Mapping the genomic landscape of Prunus spp. with PrunusMap

Abstract

Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features ‘Find markers’, ‘Align sequences’, ‘Align proteins’, and ‘Locate by position’, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap’s versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.

Acknowledgments

The authors would like to thank Dr Veronica Guajardo for providing data on ‘Adafuel’ SNPs and Bixente Sehabiague for his technical assistance. This work was funded by CSIC [grants 2020AEP119 & FAS2022_052], the Spanish Research Agency [grants AGL2017-83358-R & PID2023-146749OB-I00, funded by MCIN/AEI/10.13039/501100011033 ‘A way of making Europe’] and the Government of Aragón [grants A44, A09_23R, A10_23R, and PhD contract to Najla Ksouri 2018-2023], which were cofinanced with FEDER funds.

Author contributions

Y.G. and B.C-M. conceived the project and its components. M.-A.M. provided genetic data; B.C.-M. created and maintained the PrunusMap virtual machine and added support to protein alignments; N.K. created the datasets, analyzed results, and wrote the draft manuscript; and B.C-M. and Y.G. discussed and revised the manuscript. All authors read and approved the final manuscript.

Data availability statement

PrunusMap is freely accessible at https://prunusmap.eead.csic.es. Instructions for configuring and using the Web application can be found at https://github.com/eead-csic-compbio/prunusmap_web. All sets of curated SNP markers mapped using PrunusMap are accessible at https://github.com/eead-csic-compbio/prunusmap_web/tree/master/download.

Conflict of interest

None declared.

Supplementary Data

Supplementary data are available at Horticulture Research online.

References

[1] Araújo M d C, Rodrigues P, Filho SA. et al. Genetic variability in the peach palm genebank examined with RAPD markers. Crop Breed Appl Biotechnol. 2010;10:211-7

[2] Gillen AM, Bliss FA. Identification and mapping of markers linked to the Mi gene for root-knot nematode resistance in peach. J Am Soc Hortic Sci. 2005;130:24-33

[3] Wang Y, Georgi LL, Reighard GL. et al. Genetic mapping of the evergrowing gene in peach [Prunus persica (L.) Batsch]. J Hered. 2002;93:352-8

[4] Aranzana MJ, Decroocq V, Dirlewanger E. et al. Prunus genetics and applications after de novo genome sequencing: achieve-ments and prospects. Hortic Res. 2019;6:58-25

[5] Butiuc-Keul A, Coste A, Postolache D. et al. Molecular charac-terization of Prunus cultivars from Romania by microsatellite markers. Horticulturae. 2022;8:291-3

[6] Cirilli M, Rossini L, Geuna F. et al. Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). BMC Plant Biol. 2017;17:192-15

[7] Cirilli M, Flati T, Gioiosa S. et al. PeachVar-DB: a curated collec-tion of genetic variations for the interactive analysis of peach genome data. Plant Cell Physiol. 2018;59:e2-9

[8] Jung S, Jesudurai C, Staton M. et al. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics. 2004;5:1-8

[9] Jung S, Staton M, Lee T. et al. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res. 2008;36:D1034-40

[10] Jung S, Lee T, Cheng C-H. et al.15 years of GDR: new data and functionality in the genome database for Rosaceae. Nucleic Acids Res. 2019;47:D1137-45

[11] Cantalapiedra CP, Boudiar R, Casas AM. et al. BARLEYMAP: phys-ical and genetic mapping of nucleotide sequences and annota-tion of surrounding loci in barley. Mol Breed. 2015;35:1-13

[12] Duval H, Coindre E, Ramos-Onsins SE. et al. Development and evaluation of an AxiomTM 60K SNP array for almond (Prunus dulcis). Plants (Basel). 2023;12:1-12

[13] Peace C, Bassil N, Main D. et al. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One. 2012;7:1-15

[14] Guajardo V, Martínez-García PJ, Solís S. et al. QTLs identifica-tion for iron chlorosis in a segregating peach-almond progeny through double-digest sequence-based genotyping (SBG). Front Plant Sci. 2022;13:1-14

[15] Verde I, Jenkins J, Dondini L. et al. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics. 2017;18:225-18

[16] Fu W, Da Silva Linge C, Gasic K. Genome-wide association study of Brown rot (Monilinia spp.) tolerance in peach. Front Plant Sci. 2021;12:1-14

[17] Hellegouarch S. (2007). CherryPy: Essentials Rapid Python Web Application Development Design, Develop, Test, and Deploy your Python Web Applications Easily. Packt publishing Ltd. www.visionwt.com

[18] Sayers EW, Bolton EE, Brister JR. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2022;50:D20-6

[19] Goodstein DM, Shu S, Howson R. et al. Phytozome: a com-parative platform for green plant genomics. Nucleic Acids Res. 2012;40:D1178-86

[20] Boratyn GM, Camacho C, Cooper PS. et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41:W29-33

[21] Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859-75

[22] Li H. Protein-to-genome alignment with miniprot. Bioinformatics. 2023;39:1-6

[23] Verde I, Abbott AG, Scalabrin S. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45:487-94

[24] Cao K, Yang X, Li Y. et al. New high-quality peach ( Prunus persica L. Batsch) genome assembly to analyze the molecular evolution-ary mechanism of volatile compounds in peach fruits. Plant J. 2021;108:281-95

[25] Lian X, Zhang H, Jiang C. et al. De novo chromosome-level genome ofasemi-dwarfcultivarofPrunus persica identifies the aqua-porin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size. Plant Biotechnol J. 2022;20:886-902

[26] Zhang A, Zhou H, Jiang X. et al. The draft genome of a flat peach ( Prunus persica L. cv. ‘ 124 Pan’) provides insights into its good fruit flavor traits. Plan Theory. 2021;10:1-17

[27] Gladysheva-Azgari M, Petrova K, Tsygankova S. et al. A de novo genome assembly of cultivated Prunus persica cv. ‘Sovetskiy’. PLoS One. 2022;17:e0269284-13

[28] CaoK, PengZ, ZhaoX. et al. Chromosome-level genome assem-blies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biol. 2022;20:139-17

[29] Sánchez-Pérez R, Pavan S, Mazzeo R. et al. Mutation of a bHLH transcription factor allowed almond domestication. Sci-ence. 2019;364:1095-8

[30] D’Amico-Willman KM, Ouma WZ, Meulia T. et al. Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘nonpareil’. G3 (Bethesda). 2022;12:1-9

[31] Alioto T, Alexiou KG, Bardil A. et al. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J. 2020;101:455-72

[32] Castanera R, De Tomás C, Ruggieri V. et al. A phased genome of the highly heterozygous “Texas” almond uncovers patterns of allele-specific expression linked to heterozygous structural variants. Hortic Res. 2024;11:uhae106

[33] Campoy JA, Sun H, Goel M. et al. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 2020;21:306-20

[34] Shirasawa K, Isuzugawa K, Ikenaga M. et al. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res. 2017;24:499-508

[35] Wang J, Liu W, Zhu D. et al. Chromosome-scale genome assem-blyofsweet cherry ( Prunus avium L. cv. Tieton obtained using long-read and Hi-C sequencing. Hortic Res. 2020;7:122-11

[36] Zheng T, Li P, Zhuo X. et al. The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. New Phytol. 2022;235:141-56

[37] Verde I, Bassil N, Scalabrin S. et al. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One. 2012;7:1-13

[38] Mistry J, Chuguransky S, Williams L. et al.Pfam:the protein families database in 2021. Nucleic Acids Res. 2021;49:D412-9

[39] Paysan-Lafosse T, Blum M, Chuguransky S. et al. InterPro in 2022. Nucleic Acids Res. 2023;51:D418-27

[40] Fleming MB, Miller T, Fu W. et al. Ppe. XapF: high throughput KASP assays to identify fruit response to Xanthomonas arboricola pv. pruni (Xap) in peach. PLoS One. 2022;17:e0264543-17