Limits...
Assessing duplication and loss of APETALA1/FRUITFULL homologs in Ranunculales.

Pabón-Mora N, Hidalgo O, Gleissberg S, Litt A - Front Plant Sci (2013)

Bottom Line: By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades.We identified an early duplication resulting in the RanFL1 and RanFL2 clades.We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes.

View Article: PubMed Central - PubMed

Affiliation: Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia Medellín, Colombia ; The New York Botanical Garden Bronx, NY, USA.

ABSTRACT
Gene duplication and loss provide raw material for evolutionary change within organismal lineages as functional diversification of gene copies provide a mechanism for phenotypic variation. Here we focus on the APETALA1/FRUITFULL MADS-box gene lineage evolution. AP1/FUL genes are angiosperm-specific and have undergone several duplications. By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades. Functional characterization of several euAP1 and euFUL genes has shown that both function in proper floral meristem identity, and axillary meristem repression. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth, compound leaf morphogenesis and fruit development. Significant functional variation has been detected in the function of pre-duplication basal-eudicot FUL-like genes, but the underlying mechanisms for change have not been identified. FUL-like genes in the Papaveraceae encode all functions reported for euAP1 and euFUL genes, whereas FUL-like genes in Aquilegia (Ranunculaceae) function in inflorescence development and leaf complexity, but not in flower or fruit development. Here we isolated FUL-like genes across the Ranunculales and used phylogenetic approaches to analyze their evolutionary history. We identified an early duplication resulting in the RanFL1 and RanFL2 clades. RanFL1 genes were present in all the families sampled and are mostly under strong negative selection in the MADS, I and K domains. RanFL2 genes were only identified from Eupteleaceae, Papaveraceae s.l., Menispermaceae and Ranunculaceae and show relaxed purifying selection at the I and K domains. We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes.

No MeSH data available.


Sequence alignment including the end of the K domain (K) and the complete C-terminal domain of ranunculid FUL-like proteins. The alignment shows a region rich in glutamine (Q), asparagine (N) and serine (S), labeled as the QN rich zone, followed by the conserved hydrophobic motif newly identified (boxed), a region negatively charged and rich in glutamic acid (E), labeled the Negative AA region, and the FUL-like motif (boxed), typical of FUL-like and euFUL proteins. CmFL1 was excluded from the alignment because is the only sequence that has an additional insertion in the “hydrophobic motif” with 8 additional AA in between positions 229–236. Black asterisks show proteins that have been functionally characterized, red asterisk points to EscaFL3 that was not previously identified and has not been functionally characterized.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3775002&req=5

Figure 2: Sequence alignment including the end of the K domain (K) and the complete C-terminal domain of ranunculid FUL-like proteins. The alignment shows a region rich in glutamine (Q), asparagine (N) and serine (S), labeled as the QN rich zone, followed by the conserved hydrophobic motif newly identified (boxed), a region negatively charged and rich in glutamic acid (E), labeled the Negative AA region, and the FUL-like motif (boxed), typical of FUL-like and euFUL proteins. CmFL1 was excluded from the alignment because is the only sequence that has an additional insertion in the “hydrophobic motif” with 8 additional AA in between positions 229–236. Black asterisks show proteins that have been functionally characterized, red asterisk points to EscaFL3 that was not previously identified and has not been functionally characterized.

Mentions: In order to gain a better understanding of the basis of the functional diversity reported for FUL-like genes in the basal eudicot order Ranunculales, we looked at patterns of evolution among these genes. We isolated FUL-like copies from species representing the phylogenetic breadth of the Ranunculales, an order with nearly 202 genera and 4500 species (APG, 2009; Wang et al., 2009; Figures 2, 3), and reconstructed the evolutionary history of the gene lineage in this clade. Ranunculales includes the early-diverging families Eupteleaceae and Papaveraceae s.l., as well as the core Ranunculales Lardizabalaceae, Circaeasteraceae, Menispermaceae, Berberidaceae and Ranunculaceae. We generated a dataset consisting of 109 FUL-like gene sequences (Table S1) from Eupteleaceae, Papaveraceae s.l., Lardizabalaceae, Menispermaceae, Berberidaceae and Ranunculaceae, as well as the outgroup basal angiosperm and monocot families Magnoliaceae, Lauraceae, Saururaceae, Aristolochiaceae and the monocot family Poaceae. Sequences from Circeasteraceae were not included due to lack of availability of material.


Assessing duplication and loss of APETALA1/FRUITFULL homologs in Ranunculales.

Pabón-Mora N, Hidalgo O, Gleissberg S, Litt A - Front Plant Sci (2013)

Sequence alignment including the end of the K domain (K) and the complete C-terminal domain of ranunculid FUL-like proteins. The alignment shows a region rich in glutamine (Q), asparagine (N) and serine (S), labeled as the QN rich zone, followed by the conserved hydrophobic motif newly identified (boxed), a region negatively charged and rich in glutamic acid (E), labeled the Negative AA region, and the FUL-like motif (boxed), typical of FUL-like and euFUL proteins. CmFL1 was excluded from the alignment because is the only sequence that has an additional insertion in the “hydrophobic motif” with 8 additional AA in between positions 229–236. Black asterisks show proteins that have been functionally characterized, red asterisk points to EscaFL3 that was not previously identified and has not been functionally characterized.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3775002&req=5

Figure 2: Sequence alignment including the end of the K domain (K) and the complete C-terminal domain of ranunculid FUL-like proteins. The alignment shows a region rich in glutamine (Q), asparagine (N) and serine (S), labeled as the QN rich zone, followed by the conserved hydrophobic motif newly identified (boxed), a region negatively charged and rich in glutamic acid (E), labeled the Negative AA region, and the FUL-like motif (boxed), typical of FUL-like and euFUL proteins. CmFL1 was excluded from the alignment because is the only sequence that has an additional insertion in the “hydrophobic motif” with 8 additional AA in between positions 229–236. Black asterisks show proteins that have been functionally characterized, red asterisk points to EscaFL3 that was not previously identified and has not been functionally characterized.
Mentions: In order to gain a better understanding of the basis of the functional diversity reported for FUL-like genes in the basal eudicot order Ranunculales, we looked at patterns of evolution among these genes. We isolated FUL-like copies from species representing the phylogenetic breadth of the Ranunculales, an order with nearly 202 genera and 4500 species (APG, 2009; Wang et al., 2009; Figures 2, 3), and reconstructed the evolutionary history of the gene lineage in this clade. Ranunculales includes the early-diverging families Eupteleaceae and Papaveraceae s.l., as well as the core Ranunculales Lardizabalaceae, Circaeasteraceae, Menispermaceae, Berberidaceae and Ranunculaceae. We generated a dataset consisting of 109 FUL-like gene sequences (Table S1) from Eupteleaceae, Papaveraceae s.l., Lardizabalaceae, Menispermaceae, Berberidaceae and Ranunculaceae, as well as the outgroup basal angiosperm and monocot families Magnoliaceae, Lauraceae, Saururaceae, Aristolochiaceae and the monocot family Poaceae. Sequences from Circeasteraceae were not included due to lack of availability of material.

Bottom Line: By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades.We identified an early duplication resulting in the RanFL1 and RanFL2 clades.We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes.

View Article: PubMed Central - PubMed

Affiliation: Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia Medellín, Colombia ; The New York Botanical Garden Bronx, NY, USA.

ABSTRACT
Gene duplication and loss provide raw material for evolutionary change within organismal lineages as functional diversification of gene copies provide a mechanism for phenotypic variation. Here we focus on the APETALA1/FRUITFULL MADS-box gene lineage evolution. AP1/FUL genes are angiosperm-specific and have undergone several duplications. By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades. Functional characterization of several euAP1 and euFUL genes has shown that both function in proper floral meristem identity, and axillary meristem repression. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth, compound leaf morphogenesis and fruit development. Significant functional variation has been detected in the function of pre-duplication basal-eudicot FUL-like genes, but the underlying mechanisms for change have not been identified. FUL-like genes in the Papaveraceae encode all functions reported for euAP1 and euFUL genes, whereas FUL-like genes in Aquilegia (Ranunculaceae) function in inflorescence development and leaf complexity, but not in flower or fruit development. Here we isolated FUL-like genes across the Ranunculales and used phylogenetic approaches to analyze their evolutionary history. We identified an early duplication resulting in the RanFL1 and RanFL2 clades. RanFL1 genes were present in all the families sampled and are mostly under strong negative selection in the MADS, I and K domains. RanFL2 genes were only identified from Eupteleaceae, Papaveraceae s.l., Menispermaceae and Ranunculaceae and show relaxed purifying selection at the I and K domains. We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes.

No MeSH data available.