Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids

Abstract

Background: The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses 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 resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content.

Results: The Drimys, Liriodendron, and Piper plastid genomes are very similar in size at 160,604, 159,886 bp, and 160,624 bp, respectively. Gene content and order are nearly identical to many other unrearranged angiosperm plastid genomes, including Calycanthus, the other published magnoliid genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions. 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. Phylogenetic analyses using parsimony and likelihood methods and sequences of 61 protein-coding genes provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. Strong support is reported for monocots and eudicots as sister clades with magnoliids diverging before the monocot-eudicot split. The trees also provided moderate or strong support for the position of Amborella as sister to a clade including all other angiosperms.

Conclusion: Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, 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.

Figure 1

Gene map of the Drimys granatensis plastid genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction.

Figure 2

Gene map of the Piper coenoclatum plastid genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction.

Figure 3

Histogram of GC content for 34 seed plant plastid genomes, including the gymnosperm Pinus and 33 angiosperms (see Table 2 for list of genomes). Taxa are arranged phylogenetically following tree in Fig. 8. A. Overall GC content of complete genomes. B. GC content for 66 protein-coding genes, including average value for all codon positions, followed by values for the 1st, 2nd, and 3rd codon positions, respectively.

Figure 4

Graphs of GC content plotted over the entire plastid genomes of Drimys and Piper. X axis represents the proportion of GC content between 0 and 1 and the Y axis gives the coordinates in kb for the genomes. Coding and non-coding regions are indicated in blue and red, respectively. The green dashed line indicates that average GC content for the entire genome.

Figure 5

Histogram of GC content for photosynthetic and genetic system genes for 34 seed plant plastid genomes (see Table 2 for list of genomes). Taxa are arranged phylogenetically following tree in Fig. 8. GC content includes average value for all codon positions, followed by values for the 1st, 2nd, and 3rd codon positions, respectively. A. GC content for 33 photosynthetic genes. B. GC content for 22 genetic system genes.

Figure 6

Histogram of GC content for NADH and rRNA genes for 34 seed plant plastid genomes (see Table 2 for list of genomes). Taxa are arranged phylogenetically following tree in Fig. 8. A. GC content for 11 NADH genes, which includes average value for all codon positions, followed by values for the 1st, 2nd, and 3rd codon positions, respectively. B. GC content for four rRNA genes.

Figure 7

Graphs of GC content plotted over the entire plastid genomes of 34 seed plants. The graphs are organized by genomes with the same gene order and by clade in the phylogenetic trees in Figures 8 and 9. X axis represents the proportion of GC content between 0 and 1 and the Y axis gives the coordinates in kb for the genomes.

Figure 8

Phylogenetic tree of 35-taxon data set based on 61 plastid protein-coding genes using maximum parsimony. The tree has a length of 61,095, a consistency index of 0.41 (excluding uninformative characters) and a retention index of 0.57. Numbers at each node are bootstrap support values. Numbers above node indicate number of changes along each branch and numbers below nodes are bootstrap support values. Ordinal and higher level group names follow APG II [93]. Taxa in red are the three new genomes reported in this paper.

Figure 9

Phylogenetic tree of 35-taxon data set based on 61 plastid protein-coding genes using maximum likelihood. The single ML tree has an ML value of – lnL = 342478.92. Numbers at nodes are bootstrap support values ≥ 50%. Scale at base of tree indicates the number of base substitutions. Ordinal and higher level group names follow APG II [93]. Taxa in red are the three new genomes reported in this paper.