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Data released on March 20, 2017

Supporting data for "Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus"

Yang, J; Zhang, G; Zhang, J; Liu, H; Chen, W; Li, Y; Wang, X; Dong, Y; Yang, S (2017): Supporting data for "Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus" GigaScience Database. http://dx.doi.org/10.5524/100290 RIS BibTeX Text

The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus, which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus.
We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing method and next-generation sequencing method on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with the contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37,504 protein-coding genes in the E. breviscapus genome, and 8,172 shared gene families among Compositae species.
The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.

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Genomic

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Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Erigeron breviscapus flower244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791611
Alternative names:Erigeron breviscapus flower RNA,...
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Erigeron breviscapus leaf244311Chinese herbal fleabaneErigeron breviscapus Description:Genomic DNA extracted from Erigeron br...
Alternative accession-SRA_sample:SRS1782356
Alternative names:Erigeron breviscapus leaf
...
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Erigeron breviscapus leaf Q19244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791623
Alternative names:Erigeron breviscapus leaf Q19 RN...
...
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Erigeron breviscapus leaf Q2244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791619
Alternative names:Erigeron breviscapus leaf Q2 RNA
...
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Erigeron breviscapus leaf Q22244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791624
Alternative names:Erigeron breviscapus leaf Q22 RN...
...
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Erigeron breviscapus leaf Q29244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791625
Alternative names:Erigeron breviscapus leaf Q29 RN...
...
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Erigeron breviscapus leaf Q6244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791621
Alternative names:Erigeron breviscapus leaf Q6 RNA
...
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Erigeron breviscapus leaf Q8244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791622
Alternative names:Erigeron breviscapus leaf Q8 RNA
...
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Erigeron breviscapus leaf W10244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791637
Alternative names:Erigeron breviscapus leaf W10 RN...
...
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Erigeron breviscapus leaf W17244311Chinese herbal fleabaneErigeron breviscapus Description:transcribed RNA extracted from Erigero...
Alternative accession-SRA_sample:SRS1791638
Alternative names:Erigeron breviscapus leaf W17 RN...
...
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Displaying 1-10 of 16 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 
AlignmentsFASTA3.4 MB2017-03-07
otherUNKNOWN7.2 MB2017-03-07
ScriptUNKNOWN5.82 KB2017-04-17
ScriptUNKNOWN0.56 KB2017-04-17
ScriptUNKNOWN0.63 KB2017-04-17
annotationGFF430.86 MB2017-03-07
Coding sequenceFASTA40.38 MB2017-03-07
annotationGFF19.13 MB2017-03-07
protein sequenceFASTA16.19 MB2017-03-07
Genome sequenceFASTA1.15 GB2017-03-07
Displaying 1-10 of 26 File(s).

History:

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