title: Complete chloroplast genome sequence of holoparasite Cistanche deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from its host Haloxylon ammodendron (Chenopodiaceae).
abstract: The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. PRINCIPAL FINDINGS/SIGNIFICANCE: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Li
authors.forename: Ti-Cao
authors.initials: TC
authors.lastname: Zhang
authors.forename: Qin
authors.initials: Q
authors.lastname: Qiao
authors.forename: Zhumei
authors.initials: Z
authors.lastname: Ren
authors.forename: Jiayuan
authors.initials: J
authors.lastname: Zhao
authors.forename: Takahiro
authors.initials: T
authors.lastname: Yonezawa
authors.forename: Masami
authors.initials: M
authors.lastname: Hasegawa
authors.forename: M James C
authors.initials: MJ
authors.lastname: Crabbe
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Li
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhong
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019663:Chenopodiaceae / Q000235:genetics*; D031671:Cistanche / Q000235:genetics*; D017353:Gene Deletion; D023061:Gene Order; D022761:Gene Transfer, Horizontal; D017343:Genes, Plant; D054628:Genome, Chloroplast; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D018087:Plastids / Q000235:genetics; D016415:Sequence Alignment
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