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.
Highlights
In developing countries, several indigenous plant species form the basis of subsistence to many local and regional communities, providing food, animal feed and other non-food products
Our results showed a negative correlation between lignin content and gene expression
The result section is structured as follows: First, we describe the information that can be used as input for the browser; secondly, an overview of the various functionalities of the browser is given, and the usefulness and potentialities of this browser are illustrated using a biological example focusing on the orphan crop Miscanthus sinensis
Summary
Several indigenous plant species form the basis of subsistence to many local and regional communities, providing food, animal feed and other non-food products These crops are well accepted and preferred by farmers and consumers and well adapted to the local conditions. The commonly large, complex and polyploidy genomes of these ‘‘orphan crops’’ discourage further research Given these challenges, one alternative to progress in orphan crop research would be to make use of knowledge available from model species, translating findings from models to orphans. One alternative to progress in orphan crop research would be to make use of knowledge available from model species, translating findings from models to orphans To facilitate this task, breeding and biotechnological tools to study complex genomes and the transcriptomes of many orphan crops are currently being developed. Several researchers have recently explored their transcriptional profile as an alternative to whole-genome sequencing (Barling et al 2013; Chouvarine et al 2012; Kim et al 2014; Straub et al 2013a; Swaminathan et al 2012)
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