The rpl23 gene and pseudogene are hotspots of illegitimate recombination in barley chloroplast mutator seedlings

F Lencina,A R Prina,M G Pacheco,A M Landau,K Kobayashi,M E Petterson

doi:10.1038/s41598-019-46321-6

Abstract

Previously, through a TILLING (Targeting Induced Local Lesions in Genomes) approach applied on barley chloroplast mutator (cpm) seedlings a high frequency of polymorphisms in the rpl23 gene was detected. All the polymorphisms corresponded to five differences already known to exist in nature between the rpl23 gene located in the inverted repeats (IRs) and the rpl23 pseudogene located in the large single copy region (LSC). In this investigation, polymorphisms in the rpl23 gene were verified and besides, a similar situation was found for the pseudogene in cpm seedlings. On the other hand, no polymorphisms were found in any of those loci in 40 wild type barley seedlings. Those facts and the independent occurrence of polymorphisms in the gene and pseudogene in individual seedlings suggest that the detected polymorphisms initially arose from gene conversion between gene and pseudogene. Moreover, an additional recombination process involving small recombinant segments seems to occur between the two gene copies as a consequence of their location in the IRs. These and previous results support the hypothesis that the CPM protein is a component of the plastome mismatch repair (MMR) system, whose failure of the anti-recombination activity results in increased illegitimate recombination between the rpl23 gene and pseudogene.

Highlights

The plastid genome or plastome is considered more conserved evolutionarily in comparison to the nuclear genome in terms of its structural organization and gene content
Given that by a blast analysis some of these polymorphisms were found in nuclear DNA sequences, it is appropriate to discuss if the polymorphisms detected by celery juice extract (CJE) digestions in cpm seedlings correspond to molecular differences that raised under the influence of the cpm genotype in the plastid rpl[23] gene and/or the pseudogene or, on the contrary, if we detected polymorphisms already existing in the nucleus
It is proposed that illegitimate recombination occurs in cpm seedlings as a consequence of failure of the mismatch repair (MMR) system anti-recombination activity that is usually in charge of preventing promiscuous recombination[42]

Summary

Introduction

The plastid genome or plastome is considered more conserved evolutionarily in comparison to the nuclear genome in terms of its structural organization and gene content. We proved that the plastome was the location of a number of mutations isolated from cpm plants[9,10,11,12] and recently[13], we extended the molecular analysis of the plastome in cpm seedlings through a TILLING (Targeting Induced Local Lesions in Genomes) approach Following this strategy, we identified a wide range of plastome genes containing polymorphisms, consistent with our previous hypothesis about the involvement of the Cpm gene in maintaining plastome stability[6,14]. We performed a deeper analysis of the rpl[23] gene and included the rpl[23] pseudogene using the same DNA samples of cpm seedlings previously investigated by Landau et al.[13] Both regions were studied in two groups of control genotypes. The other group consisted of several barley genotypes representing a wide range of origins

Methods

Results

Discussion

Conclusion