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Data released on November 09, 2017

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

Shen, H; Jin, D; Shu, J, P; Zhou, X, L; Lei, M; Wei, R; Shang, H; Wei, H, J; Zhang, R; Liu, L; Gu, Y, F; Zhang, X, C; Yan, Y, H (2017): Supporting data for "Large scale phylogenomic analysis resolves a backbone phylogeny in ferns" GigaScience Database. http://dx.doi.org/10.5524/100353 RIS BibTeX Text

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.

Contact Submitter

Accessions (data included in GigaDB):

SRA: SRP061211

Keywords:

sporangium transcriptome phylogenomic monilophytes evolution 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100353.jpg

Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 31370234
  • Awardee - YH Yan
  • Funding body - Shanghai Landscaping & City Appearance Administrative Bureau of China
  • Award ID - F132421
  • Awardee - YH Yan
  • Funding body - Shanghai Landscaping & City Appearance Administrative Bureau of China
  • Award ID - F112422
  • Awardee - YH Yan

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RS69377229  Cheilanthes chusana Description:RNA extracted from Cheilanthes chusana...
BioSample accession:SAMN03575930 
Analyte type:RNA
...
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RS7450914  Elaphoglossum mcclurei Description:RNA extracted from Elaphoglossum mcclu...
BioSample accession:SAMN03575900 
Analyte type:RNA
...
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RS70449116  Lomagramma matthewii Description:RNA extracted from Lomagramma matthewi...
BioSample accession:SAMN03575899 
Analyte type:RNA
...
+
RS7132131  Osmolindsaea odorata Description:RNA extracted from Osmolindsaea odorat...
BioSample accession:SAMN03575905 
Analyte type:RNA
...
+
RS721649020  Aleuritopteris chrysophylla Description:RNA extracted from Aleuritopteris chry...
BioSample accession:SAMN03575929 
Analyte type:RNA
...
+
RS7713816 European water cloverMarsilea quadrifolia Description:RNA extracted from Marsilea quadrifoli...
BioSample accession:SAMN03575910 
Analyte type:RNA
...
+
RS8714478  Davallia repens Description:RNA extracted from Humata repens troph...
BioSample accession:SAMN03575882 
Analyte type:RNA
...
+
RS811524132  Tectaria morsei Description:RNA extracted from Tectaria subpedata ...
BioSample accession:SAMN03575940 
Analyte type:RNA
...
+
RS8449227 southern adder's-tongueOphioglossum vulgatum Description:RNA extracted from Ophioglossum vulgat...
BioSample accession:SAMN03575915 
Analyte type:RNA
...
+
RS8532153ladder fern Nephrolepis cordifolia Description:RNA extracted from Nephrolepis cordifo...
BioSample accession:SAMN03575911 
Analyte type:RNA
...
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Displaying 51-60 of 69 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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