title: The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.
abstract: Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro)transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst formation, novel promoter elements, and a microRNA system potentially regulating gene expression in both symbiont and coral. We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora, indicative of host-symbiont coevolution, providing a resource for studying the molecular basis and evolution of coral symbiosis.
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China. Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA. senjie.lin@uconn.edu.
authors.forename: Senjie
authors.initials: S
authors.lastname: Lin
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Hong Kong University (HKU)-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The Computer Science Department, The University of Hong Kong, Hong Kong, China. School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Song
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Lin
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Wujiao
authors.initials: W
authors.lastname: Li
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Yaqun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China.
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Ji
authors.affiliation: State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China.
authors.forename: Meichun
authors.initials: M
authors.lastname: Cai
authors.affiliation: Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
authors.forename: Yunyun
authors.initials: Y
authors.lastname: Zhuang
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Xinguo
authors.initials: X
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Lingxiao
authors.initials: L
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Zhaobao
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Yu
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.
authors.forename: Han
authors.initials: H
authors.lastname: Hao
authors.affiliation: State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China.
authors.forename: Quan
authors.initials: Q
authors.lastname: Zou
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chengxuan
authors.initials: C
authors.lastname: Chen
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Li
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Meng
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. James D. Watson Institute of Genome Science, Hangzhou, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Campbell
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Nancy R
authors.initials: NR
authors.lastname: Sturm
authors.affiliation: Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada.
authors.forename: Steve
authors.initials: S
authors.lastname: Dagenais-Bellefeuille
authors.affiliation: Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Morse
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000502:physiology*; D005075:Biological Evolution; D057894:Coral Reefs; D004141:Dinoflagellida / Q000235:genetics*; D005786:Gene Expression Regulation; D018390:Gene Targeting; D018503:Genome, Protozoan; D035683:MicroRNAs / Q000235:genetics; D013559:Symbiosis / Q000235:genetics*
chemical_list: D035683:MicroRNAs