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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
RS17334232  Dryopteris pseudocaenopteris Description:RNA extracted from Dryopteris pseudoca...
BioSample accession:SAMN03575896 
Analyte type:RNA
...
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RS18397678  Dicranopteris pedata Description:RNA extracted from Dicranopteris pedat...
BioSample accession:SAMN03575902 
Analyte type:RNA
...
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RS191353984  Haplopteris amboinensis Description:RNA extracted from Haplopteris amboine...
BioSample accession:SAMN03575935 
Analyte type:RNA
...
+
RS213240  Psilotum nudum Description:RNA extracted from Psilotum nudum spor...
BioSample accession:SAMN03575925 
Analyte type:RNA
...
+
RS24334228  Cyclopeltis crenata Description:RNA extracted from Cyclopeltis crenata...
BioSample accession:SAMN03575906 
Analyte type:RNA
...
+
RS25449818  Asplenium formosae Description:RNA extracted from Asplenium formosae ...
BioSample accession:SAMN03575875 
Analyte type:RNA
...
+
RS27341475  Lomariopsis spectabilis Description:RNA extracted from Lomariopsis spectab...
BioSample accession:SAMN03575907 
Analyte type:RNA
...
+
RS2829634  Cheiropleuria bicuspis Description:RNA extracted from Cheiropleuria bicus...
BioSample accession:SAMN03575895 
Analyte type:RNA
...
+
RS3132161  Plagiogyria japonica Description:RNA extracted from Plagiogyria japonic...
BioSample accession:SAMN03575917 
Analyte type:RNA
...
+
RS34204585  Alsophila podophylla Description:RNA extracted from Alsophila podophyll...
BioSample accession:SAMN03575880 
Analyte type:RNA
...
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Displaying 21-30 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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