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Identification of genic SSRs and SNPs from de novo transcriptome assembly of Chinese tallow (Triadica sebifera)
Transcriptome assembly of reads generated individually from the fruit coat, tallow and seed tissues of Chinese tallow fruits harvested at stage 4 (before maturity). The un-assembled reads from individual tissues were deposited at NCBI-Short Read Archive under accession numbers SRR1653572, SRR1653574 and SRR1653576. The assembled transcripts were ex... moreamined for simple sequence repeat and single nucleotide polymorphisms. Identified polymorphisms are deposited here to provide a resource for genetic development of Chinese tallow. less
Gene Expression (incl. Microarray and other genome-wide approaches)
CSIRO Data Licence
Divi, Uday (2014): Identification of genic SSRs and SNPs from de novo transcriptome assembly of Chinese tallow (Triadica sebifera). v2. CSIRO. Data Collection.
All Rights (including copyright) CSIRO Australia 2014.
The metadata and files (if any) are available to the public.
CLSD EF-RP3 CDF25.1 CESRE TSOP 2013/2014
Understanding tallow tissue development: defining regulatory gene networks for non-seed lipid accumulating tissues.
Oil in the form of triacylglycerol (TAG) is the major storage compound for fatty acids (FAs) and is the most energy-dense storage form of reduced carbon in many species (Durrett et al., 2008). Unlike most pl... moreants that accumulate oil in seed tissues, some species accumulate large amounts of TAG in other tissues, like the mesocarp of oil palm, avocado and olive. However, it is important to develop crops that will have minimal impact on world food supply and agricultural land, to be considered viable as alternative fuel. In this project, we study the TAG accumulation pathways of Chinese tallow tree (CT), Triadica sebifera, a valuable oil-producing tree that can grow in a variety of conditions without competing for food production (Jeffrey and Padley, 1991). The non-seed tallow layer of CT is known to accumulate more lipid than the kernel tissue and is rich in palmitic acid (16:0) and oleic acid (18:1), whereas the kernel is rich in linoleic and gamma-linolenic acid (Picou and Boldor, 2012). We deposit the transcriptome data here which is the first resource of any kind for this valuable crop accumulating high amounts of oil in both seed and non-seed tissues. less
Data mining for identification of molecular markers from de novo assembled trancriptome
The Chinese tallow transcriptome sequences (http://dx.doi.org/10.4225/08/547D1BF0EF9FD) were analyzed for identification of Simple Sequence Repeats (SSRs) using MicroSAtellite(MISA) software. Sequnces with mmore than 150 bp flaking regions available were selected to design primers using Primer 3 -2.3.4). SOAPsnp, a member of the SOAP (Short Oligonu... morecleotide Analysis Package) was used for identification of SNPs. less
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