Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

Abstract

Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired short, novel IRs, some of which also exhibit recombinational activity to generate genomic structural diversity. This diversity has been shown to exist between, and occasionally within, cupressophyte species, but it is not known whether multiple genomic forms coexist within individual plants. To examine the recombinational potential of the novel cupressophyte IRs within individuals and between species, we sequenced the plastomes of four closely related species of Juniperus. The four plastomes have identical gene content and genome organization except for a large 36 kb inversion between approximately 250 bp IR containing trnQ-UUG. Southern blotting showed that different isomeric versions of the plastome predominate among individual junipers, whereas polymerase chain reaction and high-throughput read-pair mapping revealed the substoichiometric presence of the alternative isomeric form within each individual plant. Furthermore, our comparative genomic studies demonstrate that the predominant and substoichiometric arrangements of this IR have changed several times in other cupressophytes as well. These results provide compelling evidence for substoichiometric shifting of plastomic forms during cupressophyte evolution and suggest that substoichiometric shifting activity in plastid genomes may be adaptive.

Passifloraplastome sequencing reveals widespread genomic rearrangements

“…Passiflora provides additional examples of parallel inversions in seed plant plastome evolution. Inversion isomers are long known to be present in seed plant plastomes (Kolodner & Tewari, ; Palmer, ) at the population level and growing evidence suggests dynamic inversion in individual plants (Guo et al, ; Gurdon & Maliga, ; Ruhlman et al, ). In addition to typical IR mediated inversion, different plastome conformations within a species can also occur by intra‐ and intermolecular recombination between large repeats in repeat rich plastomes (Ruhlman et al, ).…”

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae

“…Draft organellar genomes of C. paramensis and B. pedicularioides were assembled from the Illumina sequence reads with Velvet version 1.2.0342 using multiple combinations of kmer (61, 71, 81, 91) and expected coverage (50, 100, 200, 500, 1000) values, as described previously4344. Organellar contigs were identified in each assembly by using default blastn searches with known organellar gene sequences from related Lamiales species as queries.…”

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

“…However, recent large‐scale expansions (exceeding several kb) were reported for a few lineages, such as Pelargonium , Psilotum , and Trochodendraceae (Chumley et al ., ; Grewe et al ., ; Sun et al ., ), which transferred numerous genes from the SC regions into the IR. At the opposite extreme, some plants have lost most, or even all, of the IR, as observed for conifers, many legumes, and some species of Erodium (Palmer et al ., ; Raubeson & Jansen, ; Tsudzuki et al ., ; Guisinger et al ., ; Guo et al ., ).…”