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Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Pryer KM, Mathews S - Nat Commun (2015)

Bottom Line: Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved.Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades.Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.

ABSTRACT
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

No MeSH data available.


Related in: MedlinePlus

Phylogeny of fern and lycophyte phytochromes.Previously identified phytochromes are shown in bold. Support values associated with branches are maximum likelihood bootstrap values (BS)/Bayesian posterior probabilities (PP); these are only displayed (along with thickened branches) if BS>70 and PP>0.95. Thickened branches without numbers are 100/1.0. The position of orange circles estimates the origin of inferred gene duplications. Italicized capital letters within each circle correspond to the duplication event mentioned in the text, and the numbers/letters adjacent to each circle indicate the names of the gene duplicates.
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f5: Phylogeny of fern and lycophyte phytochromes.Previously identified phytochromes are shown in bold. Support values associated with branches are maximum likelihood bootstrap values (BS)/Bayesian posterior probabilities (PP); these are only displayed (along with thickened branches) if BS>70 and PP>0.95. Thickened branches without numbers are 100/1.0. The position of orange circles estimates the origin of inferred gene duplications. Italicized capital letters within each circle correspond to the duplication event mentioned in the text, and the numbers/letters adjacent to each circle indicate the names of the gene duplicates.

Mentions: In contrast, phytochromes in mosses are diverse, with at least four distinct clades resulting from three gene duplications (Fig. 4). The phylogeny reveals those moss phytochromes that are orthologous to the previously named P. patens phytochromes, PpPHY1–5. The Physcomitrella phytochromes and their orthologs form the following clades: moss PHY1_3 (including PpPHY1 and PpPHY3), moss PHY2_4 (including PpPHY2 and PpPHY4), and moss PHY5 (including PpPHY5A–C). An ancient duplication (‘D' in Fig. 4) gave rise to moss PHY1_3 and moss PHY2_4+PHY5 clades. The timing of this duplication is dependent on the phylogenetic position of the Takakia phytochrome, resolved here as sister to the moss PHY2_4+PHY5 clade, but without support (Fig. 4). Because Takakia (Takakiopsida) represents the earliest diverging lineage in the moss species phylogeny36, the first phytochrome duplication probably predates the origin of all extant mosses. In the moss PHY2_4+PHY5 clade, another duplication (‘E' in Fig. 5) occurred following the split of Andreaea (Andreaeopsida) but before Atrichum (Polytrichopsida) diverged, separating moss PHY2_4 and PHY5. The moss PHY5 clade had an additional duplication (‘F' in Fig. 4), probably after Physcomitrella diverged, that resulted in moss PHY5D and PHY5E subclades.


Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Pryer KM, Mathews S - Nat Commun (2015)

Phylogeny of fern and lycophyte phytochromes.Previously identified phytochromes are shown in bold. Support values associated with branches are maximum likelihood bootstrap values (BS)/Bayesian posterior probabilities (PP); these are only displayed (along with thickened branches) if BS>70 and PP>0.95. Thickened branches without numbers are 100/1.0. The position of orange circles estimates the origin of inferred gene duplications. Italicized capital letters within each circle correspond to the duplication event mentioned in the text, and the numbers/letters adjacent to each circle indicate the names of the gene duplicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525182&req=5

f5: Phylogeny of fern and lycophyte phytochromes.Previously identified phytochromes are shown in bold. Support values associated with branches are maximum likelihood bootstrap values (BS)/Bayesian posterior probabilities (PP); these are only displayed (along with thickened branches) if BS>70 and PP>0.95. Thickened branches without numbers are 100/1.0. The position of orange circles estimates the origin of inferred gene duplications. Italicized capital letters within each circle correspond to the duplication event mentioned in the text, and the numbers/letters adjacent to each circle indicate the names of the gene duplicates.
Mentions: In contrast, phytochromes in mosses are diverse, with at least four distinct clades resulting from three gene duplications (Fig. 4). The phylogeny reveals those moss phytochromes that are orthologous to the previously named P. patens phytochromes, PpPHY1–5. The Physcomitrella phytochromes and their orthologs form the following clades: moss PHY1_3 (including PpPHY1 and PpPHY3), moss PHY2_4 (including PpPHY2 and PpPHY4), and moss PHY5 (including PpPHY5A–C). An ancient duplication (‘D' in Fig. 4) gave rise to moss PHY1_3 and moss PHY2_4+PHY5 clades. The timing of this duplication is dependent on the phylogenetic position of the Takakia phytochrome, resolved here as sister to the moss PHY2_4+PHY5 clade, but without support (Fig. 4). Because Takakia (Takakiopsida) represents the earliest diverging lineage in the moss species phylogeny36, the first phytochrome duplication probably predates the origin of all extant mosses. In the moss PHY2_4+PHY5 clade, another duplication (‘E' in Fig. 5) occurred following the split of Andreaea (Andreaeopsida) but before Atrichum (Polytrichopsida) diverged, separating moss PHY2_4 and PHY5. The moss PHY5 clade had an additional duplication (‘F' in Fig. 4), probably after Physcomitrella diverged, that resulted in moss PHY5D and PHY5E subclades.

Bottom Line: Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved.Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades.Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, North Carolina 27708, USA.

ABSTRACT
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

No MeSH data available.


Related in: MedlinePlus