Bioinformatics tools

-  CLfinder-OrthNet (2018): a comparative genomics toolbox to (1) encode co-linearity among orthologous gene loci in multiple genomes as networks of orthologs (OrthNets) and (2) systematically detect gene loci with a shared evolutionary history using OrthNet topology search. DOI: https://doi.org/10.1101/236299 & downloaded from GitHub

-  GOMCL (2019): a Python tool for Gene Ontology gene sets clustering (source code:       )

-  PiP (2021):  Tool for phylogenetically informed Profiling analysis

 

Bioinformatics resources

Genome Assembly and Annotation

Schrenkiella parvula Version 2.2 (formerly Thellungiella parvula or Eutrema parvula)

Genome assembly: Genome sequence (fasta)

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

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Schrenkiella parvula Version 2.0 (Apr. 2014)

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)

​Genome assembly: Genome sequence (fasta)

​Genome annotation: CDS (fasta)

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Gene expression browser for Schrenkiella parvula transcriptome atlas

Link

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RNAseq and Transcriptome Data

1. 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)

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2. 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.

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3. Genome assembly and annotation of S. parvula, version 2.0 (2014): Updated genome assembly and annotation for S. parvula, based on additional RNA-Seq and comparative analyses.  Version 2.1 is currently under development using a combination of RNA-Seq and Iso-Seq data

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Schrenkiella parvula genomic and transcriptomic data BLAST tool

Click here

 

Orthologous gene pairs between A. thaliana & Schrenkiella parvula and A. thaliana & Eutrema salsugenium

Click here