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
RS115194885  Gymnogrammitis dareiformis Description:RNA extracted from Gymnogrammitis dare...
Alternative accession-BioSample:SAMN03575919Â
Analyte type:RNA
...
+
RS116148574  Schizaea dichotoma Description:RNA extracted from Schizaea dichotoma ...
Alternative accession-BioSample:SAMN03575939Â
Analyte type:RNA
...
+
RS119208694  Sceptridium japonicum Description:RNA extracted from Botrychium japonicu...
Alternative accession-BioSample:SAMN03575914Â
Analyte type:RNA
...
+
RS122126675  Polypodiodes niponica Description:RNA extracted from Goniophlebium nipon...
Alternative accession-BioSample:SAMN03575920Â
Analyte type:RNA
...
+
RS123872362  Arthropteris palisotii Description:RNA extracted from Arthropteris paliso...
Alternative accession-BioSample:SAMN03575941Â
Analyte type:RNA
...
+
RS1243277 ostrich fernMatteuccia struthiopteris Description:RNA extracted from Matteuccia struthio...
Alternative accession-BioSample:SAMN03575913Â
Analyte type:RNA
...
+
RS12742333  Salvinia natans Description:RNA extracted from Salvinia natans tro...
Alternative accession-BioSample:SAMN03575937Â
Analyte type:RNA
...
+
RS128120730  Woodwardia prolifera Description:RNA extracted from Woodwardia prolifer...
Alternative accession-BioSample:SAMN03575878Â
Analyte type:RNA
...
+
RS141392720  Diplazium viridescens Description:RNA extracted from Diplazium viridesce...
Alternative accession-BioSample:SAMN03575876Â
Analyte type:RNA
...
+
RS16449111  Bolbitis appendiculata Description:RNA extracted from Bolbitis appendicul...
Alternative accession-BioSample:SAMN03575898Â
Analyte type:RNA
...
+
Displaying 11-20 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