Comparative and Functional Algal Genomics.

  title={Comparative and Functional Algal Genomics.},
  author={Crysten E. Blaby-Haas and Sabeeha S. Merchant},
  journal={Annual review of plant biology},
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… 

An Insight into the Algal Evolution and Genomics

Algal genomics not only helped to understand the evolutionary history of algae but also may have an impact on the authors' future by helping to create algae-based products and future biotechnological approaches.

Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages

This work assembles a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary.

Leveraging computational genomics to understand the molecular basis of metal homeostasis.

To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed.

Comparative genomics of Chlamydomonas

An 8-species whole-genome alignment of unicellular and multicellular volvocine algae is produced and short introns are extensively overlapped by conserved elements, and likely represent an important functional class of regulatory sequence in C. reinhardtii.

Doing synthetic biology with photosynthetic microorganisms.

This mini-review provides an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms, and focuses on the latest CRISPR developments.

Widespread polycistronic gene expression in green algae

A range of independent approaches are employed to validate that multiple proteins are translated from a common transcript for hundreds of loci and coexpression analysis found nearly perfect correlation for open reading frames within polycistronic loci, consistent with expression in a shared transcript.

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.

Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

A comparative genomic approach is utilized to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae, and several novel functional clusters are identified.



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.