Plastome sequencing of ten nonmodel crop species uncovers a large insertion of mitochondrial DNA in cashew

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative rpl22 in cinnamon (Cinnamomum verum J. Presl) and other sequenced Lauraceae and an apparent functional transfer of rpl23 to the nucleus of quinoa (Chenopodium quinoa Willd.). In the orchard tree cashew (Anacardium occidentale L.), we report the insertion of an ~6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact ccmB open reading frame. Using three plastome markers for five species of Anacardium, we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated.