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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.

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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
RS115194885  Gymnogrammitis dareiformis Description:RNA extracted from Gymnogrammitis dare...
BioSample accession:SAMN03575919 
Analyte type:RNA
...
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RS116148574  Schizaea dichotoma Description:RNA extracted from Schizaea dichotoma ...
BioSample accession:SAMN03575939 
Analyte type:RNA
...
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RS119208694  Sceptridium japonicum Description:RNA extracted from Botrychium japonicu...
BioSample accession:SAMN03575914 
Analyte type:RNA
...
+
RS122126675  Polypodiodes niponica Description:RNA extracted from Goniophlebium nipon...
BioSample accession:SAMN03575920 
Analyte type:RNA
...
+
RS123872362  Arthropteris palisotii Description:RNA extracted from Arthropteris paliso...
BioSample accession:SAMN03575941 
Analyte type:RNA
...
+
RS1243277 ostrich fernMatteuccia struthiopteris Description:RNA extracted from Matteuccia struthio...
BioSample accession:SAMN03575913 
Analyte type:RNA
...
+
RS12742333  Salvinia natans Description:RNA extracted from Salvinia natans tro...
BioSample accession:SAMN03575937 
Analyte type:RNA
...
+
RS128120730  Woodwardia prolifera Description:RNA extracted from Woodwardia prolifer...
BioSample accession:SAMN03575878 
Analyte type:RNA
...
+
RS141392720  Diplazium viridescens Description:RNA extracted from Diplazium viridesce...
BioSample accession:SAMN03575876 
Analyte type:RNA
...
+
RS16449111  Bolbitis appendiculata Description:RNA extracted from Bolbitis appendicul...
BioSample accession:SAMN03575898 
Analyte type:RNA
...
+
Displaying 11-20 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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