The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

ZnuA and zinc homeostasis in pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous environmental bacterium and a clinically significant opportunistic human pathogen. Central to the ability of P. aeruginosa to colonise both environmental and host niches is the acquisition of zinc. Here we show that P. aeruginosa PAO1 acquires zinc via an ATP-binding cassette (ABC) permease in which ZnuA is the high affinity, zinc-specific binding protein. Zinc uptake in Gram-negative organisms predominantly occurs via an ABC permease, and consistent with this expectation a P. aeruginosa ΔznuA mutant strain showed an ~60% reduction in cellular zinc accumulation, while other metal ions were essentially unaffected. Despite the major reduction in zinc accumulation, minimal phenotypic differences were observed between the wild-type and ΔznuA mutant strains. However, the effect of zinc limitation on the transcriptome of P. aeruginosa PAO1 revealed significant changes in gene expression that enable adaptation to low-zinc conditions. Genes significantly up-regulated included non-zinc-requiring paralogs of zinc-dependent proteins and a number of novel import pathways associated with zinc acquisition. Collectively, this study provides new insight into the acquisition of zinc by P. aeruginosa PAO1, revealing a hitherto unrecognized complexity in zinc homeostasis that enables the bacterium to survive under zinc limitation.Victoria G. Pederick, Bart A. Eijkelkamp, Stephanie L. Begg, Miranda P. Ween, Lauren J. McAllister, James C. Paton, Christopher A. McDevit

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis\textit{Porphyra umbilicalis} (Bangiophyceae, Rhodophyta)

Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.The work conducted by the US Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the US DOE under Contract DE-AC02-05CH11231 (to S.H.B., E.G., A.R.G., and J.W.S.). Other major research support was provided by NSF 0929558 (to S.H.B. and A.R.G.); National Oceanic and Atmospheric Administration (NOAA) Contract NA060AR4170108 (to S.H.B.); German Research Foundation Grant Mi373/12-2 of FOR1261 (to M.M.); the French National Research Agency under IDEALG Grants ANR-10- BTBR-04-02 and 04-04 “Investissements d’avenir, Biotechnologies-Bioressources” (to J.C., E.F.-B., G.M., and S.M.D.); the New Hampshire Agricultural Experiment Station, Scientific Contribution No. 2694, supported by the US Department of Agriculture/National Institute of Food and Agriculture Hatch Project 1004051 (to A.S.K. and Y.C.); the Biotechnology and Biological Sciences Research Council (BBSRC BB/1013164/1) of the United Kingdom and European Union FP7 Marie Curie ITN Photo.Comm 317184 (to A.G.S. and K.E.H.); the Office of Biological and Environmental Research of the US DOE (C.E.B.-H.); the Connecticut Sea Grant College Program (R/A-38) and the NOAA National Marine Aquaculture Initiative (C.Y.); the NIH MCB 1244593 (to H.V.G.); NSF and NIH Grants NSF-MCB 1412738, NIH P20GM103418, and NIH P20GM103638 (to B.J.S.C.O.); NSF Graduate Research Fellowship under Grant 1247393 (to B.N.S.); the UK Natural Environment Research Council IOF Pump-priming + scheme Grant NE/L013223/1 (to C.M.M.G. and Y.B.); NOAA Contract NA14OAR4170072 (to S.H.B.); and The Great Barrier Reef Foundation, Australian Research Council (DP150101875) and a University of Queensland Early Career Researcher Grant (to C.X.C.)