title: Nannochloropsis genomes reveal evolution of microalgal oleaginous traits.
abstract: Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Dongmei
authors.initials: D
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Hu
authors.affiliation: Laboratory for Algae Research and Biotechnology, College of Technology and Innovation, Arizona State University, Mesa, Arizona, United States of America.
authors.forename: Danxiang
authors.initials: D
authors.lastname: Han
authors.affiliation: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zeng
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Jing
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Xiaoquan
authors.initials: X
authors.lastname: Su
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Xingzhi
authors.initials: X
authors.lastname: Chang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Anhui
authors.initials: A
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Jia
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wei
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xin
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Yinghe
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Ranran
authors.initials: R
authors.lastname: Huang
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Han
authors.affiliation: Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.
authors.forename: Kangsup
authors.initials: K
authors.lastname: Yoon
authors.affiliation: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America.
authors.forename: Russell T
authors.initials: RT
authors.lastname: Hill
authors.affiliation: Institute of Marine Environmental Technology and Department of Marine Biotechnology, University of Maryland Baltimore County, Baltimore, Maryland, United States of America.
authors.forename: Yonathan
authors.initials: Y
authors.lastname: Zohar
authors.affiliation: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.affiliation: CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
mesh_terms: D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016678:Genome; D058086:Microalgae / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D059467:Transcriptome; D014280:Triglycerides / Q000096:biosynthesis / Q000235:genetics*
chemical_list: D014280:Triglycerides