Comparative and Functional Algal Genomics.

@article{BlabyHaas2019ComparativeAF,
  title={Comparative and Functional Algal Genomics.},
  author={Crysten E. Blaby-Haas and Sabeeha S. Merchant},
  journal={Annual review of plant biology},
  year={2019},
  volume={70},
  pages={
          605-638
        }
}
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well… 

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References

SHOWING 1-5 OF 5 REFERENCES

Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity[OPEN]

How functional genomics and reverse genetics have contributed to the understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations is described.

A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism[OPEN]

A historical retrospective of the rise of C. reinhardtii is presented to illuminate its past and present and resources for current and future scientists who may wish to expand their studies to the realm of microalgae are presented.

Mining Natural Product Biosynthesis in Eukaryotic Algae

Applying informatics techniques to the algal genomes that are now available reveals new natural product biosynthetic pathways, with different groups of algae containing different types of pathways.

Alien Domains Shaped the Modular Structure of Plant NLR Proteins

The transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system, and suggest that NLRs originated in un icellular algae and may have a common origin with cell- surface LRR receptors.

Microalgal Metallothioneins and Phytochelatins and Their Potential Use in Bioremediation

The present review reports the current knowledge on microalgal MTs and PCs and describes the state of art of their use for HM bioremediation and other putative biotechnological applications, also emphasizing on techniques aimed at increasing the cellular concentrations of MTsand PCs.