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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
RS3532090  Histiopteris incisa Description:RNA extracted from Histiopteris incisa...
BioSample accession:SAMN03575892 
Analyte type:RNA
...
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RS3613821 Chinese brakePteris vittata Description:RNA extracted from Pteris vittata spor...
BioSample accession:SAMN03575926 
Analyte type:RNA
...
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RS3729588 Scythian lambCibotium barometz Description:RNA extracted from Cibotium barometz s...
BioSample accession:SAMN03575879 
Analyte type:RNA
...
+
RS3890693  Osmunda japonica Description:RNA extracted from Osmunda japonica sp...
BioSample accession:SAMN03575916 
Analyte type:RNA
...
+
RS391649021  Loxogramme chinensis Description:RNA extracted from Loxogramme chinensi...
BioSample accession:SAMN03575924 
Analyte type:RNA
...
+
RS4872616  Microlepia hookeriana Description:RNA extracted from Microlepia hookeria...
BioSample accession:SAMN03575887 
Analyte type:RNA
...
+
RS4132101bracken Pteridium aquilinum Description:RNA extracted from Pteridium aquilinum...
BioSample accession:SAMN03575891 
Analyte type:RNA
...
+
RS4232093  Hypolepis punctata Description:RNA extracted from Hypolepis punctata ...
BioSample accession:SAMN03575890 
Analyte type:RNA
...
+
RS433271  Dicksonia antarctica Description:RNA extracted from Dicksonia antarctic...
BioSample accession:SAMN03575893 
Analyte type:RNA
...
+
RS4565707  Rhachidosorus mesosorus Description:RNA extracted from Rhachidosorus mesos...
BioSample accession:SAMN03575936 
Analyte type:RNA
...
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Displaying 31-40 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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