Abstract
The magnoliids represent the largest basal angiosperm clade with four orders, 19 families and 8,500 species. Although several recent angiosperm molecular phylogenies have supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence has resulted in phylogenies supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. This is one of the most important remaining issues concerning relationships among basal angiosperms. We sequenced the chloroplast genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other completed angiosperm chloroplast genomes to assess phylogenetic relationships among magnoliids. The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp, respectively. The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper). The gene order of both taxa is nearly identical to many other unrearranged angiosperm chloroplast genomes, including Calycanthus, the other published magnoliid genome. Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions (both intergenic spacers and introns). Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Across the genome, GC content is highest in the inverted repeat due to the presence of rRNA genes and lowest in the small single copy region where most NADH genes are located. Phylogenetic analyses using maximum parsimony and maximum likelihood methods were performed on DNA sequences of 61 protein-coding genes. Trees from both analyses provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. The phylogenies also provided moderate to strong support for the basal position of Amborella, and a sister relationship of magnoliids to a clade that includes monocots and eudicots. The complete sequences of three magnoliid chloroplast genomes provide new data from the largest basal angiosperm clade. Evolutionary comparisons of these new genome sequences, combined with other published angiosperm genome, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots.
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Claims 17
Claim · model-written summary
The Drimys chloroplast genome is nearly identical in size to the Piper genome, at 160,606 bp.
DrimysOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp”
Claim · model-written summary
The Piper chloroplast genome is nearly identical in size to the Drimys genome, at 160,624 bp.
.jpg?width=60){kind=small}
PiperOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e1“The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp”
Claim · model-written summary
Drimys chloroplast genome has an inverted repeat of 26,649 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Piper chloroplast genome has an inverted repeat of 27,039 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Drimys chloroplast genome has a large single copy region of 88,685 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Piper chloroplast genome has a large single copy region of 87,666 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Drimys chloroplast genome has a small single copy region of 18,621 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Piper chloroplast genome has a small single copy region of 18,878 bp.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper)”
Claim · model-written summary
Overall GC content of angiosperm chloroplast genomes ranges from 34% to 39%.
Verbatim
e3“Overall GC content ranges from 34-39%”
e4“Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome”
Claim · model-written summary
Coding regions have a higher GC content than non-coding regions in angiosperm chloroplast genomes.
Verbatim
e4“Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome”
e5“coding regions have a substantially higher GC content than non-coding regions”
Claim · model-written summary
GC content of protein-coding genes varies by codon position, with 1st codon > 2nd codon > 3rd codon.
Verbatim
e4“Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome”
e6“Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon”
Claim · model-written summary
Photosynthetic genes have the highest GC percentage and NADH genes the lowest among functional groups.
Verbatim
e4“Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome”
e7“it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest”
Claim · model-written summary
Across the chloroplast genome, GC content is highest in the inverted repeat and lowest in the small single copy region.
Verbatim
e4“Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome”
e5“Across the genome, GC content is highest in the inverted repeat due to the presence of rRNA genes and lowest in the small single copy region where most NADH genes are located”
Claim · model-written summary
Magnoliids are strongly supported as monophyletic.
- Taxon
- magnoliidsMagnoliidaee0
- Outcome
- monophyly of magnoliidse0
- Qualifier
- strong supporte0
Verbatim
e0“Trees from both analyses provided strong support for the monophyly of magnoliids”
Claim · model-written summary
Two strongly supported magnoliid groups are Canellales/Piperales and Laurales/Magnoliales.
- Taxon
- magnoliidsMagnoliidaee0
- Outcome
- the Canellales/Piperales and the Laurales/Magnolialese1
Verbatim
e0“Trees from both analyses provided strong support for the monophyly of magnoliids”
e1“two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales”
Claim · model-written summary
Amborella has a basal position among angiosperms with moderate to strong support.
_fragment.jpg?width=60){kind=small}
AmborellaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
_fragment.jpg?width=500)
Verbatim
e0“The phylogenies also provided moderate to strong support for the basal position of Amborella, and a sister relationship of magnoliids to a clade that includes monocots and eudicots”
Claim · model-written summary
Magnoliids are sister to a clade of monocots and eudicots, with moderate to strong support.
- Taxon
- magnoliidsMagnoliidaee0
- Outcome
- sister relationship of magnoliids to a cladee0
- Qualifier
- moderate to strong supporte0
Verbatim
e0“The phylogenies also provided moderate to strong support for the basal position of Amborella, and a sister relationship of magnoliids to a clade that includes monocots and eudicots”