Orphan Crops Browser: a bridge between model and orphan crops

Molecular Breeding : New Strategies in Plant Improvement
Claire Lessa Alvim KameiLuisa M Trindade

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 m...Continue Reading

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Citations

Mar 21, 2020·Frontiers in Plant Science·Francesco Pancaldi, Luisa M Trindade
Jul 1, 2019·Planta·Jean-Marcel Ribaut, Michel Ragot
May 27, 2017·BMC Genomics·Tim van der WeijdeLuisa M Trindade
Mar 21, 2019·Frontiers in Plant Science·Pablo Bolaños-Villegas, Orlando Argüello-Miranda
Apr 11, 2021·The Plant Journal : for Cell and Molecular Biology·Hassan GhazalEzekiel Adebiyi

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Methods Mentioned

BETA
454

Software Mentioned

BlastN
ETE
FastME
ClustalW2
web
OrthoMCL
Orphan Crops Browser ( OCB )
Django
TrimAl
Orphan Crops Browser

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