title: Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae.
abstract: The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two "transitional" green algae: the photosynthetic, mixotrophic Auxenochlorella protothecoides and the non-photosynthetic, obligate heterotroph Prototheca wickerhamii. Remarkably, the plastid genome of A. protothecoides is only slightly larger than that of P. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise to A. protothecoides and P. wickerhamii diverged from one another around six million years ago.
authors.affiliation: MOE Key Laboratory of Bioinformatics and Center for Synthetic and System Biology, Tsinghua University, Beijing 100084, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Yan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Bioinformatics and Center for Synthetic and System Biology, Tsinghua University, Beijing 100084, China.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Murakami
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Shen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jianhui
authors.initials: J
authors.lastname: Gong
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjing 300308, China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.
authors.forename: David R
authors.initials: DR
authors.lastname: Smith
authors.affiliation: College of Science, Illinois Institute of Technology, Chicago, IL 60616, USA.
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Pombert
authors.affiliation: MOE Key Laboratory of Bioinformatics and Center for Synthetic and System Biology, Tsinghua University, Beijing 100084, China.
authors.forename: Junbiao
authors.initials: J
authors.lastname: Dai
authors.affiliation: MOE Key Laboratory of Bioinformatics and Center for Synthetic and System Biology, Tsinghua University, Beijing 100084, China.
authors.forename: Qingyu
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism; D023061:Gene Order; D054627:Genome, Plastid; D023281:Genomics; D009154:Mutation; D059645:Mutation Rate; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D011525:Prototheca / Q000235:genetics* / Q000378:metabolism