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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
RS1173894  Pronephrium simplex Description:RNA extracted from Pronephrium simplex...
BioSample accession:SAMN03575942 
Analyte type:RNA
...
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RS10474345  Antrophyum callifolium Blume Description:RNA extracted from Antrophyum callifol...
BioSample accession:SAMN03575934 
Analyte type:RNA
...
+
RS101450915  Oleandra hainanensis Description:RNA extracted from Oleandra musifolia ...
BioSample accession:SAMN03575912 
Analyte type:RNA
...
+
RS10332120  Woodsia polystichoides Description:RNA extracted from Woodsia polystichoi...
BioSample accession:SAMN03575943 
Analyte type:RNA
...
+
RS107231682  Equisetum diffusum D.Don Description:RNA extracted from Equisetum diffusum ...
BioSample accession:SAMN03575901 
Analyte type:RNA
...
+
RS108872581  Grammitis dorsipila Description:RNA extracted from Oreogrammitis dorsi...
BioSample accession:SAMN03575921 
Analyte type:RNA
...
+
RS1129625  Vandenboschia striata Description:RNA extracted from Vandenboschia stria...
BioSample accession:SAMN03575903 
Analyte type:RNA
...
+
RS11141974  Pleurosoriopsis makinoi Description:RNA extracted from Pleurosoriopsis mak...
BioSample accession:SAMN03575918 
Analyte type:RNA
...
+
RS1121131307  Azolla pinnata subsp. asiatica Description:RNA extracted from Azolla pinnata subs...
BioSample accession:SAMN03575938 
Analyte type:RNA
...
+
RS11432177  Taenitis blechnoides Description:RNA extracted from Taenitis blechnoide...
BioSample accession:SAMN03575927 
Analyte type:RNA
...
+
Displaying 1-10 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 
protein sequenceFASTA408.26 MB2017-10-05
AlignmentsUNKNOWN9.74 MB2017-10-05
AlignmentsUNKNOWN17.39 MB2017-10-05
AlignmentsUNKNOWN6.02 MB2017-10-05
AlignmentsFASTA35.65 MB2017-10-05
ReadmeTEXT7.4 KB2017-10-05
mixed archivearchive111.15 KB2017-10-05
Displaying 31-37 of 37 File(s).

History:

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