Abstract
BACKGROUND: The columbine genus (Aquilegia) contains many species with horticultural and pharmaceutical importance. However, a well-resolved phylogeny for this genus remains lacking owing to recent and rapid radiation. We obtained plastomes of 75 Aquilegia species and six species of other genera in Thalictroideae to reconstruct a robust phylogeny for Aquilegia. Within the phylogenetic framework, we investigated the evolutionary patterns of structural variations in Aquilegia plastomes. We also examined appropriate molecular markers for species identification of this genus. RESULTS: Plastid phylogenomic analyses show that Aquilegia is monophyletic and divided into two major clades and eight subclades, largely in agreement with species geographical distributions. Aquilegia plastomes have copy number variations (CNVs) of genes at the boundaries of IR/SC regions. An inversion was identified in the large single-copy region (LSC) plastomes of Aquilegia, Semiaquilegia, and Urophysa. The inversion was adjacent to three distinct structures (type I-III) in LSC region, each characterized by presence or absence of different short inverted repeat (sIR) regions. The most recent common ancestor of Aquilegia species was type III, and other two types were derived by shortening or loss of sIRs. Ten hypervariable regions were identified in Aquilegia plastomes. CONCLUSIONS: We present a well-resolved phylogeny for Aquilegia. The CNVs of genes were observed frequently at the boundaries of IR/SC regions and sIR regions in the genus, and the inversions and sIR in LSC regions have phylogenetic signal and lead to notable variations in gene content and length of plastomes. The new hypervariable regions can be used for phylogenetic analyses and molecular identification of Aquilegia. This study provides new insights into the structural evolution of plastome in angiosperms, and also have important implications for the conservation and utilization of Aquilegia species.
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Claims 9
Claim · model-written summary
Aquilegia is monophyletic.
- Outcome
- monophyletice1
AquilegiaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Aquilegia is monophyletic”
Claim · model-written summary
Aquilegia is divided into two major clades and eight subclades.
- Outcome
- two major clades and eight subcladese2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Aquilegia is monophyletic”
e2“divided into two major clades and eight subclades”
Claim · model-written summary
An inversion was identified in the LSC region of Aquilegia, Semiaquilegia and Urophysa plastomes.
- Organ / stage
- large single-copy region (LSC)e3
- Outcome
- inversione3
- Qualifier
- Semiaquilegia, and Urophysae3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“An inversion was identified in the large single-copy region (LSC) plastomes of Aquilegia, Semiaquilegia, and Urophysa”
Claim · model-written summary
The most recent common ancestor of Aquilegia species was type III.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“The most recent common ancestor of Aquilegia species was type III”
Claim · model-written summary
The other two LSC inversion types were derived by shortening or loss of short inverted repeats.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“The most recent common ancestor of Aquilegia species was type III”
e5“other two types were derived by shortening or loss of sIRs”
Claim · model-written summary
Copy number variations of genes were observed frequently at the boundaries of IR/SC regions in Aquilegia plastomes.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“Aquilegia plastomes have copy number variations (CNVs) of genes at the boundaries of IR/SC regions”
Claim · model-written summary
Ten hypervariable regions were identified in Aquilegia plastomes.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“Ten hypervariable regions were identified in Aquilegia plastomes”
Claim · model-written summary
The new hypervariable regions can be used for phylogenetic analyses and molecular identification of Aquilegia.
- Outcome
- phylogenetic analyses and molecular identificatione2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The new hypervariable regions can be used for phylogenetic analyses and molecular identification of Aquilegia”
Claim · model-written summary
Inversions and sIR in LSC regions carry phylogenetic signal and lead to notable variations in gene content and length of plastomes.
- Outcome
- notable variations in gene content and length of plastomese2
- Qualifier
- inversions and sIR in LSC regionse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Aquilegia is monophyletic”
e2“the inversions and sIR in LSC regions have phylogenetic signal and lead to notable variations in gene content and length of plastomes”