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Data  and tools generated in our group

Genome Assembly and Annotation

Schrenkiella parvula Version 2.0 (Apr. 2014) (formerly Thellungiella parvula or Eutrema parvula)

Genome assembly:  Genome sequence (fasta)
Genome annotation: CDS (fasta),
Protein (fasta),
Gene models and TEs (gff),  

Notes on the update:

       -  Genome contig/scaffolds and gene models renamed reflecting the chromosome model.

       -  Redundant genome contig/scaffolds were removed.

Schrenkiella parvula Version 1.0 (Aug. 2011)  (Dassanayake et al., 2011)

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Genome assembly: Genome sequence (fasta)
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Genome annotation: CDS (fasta)

RNAseq and Transcriptome Data

Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum  (Oh et al., 2015)

RNAseq reads (SRA links)
Reference transcriptome assembly (fasta)
RNAseq results (xlsx, Oh et al. 2015)

Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula (Oh et al., 2014)

RNAseq reads (root and shoot, A. thaliana and S. parvula) (SRA links) 
RNAseq results and structural variation information (xlsx, Oh et al. 2014)

      - S. parvula genome version 2.0 (see above) was used for this study.

Comparative genomics tools to identify shared evolutionary genomic variation

CL_Finder

Tool to identify and annotate orthologous genomic units including genes in multiple genomes

OrthNet

Tool to create orthology based networks

Pipeline described at doi: https://doi.org/10.1101/236299 and can be downloaded from GitHub

 

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