PLANT METABOLISM
Metabolism is the set of life-sustaining chemical transformations within the plant cell. On one hand, primary metabolism comprises all metabolic pathways that are essential to the plant's survival, generating compounds (metabolites) that are directly involved in the growth and development of the organism. On the other hand, secondary metabolism produces a large number of specialized compounds that are not essential to the functioning of the plant but are required for the plant to survive in its environment. Secondary plant metabolites are useful in the long term, often for defence purposes, they give plants characteristics such as colour, are also used in communication, signalling and regulation of primary metabolic pathways (e.g. phytohormones).
Plant metabolism
Sequencing the gigabase plant genome of the wild tomato species Solanum pennellii using Oxford Nanopore single molecule sequencing
Category: General | Date: Dec 19, 2016 | Author: Alexander Vogel
Recent updates in Oxford Nanopore technology (R9.4) have made it possible to obtain GBases of sequence data from a single flowcell. However, unlike other next generation sequencing technology, Oxford nanopore based sequencing doesn’t require any a priori capital investments. We therefore evaluated whether Oxford nanopore can be used to analyze plant genomes. To this aim, we sequenced and are assembling an accession of the wild tomato species Solanum pennellii. This accession was identified spuriously as an tomato accessions. Unlike the frequently used Solanum pennelii LA716 accession, for which we have previously generated a high quality draft genome, this new accession does not appear to exhibit any dwarfed, necrotic leaf phenotype when introgressed into modern tomato cultivars.
Here we present approximately 134 Gbases of third generation sequencing data representing a raw coverage of ca 110x. This corresponds to 110GBases of data passing the Oxford nanopores quality filter representing about 90x coverage. In addition we provide approximately 20-30x coverage of Illumina data. Average Q value represents a normal average of all Q (as delivered in e.g. FastQC) values in a read and is thus higher than the one reported by Oxford nanopores.
Data is available here: http://www.plabipd.de/portal/solanum-pennellii