Caught in the Act: Variation in plastid genome inverted repeat expansion within and between populations of Medicago minima

• Published in: Ecology and evolution 2020-11, Vol.10 (21), p.12129-12137
• Main Authors: Choi, In‐Su, Jansen, Robert, Ruhlman, Tracey
• Format: Article
• Language: English
• Subjects: Alfalfa; Deoxyribonucleic acid; DNA; Expansion; gene conversion; Genomes; Haplotypes; homologous recombination; Inverted repeat; inverted repeat expansion; Legumes; medicago; Medicago lupulina; Medicago minima; Mutation; Nitrogen; Original Research; Papilionoideae; Phylogenetics; plastid haplotype variation; plastome evolution; Plastomes; Polymerase chain reaction; Populations; Seeds
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.6839

The inverted repeat (IR) lacking clade (IRLC) is a monophyletic group within the Papilionoideae subfamily of Fabaceae where plastid genomes (plastomes) do not contain the large IR typical of land plants. Recently, an IRLC legume, Medicago minima, was found to have regrown a ~9 kb IR that contained a number of canonical IR genes, and closely related M. lupulina contained an incomplete IR of ~425 bp. Complete plastomes were generated for seven additional species, putative members of the M. minima clade. Polymerase chain reaction was employed to investigate the presence of the IR across M. minima and M. lupulina including individuals of nine and eight Eurasian and North African accessions and 15 and 14 Texas populations, respectively. While no sequence similar to the ~9 kb IR was detected among the seven newly sequenced plastomes, all Eurasian and North African accessions of M. minima contained the IR. Variation in IR extent was detected within and between the Texas populations. Expansions of 13 bp and 11 bp occurred at the boundaries of both IR/small single‐copy regions, and populations had one or the other expansion, but not both. Expansion of the IR was not detected in the accessions from Eurasia and North Africa suggesting recent mutations yielded at least two additional plastid haplotypes in M. minima. A recent study revealed the reemergence of the plastome inverted repeat (IR) in Medicago minima, which belongs to a clade of legumes defined by its absence. Seven putatively related plastomes were sequenced, and accessions/populations of M. minima from Europe, Asia, Africa, and Texas were assayed for presence of the IR and variation in its boundaries. While “Old World” populations of M. minima all contained identical IRs to the accession that was previously sequenced, variation in the IR boundaries was detected within and between Texas field‐collected populations. Range expansion, haplotype distribution, and IR expansion mechanisms are discussed.