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The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.ORCID iD: 0000-0002-8558-5655
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. The Royal Swedish Academy of Sciences, Sweden.
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. The Royal Swedish Academy of Sciences, Sweden.
2015 (English)In: Mitochondrial DNA, ISSN 1940-1736, E-ISSN 1940-1744Article in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
2015.
Keyword [en]
Chloroplast genome, Ephedra foeminea, Illumina sequencing, phylogeny
National Category
Biochemistry and Molecular Biology
Research subject
Plant Systematics
Identifiers
URN: urn:nbn:se:su:diva-128435DOI: 10.3109/19401736.2015.1122768PubMedID: 26713841OAI: oai:DiVA.org:su-128435DiVA: diva2:915006
Available from: 2016-03-28 Created: 2016-03-28 Last updated: 2016-09-14
In thesis
1. Evolutionary studies of the Gnetales
Open this publication in new window or tab >>Evolutionary studies of the Gnetales
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The Gnetales consist of three distinct genera, Ephedra, Gnetum and Welwitschia with considerable divergence among them regarding morphological, ecological and molecular characters. A longstanding debate of the similarity between the Gnetales and angiosperms and the unresolved seed plant phylogeny intrigues plant scientists to further investigate the evolutionary history of the Gnetales. The presented projects deal with interdisciplinary questions on proteomics, chloroplast genomes, phylogenetic relationships, gross morphology and taxonomy. The thesis aims to summarize general problems encountered in previous studies, and to provide new insights and future perspectives based on the results of completed and ongoing projects.   

In Ephedra, the Mediterranean species E. foeminea has been shown to be entomophilous and it possesses an important phylogenetic status as the sister of the remaining genus. Therefore, the chloroplast genome of E. foeminea was assembled and compared to that previously presented (of the anemophilous Asian species E. equisetina, nested in the core clade of Ephedra). The genome has a quadripartite structure and comprises 118 genes and 109,584 base pairs. A pairwise genome comparison was conducted between E. foeminea and E. equisetina, resulting in the detection of 2,352 variable sites, the obtained data can be used for prospective phylogenetic studies. A proteomic study was also conducted on E. foeminea along with three anemophilous Ephedra species, in order to investigate the biochemistry of the pollination drops. The results show that detected proteins in the pollination drops of Ephedra vary dramatically among species but always occur in very low amounts. The majority of the detected proteins are degradome proteins, i.e., waste products from degrading cells of the nucellus. Some secretome proteins were also found, which are putatively functional, but also these proteins occur in very low amounts. The repeatability of the proteomic studies can, however, be questioned. The sampling methods and proteomic analyses are probably problematic although some suggestions for improvement are provided. Thus I chose to continue with other projects.

In Gnetum, reconstruction of the genus phylogeny and assessments of divergence times of clades were performed using an extensive sampling of ingroup and outgroup accessions. The results show that the South American lineage separated from the remaining genus in the Late Cretaceous. The continued diversification event gave rise to an African lineage and an Asian lineage. The crown age of the Asian clade, which comprises two arborescent species sister to the remaining liaonid species, was estimated to the Cretaceous-Paleogene (K-Pg) boundary. In light of the genus phylogeny and estimated node ages, we suggest that the breakup of Gondwana influenced diversification patterns in Gnetum. Later dispersal events also contributed to the current distribution of Gnetum, and to the phylogenetic patterns within each of the major clades. From my results, it is however clear that taxonomy and species delimitations are poorly defined, and needs to be further studied for all subclades of Gnetum. I have initiated this task by studying the Chinese lianoid clade of Gnetum more in depth. Eleven chloroplast genomes were generated, aligned and compared. Based on the information, four chloroplast markers were designed and applied to further resolve the species relationships with an extensive sampling. The results show, with strong support, that G. parvifolium is sister to all the remaining species of the Chinese linaoid clade. Another five lianoid species are confirmed using both morphological and molecular data, but several names are represented by type material that cannot be considered separate species. Modified keys for identification of male and female plants are presented, based on vegetative and reproductive structures. A subsequent dating analysis indicates that diversification in the Chinese lianoid Gnetum clade took place mainly in the Neogene, during which environmental changes probably facilitated diversification in the lineage.

Place, publisher, year, edition, pages
Stockholm: Department of Ecology, Environment and Plant Sciences, Stockholm University, 2016. 44 p.
National Category
Botany
Research subject
Plant Systematics
Identifiers
urn:nbn:se:su:diva-128439 (URN)978-91-7649-371-7 (ISBN)
Public defence
2016-06-03, Vivi Täckholmsalen (Q-salen), NPQ-huset, Frescativägen 20 A, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2016-05-11 Created: 2016-03-28 Last updated: 2016-05-18Bibliographically approved

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