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Asset Tag: Algal genome

July 19, 2019  |  

Multiple independent changes in mitochondrial genome conformation in chlamydomonadalean algae

Chlamydomonadalean green algae are no stranger to linear mitochondrial genomes, particularly members of the Reinhardtinia clade. At least nine different Reinhardtinia species are known to have linear mitochondrial DNAs (mtDNAs), including the model species Chlamydomonas reinhardtii. Thus, it is no surprise that some have suggested that the most recent common ancestor of the Reinhardtinia clade had a linear mtDNA. But the recent uncovering of circular-mapping mtDNAs in a range of Reinhardtinia algae, such as Volvox carteri and Tetrabaena socialis, has shed doubt on this hypothesis. Here, we explore mtDNA sequence and structure within the colonial Reinhardtinia algae Yamagishiella unicocca and Eudorina sp. NIES-3984, which occupy phylogenetically intermediate positions between species with opposing mtDNA mapping structures. Sequencing and gel electrophoresis data indicate that Y. unicocca has a linear monomeric mitochondrial genome with long (3?kb) palindromic telomeres. Conversely, the mtDNA of Eudorina sp., despite having an identical gene order to that of Y. unicocca, assembled as a circular-mapping molecule. Restriction digests of Eudorina sp. mtDNA supported its circular map, but also revealed a linear monomeric form with a matching architecture and gene order to the Y. unicocca mtDNA. Based on these data, we suggest that there have been at least three separate shifts in mtDNA conformation in the Reinhardtinia, and that the common ancestor of this clade had a linear monomeric mitochondrial genome with palindromic telomeres.

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July 7, 2019  |  

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy’s Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

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July 7, 2019  |  

Draft nuclear genome sequence of the liquid hydrocarbon–accumulating green microalga Botryococcus braunii race B (Showa).

Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B. braunii will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism. Copyright © 2017 Browne et al.

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July 7, 2019  |  

Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production.

Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. There is interest in the unicellular green alga Chromochloris zofingiensis, because it produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. To advance understanding of its biology and facilitate commercial development, we present a C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions. The assembly, derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealed a compact genome of ~58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. The genome has uniform gene density over chromosomes, low repetitive sequence content (~6%), and a high fraction of protein-coding sequence (~39%) with relatively long coding exons and few coding introns. Functional annotation of gene models identified orthologous families for the majority (~73%) of genes. Synteny analysis uncovered localized but scrambled blocks of genes in putative orthologous relationships with other green algae. Two genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, were found in the genome, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants showed that BKT1 is required for the production of astaxanthin. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.

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July 7, 2019  |  

Insights into the red algae and eukaryotic evolution from the genome of 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.

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July 7, 2019  |  

Draft nuclear genome sequence of the halophilic and beta-carotene-accumulating green alga Dunaliella salina strain CCAP19/18.

The halotolerant alga Dunaliella salina is a model for stress tolerance and is used commercially for production of beta-carotene (=pro-vitamin A). The presented draft genome of the genuine strain CCAP19/18 will allow investigations into metabolic processes involved in regulation of stress responses, including carotenogenesis and adaptations to life in high-salinity environments. Copyright © 2017 Polle et al.

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July 7, 2019  |  

The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes.

Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture. Copyright © 2017 Elsevier Ltd. All rights reserved.

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July 7, 2019  |  

Glaucophyta

The Glaucophyta is by far the least species-rich phylum of the Archaeplastida comprising only four described genera, Glaucocystis, Cyanophora, Gloeochaete, and Cyanoptyche, and 15 species. However, recent molecular and morphological analyses reveal that glaucophytes are not as species poor as hitherto assumed with many novel lineages existing in natural environments. Glaucophytes are freshwater phototrophs of moderate to low abundance and retain many ancestral plastid traits derived from the cyanobacterial donor of this organelle, including the remnant peptidoglycan wall in their envelope. These plastids were originally named “cyanelles,” which was later changed to “muroplasts” when their shared ancestry with other Archaeplastida was recognized. The model glaucophyte, Cyanophora paradoxa, is well studied with respect to biochemistry, proteomics, and the gene content of the nuclear and organelle genomes. Investigation of the biosynthesis of cytosolic starch led to a model for the transition from glycogen to starch storage during plastid endosymbiosis. The photosynthetic apparatus, including phycobilisome antennae, resembles that of cyanobacteria. However, the carbon-concentrating mechanism is algal in nature and based on pyrenoids. Studies on protein import into muroplasts revealed a primordial Toc/Tic translocon. The peptidoglycan wall was elucidated with respect to composition, biosynthesis, and involvement of nuclear genes. The muroplast genome is distinct, not due to the number of encoded genes but, rather, because of the presence of unique genes not present on other plastid genomes. The mosaic nature of the gene-rich (27,000) nuclear genome came as a surprise, considering the relatively small genomes of unicellular red algae.

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July 7, 2019  |  

A viral immunity chromosome in the marine picoeukaryote, Ostreococcus tauri.

Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world’s oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae.

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July 7, 2019  |  

Next-generation sequencing of Haematococcus lacustris reveals an extremely large 1.35-megabase chloroplast genome.

Haematococcus lacustris is an industrially relevant microalga that is used for the production of the carotenoid astaxanthin. Here, we report the use of PacBio long-read sequencing to assemble the chloroplast genome of H. lacustris strain UTEX:2505. At 1.35?Mb, this is the largest assembled chloroplast of any plant or alga known to date. Copyright © 2018 Bauman et al.

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