Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae

Members of eustigmatophyte algae, especially Nannochloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis (60 Mb) and Vischeria (106 Mb), which are the sister groups to Nannochloropsis. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis that has only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

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Rapid Lipid Content Screening in Neochloris Oleoabundans by Carbon-Based Dielectrophoresis

Engineering Proceedings ◽

10.3390/micromachines2021-09605 ◽

2021 ◽

Vol 4 (1) ◽

pp. 41

Author(s):

Cynthia M. Galicia-Medina ◽

Matías Vázquez-Piñón ◽

Sergio Camacho-León ◽

Gibran S. Alemán-Nava ◽

Roberto C. Gallo-Villanueva ◽

...

Keyword(s):

Lipid Content ◽

Lipid Production ◽

Biofuel Production ◽

Neochloris Oleoabundans ◽

Atmospheric Concentration ◽

Machine Material ◽

Fixation Rate ◽

Screening Process ◽

High Lipid

The use of microalgae as a biomass source for biofuel production has drawn the attention of many scientists due to several associated environmental advantages over conventional terrestrial crops, including microalgae growing using wastewaters and a higher CO2 fixation rate, contributing to the reduction of atmospheric concentration. Consequently, a reliable cytoplasmic lipid screening process in microalgae is a valuable asset for harvesting optimization in mass production processes. In this study, the heterogeneous cytoplasmic lipid content of Neochloris oleoabundans was dielectrophoretically assorted in a microfluidic device using castellated carbon microelectrodes. The experiments carried out over a wide frequency window (100 kHz to 30 MHz) at a fixed amplitude of 7 VPP showed a significant contrast between the dielectrophoretic behavior of high lipid content and low lipid content cells at the low frequency range (100–800 kHz). A weak response for the mid and high frequency ranges (1–30 MHz) was also identified for high and low lipid content samples, allowing one to establish an electrokinetic footprint of the studied strain. These results suggest that the development of a reliable screening process for harvesting optimization is possible through a fast and straightforward mechanism, such as dielectrophoresis, which is a low-cost and easy-to-machine material that employs glassy carbon. The experimental setup in this study involved in vitro culturing of nitrogen-replete (N+) and nitrogen-deplete (N-) cell suspensions to promote low and high lipid production in cells, respectively. Cell populations were monitored using spectrophotometry, and the resulting lipid development among cells was quantified by Nile red fluorescence.

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Bacterial diketopiperazines stimulate diatom growth and lipid accumulation

Plant Physiology ◽

10.1093/plphys/kiab080 ◽

2021 ◽

Author(s):

John Sittmann ◽

Munhyung Bae ◽

Emily Mevers ◽

Muzi Li ◽

Andrew Quinn ◽

...

Keyword(s):

Lipid Content ◽

Phaeodactylum Tricornutum ◽

Photosynthetic Efficiency ◽

Biofuel Production ◽

Marine Diatom ◽

Diatom Cell ◽

Marine Microbes ◽

Bacillus Cereus Group ◽

Cell Lysate ◽

High Lipid

Abstract Diatoms are photosynthetic microalgae that fix a significant fraction of the world’s carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis and other members of the Bacillus cereus group, when in co-culture with the marine diatom Phaeodactylum tricornutum, significantly increase diatom cell count. Bioassay-guided purification of the mother cell lysate of B. thuringiensis led to the identification of two diketopiperazines (DKPs) that both stimulate P. tricornutum growth and increase its lipid content. These findings may be exploited to enhance P. tricornutum growth and microalgae-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterial-produced growth factors for marine microalgae.

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Nuclear Genome Assembly of the Microalga Nannochloropsis salina CCMP1776

Microbiology Resource Announcements ◽

10.1128/mra.00750-19 ◽

2019 ◽

Vol 8 (44) ◽

Cited By ~ 2

Author(s):

J. A. Ohan ◽

B. T. Hovde ◽

X. L. Zhang ◽

K. W. Davenport ◽

O. Chertkov ◽

...

Keyword(s):

Genome Assembly ◽

Nuclear Genome ◽

Biofuel Production ◽

Nannochloropsis Salina ◽

High Quality ◽

Draft Assembly ◽

Content Type ◽

High Lipid

Nannochloropsis salina is a halotolerant, high-lipid-producing microalga that is being explored as a biofuel production species. Here, we report an improved high-quality draft assembly and annotation for the nuclear genome of N. salina strain CCMP1776.

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Characterization and identification of freshwater microalgal strains toward biofuel production

BioResources ◽

10.15376/biores.7.1.686-695 ◽

2011 ◽

Vol 7 (1) ◽

pp. 686-695

Author(s):

Xun Yang ◽

Pinghuai Liu ◽

Zongdi Hao ◽

Jie Shi ◽

Sen Zhang

Keyword(s):

Oleic Acid ◽

Lipid Content ◽

Biomass Concentration ◽

Lipid Productivity ◽

Biodiesel Production ◽

Biofuel Production ◽

Mass Spectrometry Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Chlorella Sp ◽

High Lipid

Fifty-three algal cultures were isolated from freshwater lakes in Hainan, China. Four microalgal isolates were selected because they could be successfully cultivated at high density and demostrated a strong fluorescence after being stained with nile red. These cultures were identified as strains of Chlorella sp. C11, Chlamydomonas reinhardtii C22, Monoraphidium dybowskii C29, and Chlorella sp. HK12 through microscopic and 18S rDNA analysis. Under similar conditions, the lipid productivity of Chlorella sp. C11, Chla. reinhardtii C22, M. dybowskii C29 , and Chlorella sp. HK12 were 1.88, 2.79, 2.00, and 3.25 g L-1, respectively. Chla. reinhardtii C22 yielded a higher lipid content (51%), with a lower biomass concentration (5.47 g dwt L-1). Chlorella sp. HK12 reached a growth rate of 0.88 day-1 at OD540nm and yielded a biomass concentration of 7.56 g dwt L-1, with a high lipid content of 43%. Gas chromatography/ mass spectrometry analysis indicated that lipid fraction mainly comprises hydrocarbons including palmitic acid, stearic acid, oleic acid, linoleic acid, and linolenic acids. Our results suggest that Chlorella sp. HK12 is a promising species for biodiesel production, because of its high lipid productivity and a relatively high content of oleic acid.

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Development of a Screening Method for Isolation of Microalgae Strains That Accumulate Lipids Under Nitrate-replete Conditions

10.21203/rs.3.rs-86947/v1 ◽

2020 ◽

Author(s):

Tomoki Oyama ◽

Yuichi Kato ◽

Katsuya Satoh ◽

Yutaka Oono ◽

Tomohisa Hasunuma ◽

...

Keyword(s):

Lipid Content ◽

Fossil Fuels ◽

Screening Method ◽

Energy Resource ◽

Biofuel Production ◽

Sequential Procedures ◽

High Lipid ◽

Green Microalga ◽

One Step ◽

Mutant Cells

Abstract Background: Microalgae biofuels have attracted global attention as an alternative to fossil fuels as an energy resource. Microalgae generally accumulate lipids under nitrogen-depleted conditions, but cell growth is depressed under these conditions which causes decrease in lipid productivity. To realize one-step cultivation for biofuel production, microalgae that highly accumulate lipids even under nitrogen-replete conditions are needed. This study aimed to develop a screening method for microalgae mutants with high lipid content even in the presence of a nitrogen source.Results: Mutant cells were generated by irradiating the oleaginous green microalga Chlamydomonas sp. KOR1 with carbon ion beams, cultured under nitrate-replete conditions, and then subjected to FACS-based screening for lipid-rich cells. By repeatedly performing the sequential procedures of cultivation and selection, strains KAC1710 and KAC1801, which highly accumulate lipids under nitrate-replete conditions, were successfully obtained. These mutants formed significant lipid droplets in the cells even in the presence of abundant nitrate and achieved 1.5- and 2.1-fold greater lipid content compared to KOR1, respectively.Conclusion: This study developed a novel nitrogen-conditioned screening method for microalgae mutants that accumulate lipids in the presence of a nitrogen source. This method should contribute to microalgae biofuel production via one-step cultivation under nitrogen-replete conditions.

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Bacterially produced small molecules stimulate diatom growth

10.1101/2020.11.02.365239 ◽

2020 ◽

Author(s):

John Sittmann ◽

Munhyung Bae ◽

Emily Mevers ◽

Muzi Li ◽

Andrew Quinn ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Lipid Content ◽

Nutrient Recycling ◽

Biofuel Production ◽

Marine Diatom ◽

Rna Seq ◽

Marine Microbes ◽

Iron Starvation ◽

High Lipid ◽

Small Set

AbstractDiatoms are photosynthetic microalgae that fix a significant fraction of the world’s carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis when in co-culture with a marine diatom Phaeodactylum tricornutum significantly increases the diatom cell count. Bioassay-guided purification led to the identification of two diketopiperazines (DKPs) that both stimulate P. tricornutum growth and increase its lipid content. RNA-seq analysis revealed upregulation of a small set of P. tricornutum genes involved in iron starvation response and nutrient recycling when DKP was added to the diatom culture. This work demonstrates that two DKPs produced by a bacterium could positively impact P. tricornutum growth and lipid content, offering new approaches to enhance P. tricornutum-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterially produced growth factors for marine microalgae.One sentence summaryTwo diketopiperazines (DKPs) produced by sporulating bacterium Bacillus thuringiensis stimulate diatom P. tricornutum growth and increase diatom lipid content.

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Faculty Opinions recommendation of New components of the spliced leader RNP required for nematode trans-splicing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1007589.95659 ◽

2002 ◽

Author(s):

Thomas Blumenthal

Keyword(s):

Spliced Leader ◽

Trans Splicing

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Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab034 ◽

2021 ◽

Vol 3 (2) ◽

Author(s):

Jean-Marc Aury ◽

Benjamin Istace

Keyword(s):

Single Molecule ◽

Direct Consequence ◽

High Quality ◽

Sequencing Errors ◽

Coding Regions ◽

Sequencing Technologies ◽

Long Reads ◽

Oxford Nanopore ◽

Long Read ◽

Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

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