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
RS69377229  Cheilanthes chusana Description:RNA extracted from Cheilanthes chusana...
Alternative accession-BioSample:SAMN03575930Â
Analyte type:RNA
...
+
RS7450914  Elaphoglossum mcclurei Description:RNA extracted from Elaphoglossum mcclu...
Alternative accession-BioSample:SAMN03575900Â
Analyte type:RNA
...
+
RS70449116  Lomagramma matthewii Description:RNA extracted from Lomagramma matthewi...
Alternative accession-BioSample:SAMN03575899Â
Analyte type:RNA
...
+
RS7132131  Osmolindsaea odorata Description:RNA extracted from Osmolindsaea odorat...
Alternative accession-BioSample:SAMN03575905Â
Analyte type:RNA
...
+
RS721649020  Aleuritopteris chrysophylla Description:RNA extracted from Aleuritopteris chry...
Alternative accession-BioSample:SAMN03575929Â
Analyte type:RNA
...
+
RS7713816 European water cloverMarsilea quadrifolia Description:RNA extracted from Marsilea quadrifoli...
Alternative accession-BioSample:SAMN03575910Â
Analyte type:RNA
...
+
RS8714478  Davallia repens Description:RNA extracted from Humata repens troph...
Alternative accession-BioSample:SAMN03575882Â
Analyte type:RNA
...
+
RS811524132  Tectaria morsei Description:RNA extracted from Tectaria subpedata ...
Alternative accession-BioSample:SAMN03575940Â
Analyte type:RNA
...
+
RS8449227 southern adder's-tongueOphioglossum vulgatum Description:RNA extracted from Ophioglossum vulgat...
Alternative accession-BioSample:SAMN03575915Â
Analyte type:RNA
...
+
RS8532153ladder fern Nephrolepis cordifolia Description:RNA extracted from Nephrolepis cordifo...
Alternative accession-BioSample:SAMN03575911Â
Analyte type:RNA
...
+
Displaying 51-60 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