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

Abstract

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. Here, 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 undermore » 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. Finally, the high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.« less

Authors:
 [1];  [2];  [3];  [4];  [2];  [5];  [6];  [6];  [4];  [3];  [2]; ORCiD logo [6]
  1. Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst., Dept. of Plant and Microbial Biology
  2. Univ. of California, Los Angeles, CA (United States). Dept. of Molecular, Cell and Developmental Biology
  3. Univ. of California, Los Angeles, CA (United States). Dept. of Chemistry and Biochemistry and Inst. for Genomics and Proteomics
  4. Univ. of California, San Francisco, CA (United States). Dept. of Anatomy; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for X-ray Tomography
  5. Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst., Dept. of Plant and Microbial Biolog; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  6. Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst., Dept. of Plant and Microbial Biolog; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
National Institutes of Health (NIH); Gordon and Betty Moore Foundation; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379858
DOE Contract Number:  
AC02-05CH11231; GBMF3070; FC02-02ER63421; 2013-67012-21272
Resource Type:
Journal Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 21; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; Chlorophyceae; carotenoid biosynthesis; de novo genome; genome mapping; RNA-Seq

Citation Formats

Roth, Melissa S., Cokus, Shawn J., Gallaher, Sean D., Walter, Andreas, Lopez, David, Erickson, Erika, Endelman, Benjamin, Westcott, Daniel, Larabell, Carolyn A., Merchant, Sabeeha S., Pellegrini, Matteo, and Niyogi, Krishna K. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. United States: N. p., 2017. Web. doi:10.1073/pnas.1619928114.
Roth, Melissa S., Cokus, Shawn J., Gallaher, Sean D., Walter, Andreas, Lopez, David, Erickson, Erika, Endelman, Benjamin, Westcott, Daniel, Larabell, Carolyn A., Merchant, Sabeeha S., Pellegrini, Matteo, & Niyogi, Krishna K. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. United States. doi:10.1073/pnas.1619928114.
Roth, Melissa S., Cokus, Shawn J., Gallaher, Sean D., Walter, Andreas, Lopez, David, Erickson, Erika, Endelman, Benjamin, Westcott, Daniel, Larabell, Carolyn A., Merchant, Sabeeha S., Pellegrini, Matteo, and Niyogi, Krishna K. Mon . "Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production". United States. doi:10.1073/pnas.1619928114. https://www.osti.gov/servlets/purl/1379858.
@article{osti_1379858,
title = {Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production},
author = {Roth, Melissa S. and Cokus, Shawn J. and Gallaher, Sean D. and Walter, Andreas and Lopez, David and Erickson, Erika and Endelman, Benjamin and Westcott, Daniel and Larabell, Carolyn A. and Merchant, Sabeeha S. and Pellegrini, Matteo and Niyogi, Krishna K.},
abstractNote = {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. Here, 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. Finally, the high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.},
doi = {10.1073/pnas.1619928114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 21,
volume = 114,
place = {United States},
year = {2017},
month = {5}
}

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    Works referencing / citing this record:

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    A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
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