10.5061/DRYAD.N976P
Sinn, Brandon Tyler
The Ohio State University
Sedmak, Dylan D.
The Ohio State University
Kelly, Lawrence M.
New York Botanical Garden
Freudenstein, John V.
The Ohio State University
Data from: Total duplication of the small single copy region in the
angiosperm plastome: rearrangement and inverted repeat instability in
Asarum
Dryad
dataset
2018
Magnoliid
Aristolochia debilis
Asarum canadense
Asarum delavayi
Liriodendron tulipifera
Persea americana
Asarum epigynum
Piper cenocladum
Asarum minus
Asarum megacalyx
Litsea glutinosa
Piper kadsura
Drimys granadensis
Phoebe sheareri
Amborella trichopoda
Aristolochia contorta
Calycanthus floridus var. glaucus
Liriodendron chinense
Magnolia liliifera
Inverted Repeat Region
Asarum sieboldii
Saruma henryi
Chloranthus spicatus
Annona cherimola
Small Single Copy Region
Machilus balansae
Asarum
Magnolia officinalis
Cinnamomum micranthum f. kanehirae
National Science Foundation
https://ror.org/021nxhr62
DEB-1406732
2018-11-29T00:00:00Z
2018-11-29T00:00:00Z
en
https://doi.org/10.1002/ajb2.1001
3396846 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Premise of the Study: As more plastomes are assembled, it is evident that
rearrangements, losses, intergenic spacer expansion and contraction, and
syntenic breaks within otherwise functioning plastids are more common than
was thought previously, and such changes have developed independently in
disparate lineages. However, to date, the magnoliids remain characterized
by their highly conserved plastid genomes (plastomes). Methods: Illumina
HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma
henryi and those of representative species from each of the six taxonomic
sections of Asarum. Sequenced plastomes were compared in a phylogenetic
context provided by maximum likelihood and parsimony inferences made using
an additional 18 publicly available plastomes from early‐diverging
angiosperm lineages. Key Results: In contrast to previously published
magnoliid plastomes and the newly sequenced Saruma henryi plastome
published here, Asarum plastomes have undergone extensive disruption and
contain extremely lengthy AT‐repeat regions. The entirety of the small
single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii
has been incorporated into the inverted repeat regions (IR), and the SSC
of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an
inversion of a large portion of the large single copy region (LSC) such
that trnE‐UUC is adjacent to the LSC‐IR boundary. Conclusions: Plastome
divergence in Asarum appears to be consistent with trends seen in highly
rearranged plastomes of the monocots and eudicots. We propose that
plastome instability in Asarum is due to repetitive motifs that serve as
recombinatory substrates and reduce genome stability.
Magnoliids_alignment25 Magnoliid plastomes, with a single IR region
removed, aligned using MAFFT and processed using
Gblocks.Asaroideae_alignmentAsaroideae plastomes, with a single IR region
removed, aligned using MAFFT and processed using
Gblocks.trnH_alignmenttrnH(GUG) from plastomes and mitochondrial genomes
throughout the Piperales aligned using MAFFT and processed using Gblocks.