Supporting data for "Large scale phylogenomic analysis resolves a backbone phylogeny in ferns"

Dataset type: Genomic, Transcriptomic
Data released on November 09, 2017

Shen H; Jin D; Shu JP; Zhou XL; Lei M; Wei R; Shang H; Wei HJ; Zhang R; Liu L; Gu YF; Zhang XC; Yan YH (2017): Supporting data for "Large scale phylogenomic analysis resolves a backbone phylogeny in ferns" GigaScience Database. http://dx.doi.org/10.5524/100353

DOI10.5524/100353

Ferns originated about 360 million years ago is the sister group of seed plants. Despite remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidences and different morphological interpretations, relationships among major fern lineages remain controversial.
With the aim to obtain a robust fern phylogeny, we carried large scale phylogenomic analysis using high-quality transcriptome sequencing data which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotides and amino acids sequences in species tree estimation. Among the mainly consistent and strongly supported cladograms, coalescent-based method using nucleotides sequence yielded the most robust cladogram.
Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships new to the current view of fern phylogeny, including that Psilotaceae and Ophioglossaceae form a monophyletic clade which is sister to Marattiaceae; Gleicheniaceae and Hymenophyllaceae form a monophyletic clade which is sister to Dipteridaceae; and that Aspleniaceae is sister to the rest groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangia annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.

Additional details

Read the peer-reviewed publication(s):

Shen, H., Jin, D., Shu, J.-P., Zhou, X.-L., Lei, M., Wei, R., … Yan, Y.-H. (2017). Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns. GigaScience, 7(2). doi:10.1093/gigascience/gix116

Accessions (data included in GigaDB):

SRA: SRP061211





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RS3613821 Chinese brakePteris vittata Description:RNA extracted from Pteris vittata spor...
Alternative accession-BioSample:SAMN03575926Â
Analyte type:RNA
...
+
RS9029594 coast leather fernAcrostichum aureum Description:RNA extracted from Acrostichum aureum ...
Alternative accession-BioSample:SAMN03575928Â
Analyte type:RNA
...
+
RS7713816 European water cloverMarsilea quadrifolia Description:RNA extracted from Marsilea quadrifoli...
Alternative accession-BioSample:SAMN03575910Â
Analyte type:RNA
...
+
RS1243277 ostrich fernMatteuccia struthiopteris Description:RNA extracted from Matteuccia struthio...
Alternative accession-BioSample:SAMN03575913Â
Analyte type:RNA
...
+
RS3729588 Scythian lambCibotium barometz Description:RNA extracted from Cibotium barometz s...
Alternative accession-BioSample:SAMN03575879Â
Analyte type:RNA
...
+
RS8449227 southern adder's-tongueOphioglossum vulgatum Description:RNA extracted from Ophioglossum vulgat...
Alternative accession-BioSample:SAMN03575915Â
Analyte type:RNA
...
+
RS1129625  Vandenboschia striata Description:RNA extracted from Vandenboschia stria...
Alternative accession-BioSample:SAMN03575903Â
Analyte type:RNA
...
+
RS108872581  Grammitis dorsipila Description:RNA extracted from Oreogrammitis dorsi...
Alternative accession-BioSample:SAMN03575921Â
Analyte type:RNA
...
+
RS101450915  Oleandra hainanensis Description:RNA extracted from Oleandra musifolia ...
Alternative accession-BioSample:SAMN03575912Â
Analyte type:RNA
...
+
RS107231682  Equisetum diffusum D.Don Description:RNA extracted from Equisetum diffusum ...
Alternative accession-BioSample:SAMN03575901Â
Analyte type:RNA
...
+
Displaying 1-10 of 69 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsFASTA0.22 KB2017-10-05
AlignmentsFASTA21.83 MB2017-10-05
AlignmentsFASTA14.61 MB2017-10-05
AlignmentsUNKNOWN27.92 MB2017-10-05
AlignmentsUNKNOWN9.75 MB2017-10-05
AlignmentsUNKNOWN17.39 MB2017-10-05
AlignmentsUNKNOWN6.02 MB2017-10-05
AlignmentsUNKNOWN30.85 KB2017-10-05
AlignmentsUNKNOWN0.04 KB2017-10-05
Phylogenetic treeUNKNOWN4.51 KB2017-10-05
Displaying 1-10 of 37 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China YH Yan 31370234
Shanghai Landscaping & City Appearance Administrative Bureau of China YH Yan F132421
Shanghai Landscaping & City Appearance Administrative Bureau of China YH Yan F112422
Date Action
November 9, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix116
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix105
January 9, 2018 Manuscript Link removed : 10.1093/gigascience/gix105