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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
RS8637213  Microlepia platyphylla Description:RNA extracted from Microlepia platyphy...
BioSample accession:SAMN03575888 
Analyte type:RNA
...
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RS8885330  Lygodium flexuosum Description:RNA extracted from Lygodium flexuosum ...
BioSample accession:SAMN03575908 
Analyte type:RNA
...
+
RS8965731  Hypodematium crenatum Description:RNA extracted from Hypodematium crenat...
BioSample accession:SAMN03575904 
Analyte type:RNA
...
+
RS9029594 coast leather fernAcrostichum aureum Description:RNA extracted from Acrostichum aureum ...
BioSample accession:SAMN03575928 
Analyte type:RNA
...
+
RS911073774  Adiantum caudatum Description:RNA extracted from Adiantum caudatum s...
BioSample accession:SAMN03575931 
Analyte type:RNA
...
+
RS921691969  Parahemionitis cordata Description:RNA extracted from Parahemionitis cord...
BioSample accession:SAMN03575933 
Analyte type:RNA
...
+
RS93449865  Microlepia speluncae Description:RNA extracted from Microlepia spelunca...
BioSample accession:SAMN03575889 
Analyte type:RNA
...
+
RS9732079  Stenochlaena palustris Description:RNA extracted from Stenochlaena palust...
BioSample accession:SAMN03575877 
Analyte type:RNA
...
+
RS9829596  Ceratopteris thalictroides Description:RNA extracted from Ceratopteris thalic...
BioSample accession:SAMN03575932 
Analyte type:RNA
...
+
Displaying 61-69 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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