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Abstract 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 relatedM. lupulinacontained an incomplete IR of ~425 bp. Complete plastomes were generated for seven additional species, putative members of theM. minimaclade. Polymerase chain reaction was employed to investigate the presence of the IR acrossM. minimaandM. lupulinaincluding 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 ofM. minimacontained 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 inM. minima.
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The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes
Summary The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR‐lacking clade (IRLC) and the plant modelMedicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non‐papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early‐branching papilionoid clades. A number of IR‐related and repeat‐mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated withycf2resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non‐IR repeats in the progression of plastome change is discussed.
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- Award ID(s):
- 1853024
- PAR ID:
- 10449648
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 107
- Issue:
- 3
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 861-875
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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