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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 phytochromes.Terminal clades are collapsed into higher taxonomic units (usually orders or classes) for display purposes. Orange circles indicate inferred gene duplications. Italicized capital letters within each circle correspond to duplication events mentioned in the text, and the numbers/letters adjacent to each orange circle are the names of gene duplicates. Canonical plant phytochromes originated in an ancestor of streptophytes (green star), and some charophyte algae retain non-canonical phytochromes (PHYX1 and PHYX2). Phytochrome domain architectures are shown on the right. Domains that are not always present are indicated by dashed outlines. Domain names: GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA); H/KD (histidine phosphorylation site (H) in the histidine kinase domain (KD)); PAS (Per/Arnt/Sim); PHY (Phytochrome); PKC (Protein Kinase C); REC (Response Regulator); and RING (Really Interesting New Gene). *Traditional Archaeplastida do not include cryptophytes32.
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f1: Phylogeny of phytochromes.Terminal clades are collapsed into higher taxonomic units (usually orders or classes) for display purposes. Orange circles indicate inferred gene duplications. Italicized capital letters within each circle correspond to duplication events mentioned in the text, and the numbers/letters adjacent to each orange circle are the names of gene duplicates. Canonical plant phytochromes originated in an ancestor of streptophytes (green star), and some charophyte algae retain non-canonical phytochromes (PHYX1 and PHYX2). Phytochrome domain architectures are shown on the right. Domains that are not always present are indicated by dashed outlines. Domain names: GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA); H/KD (histidine phosphorylation site (H) in the histidine kinase domain (KD)); PAS (Per/Arnt/Sim); PHY (Phytochrome); PKC (Protein Kinase C); REC (Response Regulator); and RING (Really Interesting New Gene). *Traditional Archaeplastida do not include cryptophytes32.

Mentions: Stramenopiles are a large eukaryotic clade that includes brown algae (such as kelps), golden algae and diatoms, the latter being an important component of plankton. Within this group, phytochromes are known so far only from brown algae, some of their viruses and diatoms. Their sequences form a clade that is sister to fungal phytochromes (Fig. 1 and Supplementary Fig. 2). Interestingly, the phytochrome from the brown algal virus EsV-1 (ref. 33) does not group with brown algae phytochromes, but instead is more closely related to those of diatoms. This relationship was not supported in a bootstrapping analysis (Supplementary Fig. 2); it was, however, also obtained by Duanmu et al.21 (but without support). Additional phytochrome data from stramenopiles will be necessary to clarify the origin of these viral phytochromes. We also examined haptophytes, a predominantly marine lineage of phytoplankton (their relationships with stramenopiles and other protists are unclear2728). No phytochrome could be found in the haptophyte transcriptomes.


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 phytochromes.Terminal clades are collapsed into higher taxonomic units (usually orders or classes) for display purposes. Orange circles indicate inferred gene duplications. Italicized capital letters within each circle correspond to duplication events mentioned in the text, and the numbers/letters adjacent to each orange circle are the names of gene duplicates. Canonical plant phytochromes originated in an ancestor of streptophytes (green star), and some charophyte algae retain non-canonical phytochromes (PHYX1 and PHYX2). Phytochrome domain architectures are shown on the right. Domains that are not always present are indicated by dashed outlines. Domain names: GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA); H/KD (histidine phosphorylation site (H) in the histidine kinase domain (KD)); PAS (Per/Arnt/Sim); PHY (Phytochrome); PKC (Protein Kinase C); REC (Response Regulator); and RING (Really Interesting New Gene). *Traditional Archaeplastida do not include cryptophytes32.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Phylogeny of phytochromes.Terminal clades are collapsed into higher taxonomic units (usually orders or classes) for display purposes. Orange circles indicate inferred gene duplications. Italicized capital letters within each circle correspond to duplication events mentioned in the text, and the numbers/letters adjacent to each orange circle are the names of gene duplicates. Canonical plant phytochromes originated in an ancestor of streptophytes (green star), and some charophyte algae retain non-canonical phytochromes (PHYX1 and PHYX2). Phytochrome domain architectures are shown on the right. Domains that are not always present are indicated by dashed outlines. Domain names: GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA); H/KD (histidine phosphorylation site (H) in the histidine kinase domain (KD)); PAS (Per/Arnt/Sim); PHY (Phytochrome); PKC (Protein Kinase C); REC (Response Regulator); and RING (Really Interesting New Gene). *Traditional Archaeplastida do not include cryptophytes32.
Mentions: Stramenopiles are a large eukaryotic clade that includes brown algae (such as kelps), golden algae and diatoms, the latter being an important component of plankton. Within this group, phytochromes are known so far only from brown algae, some of their viruses and diatoms. Their sequences form a clade that is sister to fungal phytochromes (Fig. 1 and Supplementary Fig. 2). Interestingly, the phytochrome from the brown algal virus EsV-1 (ref. 33) does not group with brown algae phytochromes, but instead is more closely related to those of diatoms. This relationship was not supported in a bootstrapping analysis (Supplementary Fig. 2); it was, however, also obtained by Duanmu et al.21 (but without support). Additional phytochrome data from stramenopiles will be necessary to clarify the origin of these viral phytochromes. We also examined haptophytes, a predominantly marine lineage of phytoplankton (their relationships with stramenopiles and other protists are unclear2728). No phytochrome could be found in the haptophyte transcriptomes.

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