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
RS8637213  Microlepia platyphylla Description:RNA extracted from Microlepia platyphy...
Alternative accession-BioSample:SAMN03575888Â
Analyte type:RNA
...
+
RS8885330  Lygodium flexuosum Description:RNA extracted from Lygodium flexuosum ...
Alternative accession-BioSample:SAMN03575908Â
Analyte type:RNA
...
+
RS8965731  Hypodematium crenatum Description:RNA extracted from Hypodematium crenat...
Alternative accession-BioSample:SAMN03575904Â
Analyte type:RNA
...
+
RS9029594 coast leather fernAcrostichum aureum Description:RNA extracted from Acrostichum aureum ...
Alternative accession-BioSample:SAMN03575928Â
Analyte type:RNA
...
+
RS911073774  Adiantum caudatum Description:RNA extracted from Adiantum caudatum s...
Alternative accession-BioSample:SAMN03575931Â
Analyte type:RNA
...
+
RS921691969  Parahemionitis cordata Description:RNA extracted from Parahemionitis cord...
Alternative accession-BioSample:SAMN03575933Â
Analyte type:RNA
...
+
RS93449865  Microlepia speluncae Description:RNA extracted from Microlepia spelunca...
Alternative accession-BioSample:SAMN03575889Â
Analyte type:RNA
...
+
RS9732079  Stenochlaena palustris Description:RNA extracted from Stenochlaena palust...
Alternative accession-BioSample:SAMN03575877Â
Analyte type:RNA
...
+
RS9829596  Ceratopteris thalictroides Description:RNA extracted from Ceratopteris thalic...
Alternative accession-BioSample:SAMN03575932Â
Analyte type:RNA
...
+
Displaying 61-69 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