(Map markers to the barley genome - Morex Genome 2017 edition)

Latest changes

· Added a dataset of NCBI genes to the Morex Genome map. This dataset includes genes like HvCO1, Int-c, Btr1, Vrs1, PhyB, HvCEN, etc... to a total of 894 entries.

· Support for the Illumina50K[4] markers, which can now be searched in the IBSC[1], POPSEQ[2] and Morex Genome[3] released in 2017, through the Find markers option.

[4]Bayer et al. 2017 Development and Evaluation of a Barley 50k iSelect SNP Array Frontiers in Plant Science. 8:1792. doi:10.3389/fpls.2017.01792

Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC[1]) and the POPSEQ map (Mascher et al.[2]). The current version was updated to work with the Morex Genome (released in 2017)[3].

All the public data used by Barleymap can be found at MIPS FTP server , IPK FTP server, and FTP server for Morex Genome 2017 data.

The Find markers option allows to find the position of markers by using their identifiers as input.
Note that those markers must be part of one of the precalculated datasets available (e.g.: Illumina 50K markers).

To use the Align sequences option you must provide nucleotide sequences of the markers (in FASTA format).
These will be used to retrieve their positions through sequence alignment to the selected map (IBSC2012, POPSEQ or MorexGenome).

The Locate by position option allows to examine the map context of specific positions, which must be provided as tuples with chromosome (or contig) and position (local position, within the chromosome or contig, in base pairs). For example, an user could provide as input "chr1H 10000" to find out which genes are in that specific region of chromosome 1H.

In addition to locate a list of markers or sequences, information of genes, genetic markers, and anchored features, that enrich the context around or between the queries will be shown.

Barleymap web works on top of barleymap core API, used also in a standalone application that allows loading custom databases, maps and datasets, among other features.
Such application can be used with data from any organism for which sequences anchored to a genetic/physical background are available.

Further information about how this tool works and help on using it can be found here.
Or you may wish to contact the Laboratory of Computational Biology (EEAD - CSIC):
Carlos P Cantalapiedra
Bruno Contreras-Moreira

Citation: Cantalapiedra CP, Boudiar R, Casas AM, Igartua E, Contreras-Moreira B. BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Mol Breeding (2015) 35:13 DOI 10.1007/s11032-015-0253-1

[1]IBSC. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-16. doi:10.1038/nature11543
[2]Mascher et al. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal, 76: 718–727. doi:10.1111/tpj.12319
[3]Mascher et al. 2017 A chromosome conformation capture ordered sequence of the barley genome Nature. 544:427-433. doi:10.1038/nature22043