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
RS46272673  Aglaomorpha bonii Description:RNA extracted from Drynaria bonii spor...
Alternative accession-BioSample:SAMN03575922Â
Analyte type:RNA
...
+
RS47187371  Platycerium bifurcatum Description:RNA extracted from Platycerium bifurca...
Alternative accession-BioSample:SAMN03575923Â
Analyte type:RNA
...
+
RS48397666  Angiopteris fokiensis Description:RNA extracted from Angiopteris fokiens...
Alternative accession-BioSample:SAMN03575909Â
Analyte type:RNA
...
+
RS51111060  Diplaziopsis brunoniana Description:RNA extracted from Diplaziopsis brunon...
Alternative accession-BioSample:SAMN03575894Â
Analyte type:RNA
...
+
RS50872515  Dennstaedtia hirsuta Description:RNA extracted from Dennstaedtia pilose...
Alternative accession-BioSample:SAMN03575885Â
Analyte type:RNA
...
+
RS5132150  Monachosorum henryi Description:RNA extracted from Monachosorum henryi...
Alternative accession-BioSample:SAMN03575884Â
Analyte type:RNA
...
+
RS5286705  Acystopteris japonica Description:RNA extracted from Acystopteris japoni...
Alternative accession-BioSample:SAMN03575881Â
Analyte type:RNA
...
+
RS53872622  Monachosorum maximowiczii Description:RNA extracted from Monachosorum maximo...
Alternative accession-BioSample:SAMN03575883Â
Analyte type:RNA
...
+
RS54529617  Dennstaedtia scabra Description:RNA extracted from Dennstaedtia scabra...
Alternative accession-BioSample:SAMN03575886Â
Analyte type:RNA
...
+
RS561649022  Arachniodes nigrospinosa Description:RNA extracted from Arachniodes nigrosp...
Alternative accession-BioSample:SAMN03575897Â
Analyte type:RNA
...
+
Displaying 41-50 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