Bioinformatics Tools enables plant genome analysis

Bioinformatics Tools enables plant genome analysis and hence enables the scientific attraction to the newest inventions.

A Review of Bioinformatics Tools

The ability to detect sequence variability and gene expression was greatly enhanced by next-generation sequencing and microarray. Specific bioinformatics tools are needed to extract information from the raw data.

The NGS pipelines work on three basic levels for human data analysis: sequence generation, reference genome alignment and results in interpretation. During the analysis, NGS data sets unique to the target / whole-genome or RNA-sequencing are widely available for several bio-Informatics methods.

Big data analysis, made possible through high-performance sequencing, was important for system biology, especially in the areas of gene regulatory networks (GRNs).

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Scientists have been allowed to develop Next Generation Sequencing (NGS) that has historically been deemed too difficult or too expensive to examine genomes. The study of complex plant genomes, which often have large repeat sequences, remains a challenge.

Therefore, researchers in bioinformatics from the Leibniz Institute of Plant Genetics and Plant Science (IPK), Martin-Luther University Halle-Wittenberg (MLU), and the Leibniz Institute of Plant Biochemistry (IBB) have now released the Kmasker Plants project.

The term “k” is used in bioinformatics to describe a nucleotide of a certain length “k.” Through recognizing and counting sequences of this kind, researchers will measure and assign repetitive sequences in the genome they sample.

As early as 2014, IPK researchers in Gatersleben used this approach to develop the “Kmasker” in silicon tool. Repetitions were detected when the barley genome was characterised (Schmutzer et al., 2014).

The use of NGS is increasingly important, but it is still difficult to compose complex genomes with the results of NGS without problems. That’s why the researchers have just agreed that this first proof of concept project should be resurrected and expanded.

The MLU, the IPK, the Wageningen University & Research and the IPB Halle have been involved in a partnership with Dr. Thomas Schmutzer, formerly of the research team “Bioinformatics and Information Technology” at IPK and now working with the MLU, to redesign and grow “Kmasker plants.”

This collaboration was largely supported by the two service centres “GCBN” and “CiBi” from the German Network for Bioinformatics Infrastructure “de.NBI”.

“Kmasker plants” allows for the rapid and reference-free screening of nucleotide sequences using genome-wide derived k-mers.

In extension to the previous version, the bioinformatics tool now also enables comparative studies between different cultivars or closely related species and supports the identification of sequences suitable as fluorescence in situ hybridisation (FISH) probes or CRISPR/Cas9-specific guide RNAs.

Furthermore, “Kmasker plants” has been published with a web service that contains the pre-computed indices for selected economically important crop plants, such as barley or wheat. Dr Schmutzer emphasises that “this tool will enable plant researchers all over the world to test plant genomes and thus, for example, identify repeat free parts of their sequence of interest.”

Instead, he considers that the enhanced functionality allows the identification of sequence candidate regions which, but lack other species in the genome or occur in smaller numbers, have increased in the genome of one species.

It contributes to a phenotypical agronomic difference in various crops. This is a common effect. The Vrn-H2 gene, present in one single copy in winter barley, is an important example and is absent in barley spring lines.

As part of the IPK Crop Analysis Tool Suite (CATS), and thus as part for the De. NBI Service Portal, the web service “Kmasker Plants” is currently available.

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