007 ; Lukens et al ., 2006 ; Ran et al ., 2016 ; Xu et al ., 2009 ), transposable element activation and small RNA changes (Albertin et al ., 2006 ; Fu et al ., 2016 ; Hurgobin et al ., 2018 ; Palacios et al ., 2019 ), changes in tRNA (Wei et al ., 2014 ), and the rapid mutation of repetitive sequences (Gao et al ., 2014 ). Synthetic B. napus (A r A r C c C c ), whose genome was mostly replaced by B. rapa and B. carinata , showed a stable genome after generations of self‐pollination and recurrent selection but still contained numerous structural variation that was significantly different from that of traditional B. napus (Hu et al ., 2019 ; Zou et al ., 2018 ).…”