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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
RS46272673  Aglaomorpha bonii Description:RNA extracted from Drynaria bonii spor...
BioSample accession:SAMN03575922 
Analyte type:RNA
...
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RS47187371  Platycerium bifurcatum Description:RNA extracted from Platycerium bifurca...
BioSample accession:SAMN03575923 
Analyte type:RNA
...
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RS48397666  Angiopteris fokiensis Description:RNA extracted from Angiopteris fokiens...
BioSample accession:SAMN03575909 
Analyte type:RNA
...
+
RS51111060  Diplaziopsis brunoniana Description:RNA extracted from Diplaziopsis brunon...
BioSample accession:SAMN03575894 
Analyte type:RNA
...
+
RS50872515  Dennstaedtia hirsuta Description:RNA extracted from Dennstaedtia pilose...
BioSample accession:SAMN03575885 
Analyte type:RNA
...
+
RS5132150  Monachosorum henryi Description:RNA extracted from Monachosorum henryi...
BioSample accession:SAMN03575884 
Analyte type:RNA
...
+
RS5286705  Acystopteris japonica Description:RNA extracted from Acystopteris japoni...
BioSample accession:SAMN03575881 
Analyte type:RNA
...
+
RS53872622  Monachosorum maximowiczii Description:RNA extracted from Monachosorum maximo...
BioSample accession:SAMN03575883 
Analyte type:RNA
...
+
RS54529617  Dennstaedtia scabra Description:RNA extracted from Dennstaedtia scabra...
BioSample accession:SAMN03575886 
Analyte type:RNA
...
+
RS561649022  Arachniodes nigrospinosa Description:RNA extracted from Arachniodes nigrosp...
BioSample accession:SAMN03575897 
Analyte type:RNA
...
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Displaying 41-50 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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