The NanDeSyn database for $Nannochloropsis$ systems and synthetic biology

Yanhai Gong (1, 2) , Nam K. Kang (3) , Young U. Kim (3) , Zengbin Wang (2) , Li Wei (1) , Yi Xin (1, 2) , Chen Shen (2, 1) , Qintao Wang (2, 1) , Wuxin You (1, 4, 5) , Jong‐min Lim (6) , Suk‐won Jeong (7) , Youn‐il Park (7) , Hee‐mock Oh (6) , Kehou Pan (2, 8) , Eric Poliner (9, 10) , Guanpin Yang (8) , Yonghua Li-Beisson (11, 12) , Yantao Li (13) , Qiang Hu (4) , Ansgar Poetsch (2, 5) , Eva M. Farre (10) , Yong Chang (3) , Won‐joong Jeong (6) , Byeong‐ryool Jeong (3) , Jian Xu (1)

1 UCAS - University of Chinese Academy of Sciences [Beijing]
2 Qingdao National Laboratory for Marine Science and Technology
3 KAIST - Department of Electrical Engineering [Korea Advanced Institute of Science and Technology]
4 CAS - Chinese Academy of Sciences [Beijing]
5 RUB - Ruhr University Bochum = Ruhr-Universität Bochum
6 KRIBB - Korea Research Institute of Bioscience & Biotechnology
7 CNU - Chungnam National University
8 OUC - Ocean University of China
9 MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology
10 Michigan State University [East Lansing]
11 EBMP - Environnement, Bioénergie, Microalgues et Plantes
12 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
13 UMCES - University of Maryland Center for Environmental Science

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.

Domaines: Sciences du Vivant [q-bio]

Yanhai Gong, Nam K. Kang, Young U. Kim, Zengbin Wang, Li Wei, et al.. The NanDeSyn database for $Nannochloropsis$ systems and synthetic biology. Plant Journal, 2020, 104 (6), pp.1736-1745. ⟨10.1111/tpj.15025⟩. ⟨hal-03429770⟩