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Genomic characterization of the LEED..PEEDs, a gene family unique to the medicago lineage.

Trujillo DI, Silverstein KA, Young ND - G3 (Bethesda) (2014)

Bottom Line: Synteny comparisons between R108 and A17 confirm that gene order is conserved between the two subspecies, although a further duplication occurred solely in A17.In M. truncatula A17, all 13 LPs are exclusively transcribed in nodules and absent from other plant tissues, including roots, leaves, flowers, seeds, seed shells, and pods.The recent expansion of LP genes in Medicago spp. and their timing and location of expression suggest a novel function in nodulation, possibly as an aftermath of the evolution of bacteroid terminal differentiation or potentially associated with rhizobial-host specificity.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.

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Evolutionary expansion of the LP gene family. The phylogenetic tree of A17, HM056, and R108 LP nucleotide sequences was generated through a Bayesian phylogenetic approach (A). Posterior probability values of the clades are indicated at the nodes. The heatmap insets show spatial (microdissected nodule sections) (Roux et al. 2014) and temporal (nodule samples taken at various time points after inoculation) (Benedito et al. 2008 and Carvalho et al. unpublished data at http://mtgea.noble.org/v3/) expression patterns for LP genes, with dark red indicating a higher transcription level for each time point or nodule section. The duplication history for A17 LP genes was inferred for the Bayesian Inference trees using DILTAG software (B). Rounded squares indicate duplication events, whereas the rounded rectangle indicates a double duplication.
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fig4: Evolutionary expansion of the LP gene family. The phylogenetic tree of A17, HM056, and R108 LP nucleotide sequences was generated through a Bayesian phylogenetic approach (A). Posterior probability values of the clades are indicated at the nodes. The heatmap insets show spatial (microdissected nodule sections) (Roux et al. 2014) and temporal (nodule samples taken at various time points after inoculation) (Benedito et al. 2008 and Carvalho et al. unpublished data at http://mtgea.noble.org/v3/) expression patterns for LP genes, with dark red indicating a higher transcription level for each time point or nodule section. The duplication history for A17 LP genes was inferred for the Bayesian Inference trees using DILTAG software (B). Rounded squares indicate duplication events, whereas the rounded rectangle indicates a double duplication.

Mentions: To determine the evolutionary relatedness of the LPs, an unrooted phylogenetic tree was constructed based on an alignment of their nucleotide sequences (Figure S1) using Bayesian Inference and Maximum Likelihood approaches. Inferred relationships between genes were largely similar using the two approaches, although the relationship of LP 7 and LP 8 was unresolved using the Maximum Likelihood approach (data not shown). Figure 4A shows the tree inferred for A17, HM056, and R108 using Bayesian Inference, with posterior probabilities at the nodes. Including M. sativa in the analysis resulted in fewer resolved nodes (Figure S5), probably due to the incomplete LP gene sequence information for this species (Figure S3).


Genomic characterization of the LEED..PEEDs, a gene family unique to the medicago lineage.

Trujillo DI, Silverstein KA, Young ND - G3 (Bethesda) (2014)

Evolutionary expansion of the LP gene family. The phylogenetic tree of A17, HM056, and R108 LP nucleotide sequences was generated through a Bayesian phylogenetic approach (A). Posterior probability values of the clades are indicated at the nodes. The heatmap insets show spatial (microdissected nodule sections) (Roux et al. 2014) and temporal (nodule samples taken at various time points after inoculation) (Benedito et al. 2008 and Carvalho et al. unpublished data at http://mtgea.noble.org/v3/) expression patterns for LP genes, with dark red indicating a higher transcription level for each time point or nodule section. The duplication history for A17 LP genes was inferred for the Bayesian Inference trees using DILTAG software (B). Rounded squares indicate duplication events, whereas the rounded rectangle indicates a double duplication.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199706&req=5

fig4: Evolutionary expansion of the LP gene family. The phylogenetic tree of A17, HM056, and R108 LP nucleotide sequences was generated through a Bayesian phylogenetic approach (A). Posterior probability values of the clades are indicated at the nodes. The heatmap insets show spatial (microdissected nodule sections) (Roux et al. 2014) and temporal (nodule samples taken at various time points after inoculation) (Benedito et al. 2008 and Carvalho et al. unpublished data at http://mtgea.noble.org/v3/) expression patterns for LP genes, with dark red indicating a higher transcription level for each time point or nodule section. The duplication history for A17 LP genes was inferred for the Bayesian Inference trees using DILTAG software (B). Rounded squares indicate duplication events, whereas the rounded rectangle indicates a double duplication.
Mentions: To determine the evolutionary relatedness of the LPs, an unrooted phylogenetic tree was constructed based on an alignment of their nucleotide sequences (Figure S1) using Bayesian Inference and Maximum Likelihood approaches. Inferred relationships between genes were largely similar using the two approaches, although the relationship of LP 7 and LP 8 was unresolved using the Maximum Likelihood approach (data not shown). Figure 4A shows the tree inferred for A17, HM056, and R108 using Bayesian Inference, with posterior probabilities at the nodes. Including M. sativa in the analysis resulted in fewer resolved nodes (Figure S5), probably due to the incomplete LP gene sequence information for this species (Figure S3).

Bottom Line: Synteny comparisons between R108 and A17 confirm that gene order is conserved between the two subspecies, although a further duplication occurred solely in A17.In M. truncatula A17, all 13 LPs are exclusively transcribed in nodules and absent from other plant tissues, including roots, leaves, flowers, seeds, seed shells, and pods.The recent expansion of LP genes in Medicago spp. and their timing and location of expression suggest a novel function in nodulation, possibly as an aftermath of the evolution of bacteroid terminal differentiation or potentially associated with rhizobial-host specificity.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.

Show MeSH
Related in: MedlinePlus