Latest changes
PrunusMap is a comprehensive tool developed to efficiently locate the positions of
Prunus genetic markers across both physical and genetic maps of various
Prunus species, including peach, almond, apricot, sweet cherry and more. By integrating data from multiple databases such as NCBI, Phytozome and GDR.
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 available (e.g.: Illumina 9K 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 maps (Pp_Lovell_NCBI_V2 by default).
To use the
Align proteins option you must provide amino acid sequences in FASTA format.
These will be used to retrieve their positions through protein-to-DNA
alignment to the selected maps (Pp_Lovell_NCBI_V2 by default).
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 "Pp01 10000" to find out which genes are in that specific region of chromosome Pp01.
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.
The frontend
prunusmap_web is a fork of
barleymap_web with
added
protein alignments.
The backend is the
standalone application,
which was added the
bamp_align_prot tools.
Further information about how this tool works and help on using it can be found
here.
Or you may wish to
contact the
Computational and structural biology group
(
EEAD -
CSIC):
compbio@eead.csic.es
Funding:
This work was funded by CSIC [grants 2020AEP119 & FAS2022_052], the Spanish Research Agency [grants AGL2017-83358-R MCIN/AEI/10.13039/501100011033 & "A way of making Europe"] and the Government of Aragón [grants A44, A09_23R, A10_23R & PhD contract to Najla Ksouri 2018-2023], which were co-financed with FEDER funds.
Citations:
Ksouri N, Moreno MA, Contreras-Moreira B, Gogorcena Y (2024) Mapping the genomic landscape of Prunus spp. with PrunusMap. Horticulture Research,uhae301
[1]International Peach Genome Initiative. 2013.
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
Nature Genetics 45(5):487-94. doi: 10.1038/ng.2586
[2]Verde et al. 2017.
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
BMC Genomics 18(1):225. doi: 10.1186/s12864-017-3606-9
[3]Alioto et al. 2020.
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.
Plant J. 101(2):455-472. doi: 10.1111/tpj.14538
[4]Verde et al. 2012.
Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.
PLoS One. 7(6). doi:10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.
IRSC 9K markers downloaded from the GDR.
[5]Gasic et al. 2022.
IRSC 16K SNP array for Prunus persica.
Unpublished.
IRSC 16K markers downloaded from the GDR.
[6]Guajardo et al. 2022
QTLs Identification for Iron Chlorosis in a Segregating Peach-Almond Progeny Through Double-Digest Sequence-Based Genotyping (SBG).
Front. Plant Sci. 13:872208. doi: 10.3389/fpls.2022.872208
[7]Duval et al. 2023
Development and Evaluation of an Axiom 60K SNP Array for Almond (Prunus dulcis).
Plants 12(2): 242. doi: 10.3390/plants12020242
[8]D'Amico-Willman et al. 2022
Whole-genome sequence and methylome profiling off the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar 'Nonpareil'.
G3 (Bethesda) 12(5):jkac065. doi: 10.1093/g3journal/jkac065
[9]Sanchez-Perez et al. 2019
Mutation of a bHLH transcription factor allowed almond domestication.
Science 364(6445):1095-1098. doi: 10.1126/science.aav8197
