Plant genomes
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Rescooped by Mathieu Rouard from Plant & Evolution
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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits | Plant genomes | Scoop.it
Sequencing and de novo assembly of seven wild relatives of soybean yields insights relevant to crop domestication and improvement.

Via Ali Taheri, Pierre-Marc Delaux
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Rescooped by Mathieu Rouard from Plant & Evolution
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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.


Via Pierre-Marc Delaux
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Pierre-Marc Delaux's curator insight, September 4, 2014 3:10 PM

When my two hobbies meet: evolution of coffee :p

Rescooped by Mathieu Rouard from Plant & Evolution
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Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

Abstract

Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in theArabidopsis thaliana lineage.


Via Pierre-Marc Delaux
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Rescooped by Mathieu Rouard from Bioinformatics Software: Sequence Analysis
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MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations


Via Mel Melendrez-Vallard
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Scooped by Mathieu Rouard
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The Origin of Flowers: DNA of Storied Plant Provides Insight Into the ... - Science Daily (press release)

The Origin of Flowers: DNA of Storied Plant Provides Insight Into the ... - Science Daily (press release) | Plant genomes | Scoop.it
The Origin of Flowers: DNA of Storied Plant Provides Insight Into the ...
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