Orphan Crops Browser: a bridge between model and orphan crops

Abstract

Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information. Our goal was to develop a tool that enables molecular breeders, without extensive bioinformatics knowledge, to efficiently study de novo transcriptome data from any orphan crop (http://www.bioinformatics.nl/denovobrowser/db/species/index). The Orphan Crops Browser has been designed to facilitate the following tasks (1) search and identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data from a set of related species and (2) design specific and degenerate primers for expression studies in the orphan crop of interest. To demonstrate the usability and reliability of the browser, it was used to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis. Expression studies in miscanthus stem internode tissue differing in maturation were subsequently carried out, to follow the expression of these genes during lignification. Our results showed a negative correlation between lignin content and gene expression. The present data are in agreement with recent findings in maize and other crops, and it is further discussed in this paper.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0430-2) contains supplementary material, which is available to authorized users.

The hot, the cold and the tulip : the regulation of flowering time and dormancy release

“…Most of the publicly available software tools offer limited options, forcing researchers to use a combination of open software packages, requiring in general different formats and operational systems (Deng, 2011). Based on the identification of the putative TCP transcripts for both bulbous species, we confirmed that the Transcriptome Browser (Kamei et al, 2016) represents a reliable and user-friendly web based interface, able to identify gene families and build phylogenetic relationships with other species.…”

“…To support in mining data using open sources, we decided to deposit our generated transcriptomes in a web-browser (http://www.bioinformatics.nl/bulbs/db/species/index) based on recently developed open software (Kamei et al, 2016). This web-based interface offers basic bioinformatics search tools, identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data and design of specific and degenerate primers for expression studies of transcripts of interest (Fig.…”

“…Last, we tested the capacity of the 'specific primer design tool' offered in the Transcriptome Browser (Kamei et al, 2016). This tool designs primers in unique regions, given a set of similar sequences.…”

Application of next-generation sequencing in plant breeding

“…Kamei et al (2016) developed a tool that enables molecular breeders even without extensive bioinformatics knowledge to efficiently study de novo transcriptome data from any crop (Orphan Crop Browser; http://www.bioinformatics.nl) with a large and complex genome. They used that tool to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis Andersson.…”

Mechanisms of vegetative propagation in bulbs : a molecular approach

“…Subsequently, a web-based interface (Kamei et al 2016), which we call Transcriptome Browser, was implemented for data presentation and mining.…”