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,
- Award ID(s):
- 1853010
- NSF-PAR ID:
- 10472502
- Publisher / Repository:
- Nature.com
- Date Published:
- Journal Name:
- Scientific Reports
- Edition / Version:
- 1
- Volume:
- 12
- Issue:
- 1
- ISSN:
- 2045-2322
- Page Range / eLocation ID:
- 21172
- Subject(s) / Keyword(s):
- Medicago truncatula plastid phylogenomics germplasm accessions phylogenetics
- Format(s):
- Medium: X Size: 3.8MB Other: pdf
- Size(s):
- 3.8MB
- Sponsoring Org:
- National Science Foundation
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Abstract Medicago minima , was found to have regrown a ~9 kb IR that contained a number of canonical IR genes, and closely relatedM. lupulina contained an incomplete IR of ~425 bp. Complete plastomes were generated for seven additional species, putative members of theM. minima clade. Polymerase chain reaction was employed to investigate the presence of the IR acrossM. minima andM. 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 ofM. 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 inM. minima . -
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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 model
Medicago 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 withycf2 resulted 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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SUMMARY Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31
Medicago taxa we detected exceptionally high post‐IGT amplification of mitochondrial (mt) DNA sequences containingrps10 in the nuclear genome ofMedicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in theM. polymorpha nuclear genome. The mtrps10‐ like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6–3.0% of total genomic DNA, a value approximately three‐fold greater than the entire mitogenome inM. polymorpha . Compared to a typical mt gene, the mtrps10 ‐like sequence coverage level was 691.5–7198‐fold higher inM. polymorpha and closely related species. In addition to the post‐IGT amplification, our analysis identified the canonical telomeric repeat and the species‐specific satellite arrays that are likely attributable to an ancestral chromosomal fusion inM. polymorpha . A possible relationship between chromosomal instability and the mtrps10 ‐like tandem repeat family in theM. polymorpha clade is discussed. -
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Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics.
Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information.
Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of
rps16 andrpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%.Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.
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Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum , Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.more » « less
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- https://doi.org/10.1038/s41598-022-25381-1
