title: The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.
abstract: This study presents the chloroplast genome of Ephedra foeminea, an entomophilous gymnosperm, sister to the remaining (wind-pollinated) species of Ephedra (Ephedraceae, Gnetales). Based on the reference-guided assembly, the length of the chloroplast genome was estimated to be 109 584 bp, comprising a large single copy region of 60 027 bp, a small single copy 8079 bp, and inverted repeat regions of 20 739 bp. In total, 118 genes were detected, including 73 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene density is 1.076 (genes/kb) and the GC content is 36.7%. The genomic sequence of the entomophilous, Mediterranean species E. foeminea, differs from that of the anemophilous, Asian species E. equisetina by 1018 point mutations and 1334 indels. The detected variation is useful for future development of new plastid markers for phylogenetic purposes. Our phylogenetic analysis based on 55 protein-coding chloroplast genes resolve Ephedra as monophyletic and sister to a Gnetum-Welwitschia clade. The Gnetales are sister to Cupressophytes.
authors.affiliation: a Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden.
authors.forename: Chen
authors.initials: C
authors.lastname: Hou
authors.affiliation: b Bergius Foundation, the Royal Swedish Academy of Sciences and Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden.
authors.forename: Niklas
authors.initials: N
authors.lastname: Wikström
authors.affiliation: b Bergius Foundation, the Royal Swedish Academy of Sciences and Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden.
authors.forename: Catarina
authors.initials: C
authors.lastname: Rydin
mesh_terms: D032462:Cycadopsida / Q000235:genetics*; D029789:Ephedra / Q000235:genetics*; D054628:Genome, Chloroplast / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D012335:RNA, Ribosomal
keywords: Chloroplast genome; Ephedra foeminea; Illumina sequencing; phylogeny