The NanDeSyn database for Nannochloropsis systems and synthetic biology

Yanhai Gong; Nam K Kang; Young U Kim; Zengbin Wang; Li Wei; Yi Xin; Chen Shen; Qintao Wang; Wuxin You; Jong-Min Lim; Suk-Won Jeong; Youn-Il Park; Hee-Mock Oh; Kehou Pan; Eric Poliner; Guanpin Yang; Yonghua Li-Beisson; Yantao Li; Qiang Hu; Ansgar Poetsch; Eva M Farre; Yong K Chang; Won-Joong Jeong; Byeong-Ryool Jeong; Jian Xu

doi:10.1111/tpj.15025

The NanDeSyn database for Nannochloropsis systems and synthetic biology

Plant J. 2020 Dec;104(6):1736-1745. doi: 10.1111/tpj.15025. Epub 2020 Nov 27.

Authors

Yanhai Gong^#^{1

2

3}, Nam K Kang^#^{4

5}, Young U Kim⁴, Zengbin Wang^{1

2

3}, Li Wei^{1

2

3}, Yi Xin^{1

2

3}, Chen Shen^{1

2

3}, Qintao Wang^{1

2

3}, Wuxin You^{1

6}, Jong-Min Lim⁷, Suk-Won Jeong⁸, Youn-Il Park⁸, Hee-Mock Oh⁹, Kehou Pan^{3

10}, Eric Poliner¹¹, Guanpin Yang^{3

12

13}, Yonghua Li-Beisson¹⁴, Yantao Li¹⁵, Qiang Hu¹⁶, Ansgar Poetsch^{3

6

12}, Eva M Farre¹⁷, Yong K Chang⁴, Won-Joong Jeong⁷, Byeong-Ryool Jeong^{1

2

4

18}, Jian Xu^{1

2

3}

Affiliations

¹ Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
⁴ Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
⁵ Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
⁶ Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.
⁷ Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
⁸ Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea.
⁹ Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.
¹⁰ Laboratory of Applied Microalgae, College of Fisheries, Ocean University of China, Qingdao, 266003, China.
¹¹ MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
¹² College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China.
¹³ Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, 266003, China.
¹⁴ Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France.
¹⁵ Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, University of Maryland, Baltimore County, Baltimore, MD, 21202, USA.
¹⁶ Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
¹⁷ Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
¹⁸ School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.

^# Contributed equally.

PMID: 33103271
DOI: 10.1111/tpj.15025

Abstract

Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.

Keywords: Nannochloropsis; Tripal; functional genomics; genomic database; industrial oleaginous microalgae.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases as Topic
Epigenomics
Genome / genetics
Genomics
Internet
Metabolic Networks and Pathways
Microalgae / genetics
Microalgae / metabolism*
Proteomics
RNA, Small Cytoplasmic
Synthetic Biology
Transcriptome / genetics

Substances

RNA, Small Cytoplasmic